NPASS Compound

Structure

CID103409 OpenBabel06191715452D 23 25 0 0 1 0 0 0 0 0999 V2000 -2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1962 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 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 2 0 0 0 0 1 7 1 0 0 0 0 2 4 2 0 0 0 0 2 7 1 0 0 0 0 3 8 1 0 0 0 0 4 11 1 0 0 0 0 5 8 2 0 0 0 0 5 9 1 0 0 0 0 6 16 1 0 0 0 0 7 9 2 0 0 0 0 8 21 1 0 0 0 0 9 22 1 0 0 0 0 10 6 1 6 0 0 0 10 12 1 0 0 0 0 10 23 1 0 0 0 0 11 17 2 0 0 0 0 11 22 1 0 0 0 0 12 13 1 0 0 0 0 12 18 1 1 0 0 0 13 14 1 0 0 0 0 13 19 1 6 0 0 0 14 15 1 0 0 0 0 14 20 1 1 0 0 0 15 21 1 6 0 0 0 15 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	324.08
Volume:	299.466
LogP:	-0.36
LogD:	-0.28
LogS:	-1.952
# Rotatable Bonds:	3
TPSA:	129.59
# H-Bond Aceptor:	8
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.528
Synthetic Accessibility Score:	3.567
Fsp3:	0.4
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.589
MDCK Permeability:	3.528717934386805e-05
Pgp-inhibitor:	0.002
Pgp-substrate:	0.17
Human Intestinal Absorption (HIA):	0.291
20% Bioavailability (F20%):	0.011
30% Bioavailability (F30%):	0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.227
Plasma Protein Binding (PPB):	68.37468719482422%
Volume Distribution (VD):	0.742
Pgp-substrate:	25.831647872924805%

ADMET: Metabolism

CYP1A2-inhibitor:	0.159
CYP1A2-substrate:	0.098
CYP2C19-inhibitor:	0.037
CYP2C19-substrate:	0.104
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.309
CYP2D6-inhibitor:	0.106
CYP2D6-substrate:	0.507
CYP3A4-inhibitor:	0.013
CYP3A4-substrate:	0.056

ADMET: Excretion

Clearance (CL):	2.438
Half-life (T1/2):	0.608

ADMET: Toxicity

hERG Blockers:	0.222
Human Hepatotoxicity (H-HT):	0.109
Drug-inuced Liver Injury (DILI):	0.737
AMES Toxicity:	0.139
Rat Oral Acute Toxicity:	0.073
Maximum Recommended Daily Dose:	0.007
Skin Sensitization:	0.166
Carcinogencity:	0.896
Eye Corrosion:	0.004
Eye Irritation:	0.256
Respiratory Toxicity:	0.023

Download Data

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

Natural Product: NPC103409

Natural Product ID:	NPC103409
*Common Name:**	Skimmin
IUPAC Name:	7-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxychromen-2-one
Synonyms:	Skimmin
Standard InCHIKey:	VPAOSFFTKWUGAD-TVKJYDDYSA-N
Standard InCHI:	InChI=1S/C15H16O8/c16-6-10-12(18)13(19)14(20)15(23-10)21-8-3-1-7-2-4-11(17)22-9(7)5-8/h1-5,10,12-16,18-20H,6H2/t10-,12-,13+,14-,15-/m1/s1
SMILES:	OC[C@H]1O[C@@H](Oc2ccc3c(c2)oc(=O)cc3)[C@@H]([C@H]([C@@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL526377
PubChem CID:	99693
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000145] Coumarins and derivatives [CHEMONTID:0001743] Coumarin glycosides

