NPASS Compound

Structure

CID93739 OpenBabel06191715432D 34 36 0 0 0 0 0 0 0 0999 V2000 6.0869 4.0990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7327 -5.4805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2209 4.5990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2989 -4.5796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3548 4.0990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3017 -4.5048 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3548 3.0990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8678 -3.6039 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4888 2.5990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1294 -3.5291 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6228 1.0990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4888 -0.4010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6228 -1.9010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4311 -0.8262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6228 0.0990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4888 1.5990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4888 -1.4010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5633 -2.6282 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9944 -1.6525 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7568 -1.4010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4339 -0.9010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7568 -0.4010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5605 -2.5534 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.8019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1238 -3.3797 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9749 0.2225 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3548 1.0990 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3548 -1.9010 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9916 -1.5777 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6900 -4.2807 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1210 -3.3050 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1974 1.1974 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9749 -2.0245 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 0 0 0 0 2 4 1 0 0 0 0 3 5 1 0 0 0 0 4 6 1 0 0 0 0 5 7 1 0 0 0 0 6 8 1 0 0 0 0 7 9 1 0 0 0 0 8 10 1 0 0 0 0 9 16 1 0 0 0 0 10 18 1 0 0 0 0 11 15 1 0 0 0 0 11 16 1 0 0 0 0 12 15 2 0 0 0 0 12 17 1 0 0 0 0 13 17 2 0 0 0 0 13 20 1 0 0 0 0 14 19 2 0 0 0 0 14 21 1 0 0 0 0 15 22 1 0 0 0 0 16 27 2 0 0 0 0 17 28 1 0 0 0 0 18 23 2 0 0 0 0 18 24 1 0 0 0 0 19 23 1 0 0 0 0 19 29 1 0 0 0 0 20 22 2 0 0 0 0 20 33 1 0 0 0 0 21 24 2 0 0 0 0 21 34 1 0 0 0 0 22 26 1 0 0 0 0 23 25 1 0 0 0 0 24 33 1 0 0 0 0 25 30 2 0 0 0 0 25 31 1 0 0 0 0 26 32 2 0 0 0 0 26 34 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	470.19
Volume:	479.176
LogP:	6.132
LogD:	3.521
LogS:	-3.527
# Rotatable Bonds:	11
TPSA:	130.36
# H-Bond Aceptor:	8
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.221
Synthetic Accessibility Score:	3.076
Fsp3:	0.423
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.478
MDCK Permeability:	2.4953773390734568e-05
Pgp-inhibitor:	0.262
Pgp-substrate:	0.978
Human Intestinal Absorption (HIA):	0.025
20% Bioavailability (F20%):	0.979
30% Bioavailability (F30%):	0.275

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.024
Plasma Protein Binding (PPB):	99.15435028076172%
Volume Distribution (VD):	0.245
Pgp-substrate:	0.7520095109939575%

ADMET: Metabolism

CYP1A2-inhibitor:	0.397
CYP1A2-substrate:	0.131
CYP2C19-inhibitor:	0.161
CYP2C19-substrate:	0.054
CYP2C9-inhibitor:	0.696
CYP2C9-substrate:	0.42
CYP2D6-inhibitor:	0.297
CYP2D6-substrate:	0.135
CYP3A4-inhibitor:	0.138
CYP3A4-substrate:	0.027

ADMET: Excretion

Clearance (CL):	2.812
Half-life (T1/2):	0.866

ADMET: Toxicity

hERG Blockers:	0.04
Human Hepatotoxicity (H-HT):	0.306
Drug-inuced Liver Injury (DILI):	0.973
AMES Toxicity:	0.025
Rat Oral Acute Toxicity:	0.25
Maximum Recommended Daily Dose:	0.907
Skin Sensitization:	0.759
Carcinogencity:	0.041
Eye Corrosion:	0.003
Eye Irritation:	0.161
Respiratory Toxicity:	0.889

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC93739

Natural Product ID:	NPC93739
*Common Name:**	Physodic Acid
IUPAC Name:	3,9-dihydroxy-6-oxo-7-(2-oxoheptyl)-1-pentylbenzo[b][1,4]benzodioxepine-2-carboxylic acid
Synonyms:	NSC-685589
Standard InCHIKey:	KVTYWHGIZSCFLG-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C26H30O8/c1-3-5-7-9-16(27)11-15-12-17(28)13-20-22(15)26(32)34-21-14-19(29)23(25(30)31)18(24(21)33-20)10-8-6-4-2/h12-14,28-29H,3-11H2,1-2H3,(H,30,31)
SMILES:	CCCCCC(=O)Cc1cc(cc2c1C(=O)Oc1cc(c(c(CCCCC)c1O2)C(=O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL171637
PubChem CID:	65751
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0001645] Depsides and depsidones

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO40010	Alectoria sarmentosa	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7964789]
NPO4334	Garcinia griffithii	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8465	Maesa indica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8465	Maesa indica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4334	Garcinia griffithii	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1286	Parmelia furfuracea	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6552	Astrocasia phyllanthoides	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4517	Laggera tomentosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4334	Garcinia griffithii	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9731	Roccella fuciformis	Species	Roccellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5847	Moghania faginea	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO9715	Hypericum richeri	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24532	Ula pilosa	Species	Pediciidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9084	Rumex confertus	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8465	Maesa indica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7203	Lindera lucida	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6307	Salix lasiolepis	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3334	Dicranum japonicum	Species	Dicranaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18984	Aster lautureanus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4891	Lentinellus ursinus	Species	Auriscalpiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
AC50	2
EC50	10
ED50	1
IC50	12
Others	25
Potency	28

Activity Type	# Activity
Cell Line	1
Individual Protein	39
NON-MOLECULAR	5
Organism	6
Others	9
SINGLE PROTEIN	18

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT12	Individual Protein	Human immunodeficiency virus type 1 integrase	Human immunodeficiency virus 1	Inhibition	=	94.0	%	PMID[521443]
NPT12	Individual Protein	Human immunodeficiency virus type 1 integrase	Human immunodeficiency virus 1	Inhibition	=	79.5	%	PMID[521443]
NPT12	Individual Protein	Human immunodeficiency virus type 1 integrase	Human immunodeficiency virus 1	IC50	=	38500.0	nM	PMID[521443]
NPT12	Individual Protein	Human immunodeficiency virus type 1 integrase	Human immunodeficiency virus 1	IC50	=	30900.0	nM	PMID[521443]
NPT12	Individual Protein	Human immunodeficiency virus type 1 integrase	Human immunodeficiency virus 1	IC50	=	32500.0	nM	PMID[521443]
NPT47	Individual Protein	ATP-dependent DNA helicase Q1	Homo sapiens	Potency	=	15848.9	nM	PMID[521445]
NPT48	Individual Protein	Lysine-specific demethylase 4D-like	Homo sapiens	Potency	=	39810.7	nM	PMID[521445]
NPT51	Individual Protein	Microtubule-associated protein tau	Homo sapiens	Potency	=	28183.8	nM	PMID[521445]
NPT3	Individual Protein	Thioredoxin glutathione reductase	Schistosoma mansoni	Potency	=	35481.3	nM	PMID[521445]
NPT55	Individual Protein	Putative fructose-1,6-bisphosphate aldolase	Giardia intestinalis	Potency	=	25059.4	nM	PMID[521445]
NPT1254	Individual Protein	Streptokinase A	Streptococcus pyogenes serotype M1	EC50	=	6670.0	nM	PMID[521445]
NPT60	Individual Protein	Lysosomal alpha-glucosidase	Homo sapiens	Potency	=	44668.4	nM	PMID[521445]
NPT58	Individual Protein	Bloom syndrome protein	Homo sapiens	Potency	=	3981.1	nM	PMID[521445]
NPT1254	Individual Protein	Streptokinase A	Streptococcus pyogenes serotype M1	EC50	=	15899.0	nM	PMID[521445]
NPT59	Individual Protein	DNA polymerase beta	Homo sapiens	Potency	=	44668.4	nM	PMID[521445]
NPT532	Individual Protein	Lysine-specific demethylase 4A	Homo sapiens	Potency	n.a.	79432.8	nM	PMID[521445]
NPT1039	Individual Protein	Envelope glycoprotein gp160	Human immunodeficiency virus 1	IC50	=	4100.0	nM	PMID[521445]
NPT63	Individual Protein	Bromodomain adjacent to zinc finger domain protein 2B	Homo sapiens	Potency	n.a.	79432.8	nM	PMID[521445]
NPT198	Individual Protein	Vitamin D receptor	Homo sapiens	Potency	n.a.	89125.1	nM	PMID[521445]
NPT2866	Individual Protein	Replicative DNA helicase	Mycobacterium tuberculosis	AC50	=	2050.0	nM	PMID[521445]
NPT2867	Individual Protein	Protein RecA	Mycobacterium tuberculosis	EC50	=	3230.0	nM	PMID[521445]
NPT65	Cell Line	HepG2	Homo sapiens	Potency	n.a.	35481.3	nM	PMID[521445]
NPT199	Individual Protein	DNA polymerase kappa	Homo sapiens	Potency	n.a.	79432.8	nM	PMID[521445]
NPT2866	Individual Protein	Replicative DNA helicase	Mycobacterium tuberculosis	AC50	=	6087.0	nM	PMID[521445]
NPT154	Individual Protein	Mothers against decapentaplegic homolog 3	Homo sapiens	Potency	n.a.	35481.3	nM	PMID[521445]
NPT10	Individual Protein	Geminin	Homo sapiens	Potency	n.a.	1835.6	nM	PMID[521445]