*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
NPO13278	Strychnos spinosa	Species	Loganiaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[17637068]
NPO15233	Balanophora japonica	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18302336]
NPO33433	adina cordifolia	Species	Rubiaceae	Eukaryota	root bark	n.a.	n.a.	PMID[18675491]
NPO12339	Daphne feddei	Species	Thymelaeaceae	Eukaryota	stem bark	Kunming, Yunnan Province, China	n.a.	PMID[18986199]
NPO5470	Cynoglossum amabile	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22432912]
NPO15650	Picea neoveitchii	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22901896]
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24813739]
NPO2330	Alchornea cordifolia	Species	Euphorbiaceae	Eukaryota	n.a.	stem	n.a.	PMID[26724423]
NPO2330	Alchornea cordifolia	Species	Euphorbiaceae	Eukaryota	n.a.	root	n.a.	PMID[26724423]
NPO13278	Strychnos spinosa	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15233	Balanophora japonica	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5470	Cynoglossum amabile	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12487	Juniperus horizontalis	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5470	Cynoglossum amabile	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23754	Solanum aculeatissimum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15233	Balanophora japonica	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23772	Tetradium glabrifolium	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10098	Glycosmis pseudoracemosa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13278	Strychnos spinosa	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5470	Cynoglossum amabile	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1759	Alexandrium excavatum	Species	Gonyaulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10211	Pajanelia multijuga	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO15650	Picea neoveitchii	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1109	Corydalis persica	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18873.2	Salmonella enterica subsp. enterica serovar bovismorbificans	Subspecies	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO23772	Tetradium glabrifolium	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21329	Ilyonectria destructans	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13278	Strychnos spinosa	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15145	Rauvolfia salicifolia	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5470	Cynoglossum amabile	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3965	Corynanthe pachyceras	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12487	Juniperus horizontalis	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16801	Cota tinctoria	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12339	Daphne feddei	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10098	Glycosmis pseudoracemosa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15233	Balanophora japonica	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14526	Plectranthus caninus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15329	Rhizoplaca baranowii	Species	Lecanoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13848	Amomum daniellii	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13647	Calcarisporium thermophilum	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2330	Alchornea cordifolia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23754	Solanum aculeatissimum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5398	Peucedanum oroselinum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14947	Lathyrus tingitanus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7521	Hygrophorus eburneus	Species	Hygrophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6906	Atalantia wightii	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11430	Inula grantioides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3761	Plectosphaerella cucumerina	Species	Plectosphaerellaceae	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
IC50	1
Others	9

Activity Type	# Activity
NON-MOLECULAR	1
Organism	9

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT992	Organism	Entamoeba histolytica	Entamoeba histolytica	IC50	=	4150000.0	nM	PMID[489626]
NPT1493	Organism	Ceratocystis paradoxa	Ceratocystis paradoxa	GI	=	5.8	%	PMID[489627]
NPT1494	Organism	Alternaria mali	Alternaria mali	GI	=	0.0	%	PMID[489627]
NPT722	Organism	Athelia rolfsii	Athelia rolfsii	GI	=	24.1	%	PMID[489627]
NPT1198	Organism	Magnaporthe grisea	Magnaporthe grisea	GI	=	0.0	%	PMID[489627]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	GI	=	15.3	%	PMID[489627]
NPT1493	Organism	Ceratocystis paradoxa	Ceratocystis paradoxa	IZ	=	1.5	mm	PMID[489627]
NPT1494	Organism	Alternaria mali	Alternaria mali	IZ	=	0.0	mm	PMID[489627]
NPT722	Organism	Athelia rolfsii	Athelia rolfsii	IZ	=	2.8	mm	PMID[489627]
NPT1198	Organism	Magnaporthe grisea	Magnaporthe grisea	IZ	=	0.0	mm	PMID[489627]