NPT478	Individual Protein	Ataxin-2	Homo sapiens	Potency	n.a.	39810.7	nM	PMID[521445]
NPT101	Individual Protein	Glucagon-like peptide 1 receptor	Homo sapiens	Potency	n.a.	28183.8	nM	PMID[521445]
NPT50	Individual Protein	Tyrosyl-DNA phosphodiesterase 1	Homo sapiens	Potency	n.a.	32642.7	nM	PMID[521445]
NPT50	Individual Protein	Tyrosyl-DNA phosphodiesterase 1	Homo sapiens	Potency	n.a.	29092.9	nM	PMID[521445]
NPT444	Individual Protein	Ubiquitin carboxyl-terminal hydrolase 1	Homo sapiens	Potency	n.a.	50118.7	nM	PMID[521445]
NPT161	Individual Protein	Rap guanine nucleotide exchange factor 4	Homo sapiens	Potency	n.a.	15848.9	nM	PMID[521445]
NPT446	Individual Protein	Rap guanine nucleotide exchange factor 3	Homo sapiens	Potency	n.a.	39810.7	nM	PMID[521445]
NPT30	Individual Protein	Cyclooxygenase-1	Homo sapiens	IC50	>	30000.0	nM	PMID[521447]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	Activity	=	25.0	ug ml-1	PMID[521444]
NPT602	Organism	Mycobacterium smegmatis	Mycobacterium smegmatis	Activity	=	100.0	ug ml-1	PMID[521444]
NPT174	Organism	Streptococcus	Streptococcus	EC50	>	150000.0	nM	PMID[521445]
NPT1252	Organism	Streptococcus sp. 'group A'	Streptococcus sp. 'group A'	EC50	=	2358.0	nM	PMID[521445]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Potency	n.a.	9285.0	nM	PMID[521445]
NPT803	Individual Protein	Flap endonuclease 1	Homo sapiens	Potency	n.a.	22387.2	nM	PMID[521445]
NPT8	Individual Protein	DNA polymerase iota	Homo sapiens	Potency	n.a.	70794.6	nM	PMID[521445]
NPT9	Individual Protein	DNA polymerase eta	Homo sapiens	Potency	n.a.	17782.8	nM	PMID[521445]
NPT821	Individual Protein	Werner syndrome ATP-dependent helicase	Homo sapiens	Potency	n.a.	44668.4	nM	PMID[521445]
NPT776	Organism	Spodoptera littoralis	Spodoptera littoralis	ED50	>	110.0	uM	PMID[521446]
NPT831	Individual Protein	Serine/threonine-protein kinase PLK1	Homo sapiens	Potency	n.a.	23778.1	nM	PMID[521445]
NPT956	Individual Protein	Prostaglandin E synthase	Homo sapiens	IC50	=	430.0	nM	PMID[521447]
NPT26023	SINGLE PROTEIN	Kinesin-like protein KIF20B	Homo sapiens	IC50	=	9900.0	nM	PMID[521448]
NPT26023	SINGLE PROTEIN	Kinesin-like protein KIF20B	Homo sapiens	Imax	=	85.0	%	PMID[521448]
NPT26023	SINGLE PROTEIN	Kinesin-like protein KIF20B	Homo sapiens	IC50	=	5800.0	nM	PMID[521448]
NPT26023	SINGLE PROTEIN	Kinesin-like protein KIF20B	Homo sapiens	Imax	=	90.0	%	PMID[521448]
NPT26023	SINGLE PROTEIN	Kinesin-like protein KIF20B	Homo sapiens	IC50	=	10400.0	nM	PMID[521448]
NPT26023	SINGLE PROTEIN	Kinesin-like protein KIF20B	Homo sapiens	IC50	=	4600.0	nM	PMID[521448]
NPT26023	SINGLE PROTEIN	Kinesin-like protein KIF20B	Homo sapiens	Imax	=	95.0	%	PMID[521448]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	EC50	>	50000.0	nM	PMID[521448]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	EC50	=	38200.0	nM	PMID[521448]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	EC50	=	31800.0	nM	PMID[521448]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	EC50	=	32600.0	nM	PMID[521448]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	EC50	=	37300.0	nM	PMID[521448]
NPT35	Others	n.a.		Solubility	=	3750.0	nM	PMID[521448]
NPT35	Others	n.a.		Solubility	=	65000.0	nM	PMID[521448]
NPT35	Others	n.a.		Solubility	>	100000.0	nM	PMID[521448]
NPT35	Others	n.a.		LogD	=	3.0	n.a.	PMID[521448]
NPT27	Others	Unspecified		Drug recovery	=	77.0	%	PMID[521448]
NPT27	Others	Unspecified		CLH	=	310.0	uL/min	PMID[521448]
NPT27	Others	Unspecified		CLH	=	61.6	uL/min	PMID[521448]
NPT27	Others	Unspecified		T1/2	=	0.075	hr	PMID[521448]
NPT27	Others	Unspecified		T1/2	=	0.375	hr	PMID[521448]
NPT27055	SINGLE PROTEIN	Centromere-associated protein E	Homo sapiens	IC50	=	29600.0	nM	PMID[521448]
NPT27055	SINGLE PROTEIN	Centromere-associated protein E	Homo sapiens	Imax	=	70.0	%	PMID[521448]
NPT27059	SINGLE PROTEIN	Kinesin-like protein KIF9	Homo sapiens	Inhibition	=	40.0	%	PMID[521448]
NPT27060	SINGLE PROTEIN	Chromosome-associated kinesin KIF4A	Homo sapiens	Inhibition	=	40.0	%	PMID[521448]
NPT27052	SINGLE PROTEIN	Kinesin-like protein KIF23	Homo sapiens	Inhibition	=	40.0	%	PMID[521448]
NPT27055	SINGLE PROTEIN	Centromere-associated protein E	Homo sapiens	IC50	=	91400.0	nM	PMID[521448]
NPT27055	SINGLE PROTEIN	Centromere-associated protein E	Homo sapiens	Imax	=	60.0	%	PMID[521448]
NPT27058	SINGLE PROTEIN	Kinesin-like protein KIF3B	Homo sapiens	Inhibition	=	40.0	%	PMID[521448]
NPT27059	SINGLE PROTEIN	Kinesin-like protein KIF9	Homo sapiens	Inhibition	=	50.0	%	PMID[521448]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC93739 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	406
0.1-0.2	1843
0.2-0.3	4647
0.3-0.4	10320
0.4-0.5	7488
0.5-0.6	3737
0.6-0.7	5189
0.7-0.8	5952
0.8-0.85	2468
0.85-0.9	587
0.9-0.95	53
0.95-1	7

Similarity Score	Similarity Level	Natural Product ID
0.9935	High Similarity	NPC284007
0.9871	High Similarity	NPC267153
0.9871	High Similarity	NPC8070
0.9679	High Similarity	NPC300984
0.9677	High Similarity	NPC303565
0.9608	High Similarity	NPC471800
0.943	High Similarity	NPC474350
0.9423	High Similarity	NPC238381
0.9379	High Similarity	NPC246716
0.9379	High Similarity	NPC239440
0.9379	High Similarity	NPC20543
0.9325	High Similarity	NPC139350
0.9317	High Similarity	NPC26568
0.9313	High Similarity	NPC20216
0.9308	High Similarity	NPC156082
0.9295	High Similarity	NPC54928
0.9264	High Similarity	NPC181523
0.9259	High Similarity	NPC17219
0.9259	High Similarity	NPC10576
0.9259	High Similarity	NPC1827
0.9255	High Similarity	NPC272485
0.9255	High Similarity	NPC292788
0.925	High Similarity	NPC112981
0.9207	High Similarity	NPC289147
0.9198	High Similarity	NPC99613
0.9198	High Similarity	NPC49487
0.9177	High Similarity	NPC83763
0.9177	High Similarity	NPC168616
0.9172	High Similarity	NPC274730
0.9157	High Similarity	NPC113446
0.9156	High Similarity	NPC6923
0.9141	High Similarity	NPC124470
0.9141	High Similarity	NPC109827
0.9119	High Similarity	NPC200594
0.9114	High Similarity	NPC165977
0.9114	High Similarity	NPC241904
0.9114	High Similarity	NPC300727
0.9114	High Similarity	NPC217677
0.9103	High Similarity	NPC289968
0.9097	High Similarity	NPC60413
0.9085	High Similarity	NPC158226
0.9074	High Similarity	NPC29160
0.9057	High Similarity	NPC476242
0.9057	High Similarity	NPC100123
0.9045	High Similarity	NPC475895
0.9045	High Similarity	NPC89474
0.9038	High Similarity	NPC474663
0.9018	High Similarity	NPC234331
0.9006	High Similarity	NPC8300
0.9	High Similarity	NPC228785
0.9	High Similarity	NPC320359
0.9	High Similarity	NPC474287
0.9	High Similarity	NPC56085
0.9	High Similarity	NPC475886
0.9	High Similarity	NPC14353
0.9	High Similarity	NPC200746
0.8987	High Similarity	NPC38898
0.8974	High Similarity	NPC29056
0.8963	High Similarity	NPC165979
0.8963	High Similarity	NPC163130
0.8951	High Similarity	NPC234004
0.8944	High Similarity	NPC474351
0.8944	High Similarity	NPC61010
0.8944	High Similarity	NPC66288
0.8944	High Similarity	NPC474187
0.8944	High Similarity	NPC474186
0.8944	High Similarity	NPC475883
0.8944	High Similarity	NPC278052
0.8944	High Similarity	NPC40491
0.8931	High Similarity	NPC142339
0.8931	High Similarity	NPC472456
0.8929	High Similarity	NPC240887
0.8929	High Similarity	NPC470091
0.8929	High Similarity	NPC329161
0.8924	High Similarity	NPC280937
0.8924	High Similarity	NPC250822
0.8924	High Similarity	NPC276409
0.8924	High Similarity	NPC75279
0.8917	High Similarity	NPC117579
0.8917	High Similarity	NPC226973
0.8917	High Similarity	NPC208043
0.8917	High Similarity	NPC198615
0.8917	High Similarity	NPC202157
0.891	High Similarity	NPC328119
0.8896	High Similarity	NPC130920
0.8896	High Similarity	NPC134621
0.8896	High Similarity	NPC29577
0.8896	High Similarity	NPC85057
0.8889	High Similarity	NPC25152
0.8889	High Similarity	NPC108767
0.8889	High Similarity	NPC229632
0.8882	High Similarity	NPC139036
0.8882	High Similarity	NPC143050
0.8875	High Similarity	NPC108456
0.8875	High Similarity	NPC181960
0.8875	High Similarity	NPC236796
0.8875	High Similarity	NPC469584
0.8868	High Similarity	NPC196439
0.8868	High Similarity	NPC167815
0.8868	High Similarity	NPC4455
0.8868	High Similarity	NPC138360
0.8868	High Similarity	NPC280339
0.8868	High Similarity	NPC208197
0.8868	High Similarity	NPC472909
0.8868	High Similarity	NPC183597
0.8868	High Similarity	NPC37392
0.8868	High Similarity	NPC2476
0.8868	High Similarity	NPC163780
0.8868	High Similarity	NPC201136
0.8868	High Similarity	NPC146165
0.8868	High Similarity	NPC20541
0.8868	High Similarity	NPC50715
0.8868	High Similarity	NPC92659
0.8868	High Similarity	NPC128863
0.8868	High Similarity	NPC227325
0.8854	High Similarity	NPC179183
0.8854	High Similarity	NPC151473
0.8854	High Similarity	NPC306821
0.8839	High Similarity	NPC237208
0.8834	High Similarity	NPC236132
0.8834	High Similarity	NPC270837
0.8834	High Similarity	NPC220313
0.8834	High Similarity	NPC189473
0.8834	High Similarity	NPC236521
0.8834	High Similarity	NPC133065
0.8834	High Similarity	NPC197168
0.8834	High Similarity	NPC475985
0.8834	High Similarity	NPC248638
0.8834	High Similarity	NPC152659
0.8834	High Similarity	NPC23298
0.8834	High Similarity	NPC7483
0.8831	High Similarity	NPC66404
0.8831	High Similarity	NPC95123
0.8827	High Similarity	NPC258331
0.8824	High Similarity	NPC105648
0.882	High Similarity	NPC474290
0.882	High Similarity	NPC329091
0.8812	High Similarity	NPC68093
0.8812	High Similarity	NPC474520
0.8812	High Similarity	NPC191146
0.8812	High Similarity	NPC138243
0.8812	High Similarity	NPC178854
0.8805	High Similarity	NPC160951
0.8805	High Similarity	NPC183878
0.8805	High Similarity	NPC22519
0.8805	High Similarity	NPC274327
0.8805	High Similarity	NPC47781
0.8805	High Similarity	NPC86485
0.8805	High Similarity	NPC145379
0.8805	High Similarity	NPC69394
0.8805	High Similarity	NPC176775
0.8805	High Similarity	NPC186507
0.8805	High Similarity	NPC472915
0.8805	High Similarity	NPC246204
0.8805	High Similarity	NPC255350
0.8805	High Similarity	NPC231018
0.8797	High Similarity	NPC133856
0.8797	High Similarity	NPC149614
0.8797	High Similarity	NPC308451
0.8797	High Similarity	NPC204350
0.879	High Similarity	NPC474648
0.879	High Similarity	NPC106334
0.879	High Similarity	NPC285527
0.8782	High Similarity	NPC93034
0.8782	High Similarity	NPC33265
0.8782	High Similarity	NPC119660
0.8782	High Similarity	NPC62536
0.8782	High Similarity	NPC12305
0.878	High Similarity	NPC239752
0.878	High Similarity	NPC326520
0.878	High Similarity	NPC472450
0.878	High Similarity	NPC39306
0.878	High Similarity	NPC275780
0.878	High Similarity	NPC25361
0.8774	High Similarity	NPC312789
0.8773	High Similarity	NPC294965
0.8773	High Similarity	NPC52204
0.8765	High Similarity	NPC119224
0.8765	High Similarity	NPC47623
0.8765	High Similarity	NPC45146
0.8765	High Similarity	NPC235018
0.8758	High Similarity	NPC472914
0.8758	High Similarity	NPC220106
0.8758	High Similarity	NPC222814
0.8758	High Similarity	NPC75215
0.8758	High Similarity	NPC29841
0.8758	High Similarity	NPC136674
0.8758	High Similarity	NPC474208
0.8758	High Similarity	NPC472911
0.8758	High Similarity	NPC224137
0.8758	High Similarity	NPC156057
0.8758	High Similarity	NPC235215
0.8758	High Similarity	NPC474836
0.8758	High Similarity	NPC472913
0.8758	High Similarity	NPC475267
0.8758	High Similarity	NPC78225
0.8758	High Similarity	NPC7973
0.8758	High Similarity	NPC93376
0.8758	High Similarity	NPC476981
0.8758	High Similarity	NPC472910

Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC93739 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	363
0.1-0.2	1032
0.2-0.3	1944
0.3-0.4	2631
0.4-0.5	1702
0.5-0.6	927
0.6-0.7	383
0.7-0.8	131
0.8-0.85	31
0.85-0.9	6
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8805	High Similarity	NPD2801	Approved
0.8659	High Similarity	NPD6232	Discontinued
0.8614	High Similarity	NPD7473	Discontinued
0.8571	High Similarity	NPD1465	Phase 2
0.8519	High Similarity	NPD3817	Phase 2
0.8509	High Similarity	NPD1934	Approved
0.8402	Intermediate Similarity	NPD5844	Phase 1
0.8354	Intermediate Similarity	NPD1511	Approved
0.8354	Intermediate Similarity	NPD3882	Suspended
0.8354	Intermediate Similarity	NPD4868	Clinical (unspecified phase)
0.8344	Intermediate Similarity	NPD7819	Suspended
0.8344	Intermediate Similarity	NPD2393	Clinical (unspecified phase)
0.8314	Intermediate Similarity	NPD4338	Clinical (unspecified phase)
0.8269	Intermediate Similarity	NPD970	Clinical (unspecified phase)
0.825	Intermediate Similarity	NPD1512	Approved
0.8235	Intermediate Similarity	NPD3818	Discontinued
0.8225	Intermediate Similarity	NPD6168	Clinical (unspecified phase)
0.8225	Intermediate Similarity	NPD6166	Phase 2
0.8225	Intermediate Similarity	NPD6167	Clinical (unspecified phase)
0.821	Intermediate Similarity	NPD3226	Approved
0.8204	Intermediate Similarity	NPD5494	Approved
0.814	Intermediate Similarity	NPD7074	Phase 3
0.811	Intermediate Similarity	NPD7411	Suspended
0.8084	Intermediate Similarity	NPD3749	Approved
0.8084	Intermediate Similarity	NPD7075	Discontinued
0.8081	Intermediate Similarity	NPD7054	Approved
0.8075	Intermediate Similarity	NPD2534	Approved
0.8075	Intermediate Similarity	NPD2533	Approved
0.8075	Intermediate Similarity	NPD4378	Clinical (unspecified phase)
0.8075	Intermediate Similarity	NPD2532	Approved
0.805	Intermediate Similarity	NPD3750	Approved
0.8035	Intermediate Similarity	NPD7472	Approved
0.8012	Intermediate Similarity	NPD6799	Approved
0.8	Intermediate Similarity	NPD447	Suspended
0.7989	Intermediate Similarity	NPD7993	Clinical (unspecified phase)
0.7964	Intermediate Similarity	NPD8443	Clinical (unspecified phase)
0.7964	Intermediate Similarity	NPD5402	Approved
0.7941	Intermediate Similarity	NPD6959	Discontinued
0.7941	Intermediate Similarity	NPD1247	Approved
0.7939	Intermediate Similarity	NPD6599	Discontinued
0.7911	Intermediate Similarity	NPD2935	Discontinued
0.7907	Intermediate Similarity	NPD7852	Clinical (unspecified phase)
0.7904	Intermediate Similarity	NPD7096	Clinical (unspecified phase)
0.7898	Intermediate Similarity	NPD7808	Phase 3
0.7886	Intermediate Similarity	NPD6797	Phase 2
0.787	Intermediate Similarity	NPD4381	Clinical (unspecified phase)
0.7862	Intermediate Similarity	NPD1552	Clinical (unspecified phase)
0.7862	Intermediate Similarity	NPD1550	Clinical (unspecified phase)
0.7853	Intermediate Similarity	NPD7410	Clinical (unspecified phase)
0.7849	Intermediate Similarity	NPD3926	Phase 2
0.7848	Intermediate Similarity	NPD2799	Discontinued
0.7844	Intermediate Similarity	NPD6801	Discontinued
0.7841	Intermediate Similarity	NPD7251	Discontinued
0.7833	Intermediate Similarity	NPD8397	Clinical (unspecified phase)
0.7831	Intermediate Similarity	NPD4380	Phase 2
0.7824	Intermediate Similarity	NPD919	Approved
0.7821	Intermediate Similarity	NPD1240	Approved
0.7812	Intermediate Similarity	NPD1549	Phase 2
0.7764	Intermediate Similarity	NPD2800	Approved
0.7758	Intermediate Similarity	NPD6980	Clinical (unspecified phase)
0.7738	Intermediate Similarity	NPD37	Approved
0.7736	Intermediate Similarity	NPD3748	Approved
0.7736	Intermediate Similarity	NPD1510	Phase 2
0.7733	Intermediate Similarity	NPD7199	Phase 2
0.7722	Intermediate Similarity	NPD1607	Approved
0.7719	Intermediate Similarity	NPD6234	Discontinued
0.7707	Intermediate Similarity	NPD943	Approved
0.7706	Intermediate Similarity	NPD4967	Phase 2
0.7706	Intermediate Similarity	NPD4965	Approved
0.7706	Intermediate Similarity	NPD4966	Approved
0.7688	Intermediate Similarity	NPD2796	Approved
0.7658	Intermediate Similarity	NPD230	Phase 1
0.7654	Intermediate Similarity	NPD1243	Approved
0.7654	Intermediate Similarity	NPD7421	Clinical (unspecified phase)
0.7647	Intermediate Similarity	NPD7501	Clinical (unspecified phase)
0.7644	Intermediate Similarity	NPD7184	Clinical (unspecified phase)
0.764	Intermediate Similarity	NPD2346	Discontinued
0.7625	Intermediate Similarity	NPD651	Clinical (unspecified phase)
0.7602	Intermediate Similarity	NPD7768	Phase 2
0.758	Intermediate Similarity	NPD6859	Clinical (unspecified phase)
0.758	Intermediate Similarity	NPD3268	Approved
0.7578	Intermediate Similarity	NPD1551	Phase 2
0.7571	Intermediate Similarity	NPD7804	Clinical (unspecified phase)
0.7554	Intermediate Similarity	NPD7879	Clinical (unspecified phase)
0.7545	Intermediate Similarity	NPD5403	Approved
0.7545	Intermediate Similarity	NPD920	Approved
0.7542	Intermediate Similarity	NPD6559	Discontinued
0.7516	Intermediate Similarity	NPD1509	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD4628	Phase 3
0.75	Intermediate Similarity	NPD1878	Clinical (unspecified phase)
0.7486	Intermediate Similarity	NPD5711	Approved
0.7486	Intermediate Similarity	NPD5710	Approved
0.7486	Intermediate Similarity	NPD5953	Discontinued
0.7484	Intermediate Similarity	NPD1203	Approved
0.7473	Intermediate Similarity	NPD8055	Clinical (unspecified phase)
0.747	Intermediate Similarity	NPD6143	Clinical (unspecified phase)
0.747	Intermediate Similarity	NPD7390	Discontinued
0.7469	Intermediate Similarity	NPD6099	Approved
0.7469	Intermediate Similarity	NPD6100	Approved
0.7425	Intermediate Similarity	NPD642	Clinical (unspecified phase)
0.7425	Intermediate Similarity	NPD5401	Approved
0.7423	Intermediate Similarity	NPD2344	Approved
0.7416	Intermediate Similarity	NPD7228	Approved
0.7396	Intermediate Similarity	NPD1653	Approved
0.7394	Intermediate Similarity	NPD6398	Clinical (unspecified phase)
0.7389	Intermediate Similarity	NPD1530	Clinical (unspecified phase)
0.7374	Intermediate Similarity	NPD7286	Phase 2
0.7358	Intermediate Similarity	NPD2313	Discontinued
0.7345	Intermediate Similarity	NPD5242	Approved
0.7342	Intermediate Similarity	NPD6832	Phase 2
0.7342	Intermediate Similarity	NPD1529	Clinical (unspecified phase)
0.7337	Intermediate Similarity	NPD8434	Phase 2
0.7329	Intermediate Similarity	NPD1933	Approved
0.7318	Intermediate Similarity	NPD3751	Discontinued
0.7305	Intermediate Similarity	NPD643	Clinical (unspecified phase)
0.729	Intermediate Similarity	NPD9717	Approved
0.729	Intermediate Similarity	NPD1608	Approved
0.7288	Intermediate Similarity	NPD3787	Discontinued
0.7284	Intermediate Similarity	NPD6651	Approved
0.7278	Intermediate Similarity	NPD1940	Clinical (unspecified phase)
0.7268	Intermediate Similarity	NPD8312	Approved
0.7268	Intermediate Similarity	NPD8313	Approved
0.7261	Intermediate Similarity	NPD2797	Approved
0.7261	Intermediate Similarity	NPD3267	Approved
0.7261	Intermediate Similarity	NPD3266	Approved
0.7246	Intermediate Similarity	NPD6190	Approved
0.7246	Intermediate Similarity	NPD2309	Approved
0.7226	Intermediate Similarity	NPD422	Phase 1
0.7222	Intermediate Similarity	NPD1899	Clinical (unspecified phase)
0.7207	Intermediate Similarity	NPD2403	Approved
0.7191	Intermediate Similarity	NPD7229	Phase 3
0.7188	Intermediate Similarity	NPD3027	Phase 3
0.7179	Intermediate Similarity	NPD9269	Phase 2
0.7172	Intermediate Similarity	NPD7783	Phase 2
0.7172	Intermediate Similarity	NPD7782	Clinical (unspecified phase)
0.7166	Intermediate Similarity	NPD4287	Approved
0.7165	Intermediate Similarity	NPD7435	Discontinued
0.716	Intermediate Similarity	NPD1612	Clinical (unspecified phase)
0.716	Intermediate Similarity	NPD1613	Approved
0.7157	Intermediate Similarity	NPD8151	Discontinued
0.7151	Intermediate Similarity	NPD8150	Discontinued
0.7143	Intermediate Similarity	NPD9268	Approved
0.7143	Intermediate Similarity	NPD4288	Approved
0.7143	Intermediate Similarity	NPD5353	Approved
0.7143	Intermediate Similarity	NPD3764	Approved
0.7143	Intermediate Similarity	NPD411	Approved
0.7108	Intermediate Similarity	NPD1471	Phase 3
0.7098	Intermediate Similarity	NPD6776	Approved
0.7098	Intermediate Similarity	NPD6779	Approved
0.7098	Intermediate Similarity	NPD6782	Approved
0.7098	Intermediate Similarity	NPD6781	Approved
0.7098	Intermediate Similarity	NPD6780	Approved
0.7098	Intermediate Similarity	NPD6777	Approved
0.7098	Intermediate Similarity	NPD6778	Approved
0.7097	Intermediate Similarity	NPD17	Approved
0.7091	Intermediate Similarity	NPD4308	Phase 3
0.7089	Intermediate Similarity	NPD3225	Approved
0.7069	Intermediate Similarity	NPD6386	Approved
0.7069	Intermediate Similarity	NPD6385	Approved
0.7065	Intermediate Similarity	NPD7685	Pre-registration
0.7065	Intermediate Similarity	NPD7240	Approved
0.7055	Intermediate Similarity	NPD4060	Phase 1
0.7048	Intermediate Similarity	NPD5404	Approved
0.7048	Intermediate Similarity	NPD5405	Approved
0.7048	Intermediate Similarity	NPD5406	Approved
0.7048	Intermediate Similarity	NPD5408	Approved
0.7039	Intermediate Similarity	NPD8127	Discontinued
0.7037	Intermediate Similarity	NPD1699	Clinical (unspecified phase)
0.7037	Intermediate Similarity	NPD1296	Phase 2
0.7027	Intermediate Similarity	NPD7549	Discontinued
0.7027	Intermediate Similarity	NPD4419	Clinical (unspecified phase)
0.7018	Intermediate Similarity	NPD7004	Clinical (unspecified phase)
0.7018	Intermediate Similarity	NPD7422	Clinical (unspecified phase)
0.7	Intermediate Similarity	NPD2798	Approved
0.699	Remote Similarity	NPD7698	Approved
0.699	Remote Similarity	NPD7697	Approved
0.699	Remote Similarity	NPD7696	Phase 3
0.6988	Remote Similarity	NPD7033	Discontinued
0.6975	Remote Similarity	NPD4625	Phase 3
0.6962	Remote Similarity	NPD1481	Phase 2
0.6957	Remote Similarity	NPD9494	Approved
0.6954	Remote Similarity	NPD5808	Clinical (unspecified phase)
0.6954	Remote Similarity	NPD7870	Phase 2
0.6954	Remote Similarity	NPD7871	Phase 2
0.695	Remote Similarity	NPD7874	Approved
0.695	Remote Similarity	NPD7875	Clinical (unspecified phase)
0.6946	Remote Similarity	NPD4477	Approved
0.6946	Remote Similarity	NPD4476	Approved
0.6943	Remote Similarity	NPD8090	Clinical (unspecified phase)
0.6937	Remote Similarity	NPD1470	Approved
0.6918	Remote Similarity	NPD4379	Clinical (unspecified phase)
0.6914	Remote Similarity	NPD4908	Phase 1
0.6909	Remote Similarity	NPD6355	Discontinued
0.6899	Remote Similarity	NPD1535	Discovery
0.6899	Remote Similarity	NPD1201	Approved
0.6897	Remote Similarity	NPD2370	Clinical (unspecified phase)
0.689	Remote Similarity	NPD6233	Phase 2
0.6882	Remote Similarity	NPD4110	Phase 3
0.6882	Remote Similarity	NPD4109	Clinical (unspecified phase)
0.6879	Remote Similarity	NPD6273	Approved

Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data