☑ 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 NPC103409 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	370
0.1-0.2	1689
0.2-0.3	4210
0.3-0.4	9521
0.4-0.5	9132
0.5-0.6	4239
0.6-0.7	6013
0.7-0.8	5505
0.8-0.85	1615
0.85-0.9	363
0.9-0.95	39
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9699	High Similarity	NPC215512
0.9699	High Similarity	NPC476442
0.9416	High Similarity	NPC85624
0.9281	High Similarity	NPC471764
0.9281	High Similarity	NPC87950
0.9281	High Similarity	NPC52740
0.9281	High Similarity	NPC41844
0.9281	High Similarity	NPC296377
0.9275	High Similarity	NPC226722
0.9254	High Similarity	NPC166180
0.9231	High Similarity	NPC146540
0.9214	High Similarity	NPC169510
0.9214	High Similarity	NPC96294
0.916	High Similarity	NPC295970
0.9149	High Similarity	NPC206264
0.9149	High Similarity	NPC313334
0.9149	High Similarity	NPC212670
0.9085	High Similarity	NPC114740
0.9078	High Similarity	NPC93924
0.9044	High Similarity	NPC153818
0.9044	High Similarity	NPC232246
0.903	High Similarity	NPC469449
0.9023	High Similarity	NPC29734
0.9021	High Similarity	NPC213197
0.8971	High Similarity	NPC224543
0.8971	High Similarity	NPC188380
0.8971	High Similarity	NPC78746
0.8958	High Similarity	NPC476352
0.8958	High Similarity	NPC215060
0.8951	High Similarity	NPC100818
0.8947	High Similarity	NPC113098
0.8921	High Similarity	NPC145319
0.8913	High Similarity	NPC312881
0.8905	High Similarity	NPC184861
0.8905	High Similarity	NPC225106
0.8905	High Similarity	NPC281014
0.8905	High Similarity	NPC294456
0.8905	High Similarity	NPC212124
0.8897	High Similarity	NPC185778
0.8881	High Similarity	NPC272650
0.8881	High Similarity	NPC267336
0.8864	High Similarity	NPC258567
0.8864	High Similarity	NPC121740
0.8864	High Similarity	NPC224774
0.8849	High Similarity	NPC195357
0.8849	High Similarity	NPC152771
0.8849	High Similarity	NPC287286
0.8841	High Similarity	NPC279573
0.8832	High Similarity	NPC26954
0.8832	High Similarity	NPC38099
0.8828	High Similarity	NPC53587
0.8828	High Similarity	NPC470264
0.8828	High Similarity	NPC176186
0.8828	High Similarity	NPC169404
0.8824	High Similarity	NPC326600
0.8824	High Similarity	NPC62366
0.8824	High Similarity	NPC50896
0.8824	High Similarity	NPC204353
0.8806	High Similarity	NPC474491
0.8797	High Similarity	NPC469453
0.8794	High Similarity	NPC292443
0.8768	High Similarity	NPC155963
0.8768	High Similarity	NPC124149
0.8767	High Similarity	NPC150442
0.8759	High Similarity	NPC472525
0.8732	High Similarity	NPC469701
0.8732	High Similarity	NPC476450
0.8716	High Similarity	NPC284810
0.8705	High Similarity	NPC211110
0.8705	High Similarity	NPC151946
0.8692	High Similarity	NPC226712
0.8686	High Similarity	NPC180716
0.8686	High Similarity	NPC213173
0.8686	High Similarity	NPC224475
0.8671	High Similarity	NPC107120
0.8671	High Similarity	NPC199928
0.8671	High Similarity	NPC74320
0.8662	High Similarity	NPC232228
0.8652	High Similarity	NPC245219
0.8652	High Similarity	NPC31081
0.8643	High Similarity	NPC210478
0.8633	High Similarity	NPC262328
0.8633	High Similarity	NPC87777
0.8623	High Similarity	NPC33986
0.8621	High Similarity	NPC106138
0.8615	High Similarity	NPC163200
0.8615	High Similarity	NPC469412
0.8615	High Similarity	NPC198734
0.8615	High Similarity	NPC269242
0.8613	High Similarity	NPC318400
0.8613	High Similarity	NPC133956
0.8613	High Similarity	NPC471910
0.8613	High Similarity	NPC296624
0.8613	High Similarity	NPC207002
0.8613	High Similarity	NPC31849
0.8613	High Similarity	NPC167111
0.8611	High Similarity	NPC15577
0.8592	High Similarity	NPC469367
0.8582	High Similarity	NPC300611
0.8582	High Similarity	NPC186406
0.8582	High Similarity	NPC80098
0.8562	High Similarity	NPC107197
0.8561	High Similarity	NPC37468
0.8561	High Similarity	NPC186418
0.8552	High Similarity	NPC302989
0.8552	High Similarity	NPC478237
0.8552	High Similarity	NPC218685
0.8552	High Similarity	NPC187398
0.8552	High Similarity	NPC476348
0.8551	High Similarity	NPC47163
0.8551	High Similarity	NPC98179
0.8551	High Similarity	NPC84894
0.8551	High Similarity	NPC195343
0.8551	High Similarity	NPC267412
0.8551	High Similarity	NPC319859
0.8551	High Similarity	NPC287182
0.8551	High Similarity	NPC100986
0.8551	High Similarity	NPC166672
0.8551	High Similarity	NPC18804
0.8551	High Similarity	NPC198381
0.8551	High Similarity	NPC253574
0.8551	High Similarity	NPC260265
0.8551	High Similarity	NPC74655
0.8551	High Similarity	NPC164269
0.8551	High Similarity	NPC127888
0.855	High Similarity	NPC11724
0.854	High Similarity	NPC269421
0.854	High Similarity	NPC194277
0.854	High Similarity	NPC303422
0.854	High Similarity	NPC26080
0.854	High Similarity	NPC85799
0.854	High Similarity	NPC165686
0.8538	High Similarity	NPC60589
0.8538	High Similarity	NPC469708
0.8531	High Similarity	NPC471824
0.8511	High Similarity	NPC202700
0.8503	High Similarity	NPC213723
0.85	High Similarity	NPC471069
0.85	High Similarity	NPC471068
0.8493	Intermediate Similarity	NPC287294
0.8489	Intermediate Similarity	NPC281241
0.8489	Intermediate Similarity	NPC472424
0.8489	Intermediate Similarity	NPC86892
0.8489	Intermediate Similarity	NPC471909
0.8489	Intermediate Similarity	NPC471625
0.8485	Intermediate Similarity	NPC52097
0.8483	Intermediate Similarity	NPC476347
0.8478	Intermediate Similarity	NPC294166
0.8478	Intermediate Similarity	NPC115022
0.8478	Intermediate Similarity	NPC2363
0.8477	Intermediate Similarity	NPC43761
0.8473	Intermediate Similarity	NPC302107
0.8473	Intermediate Similarity	NPC235190
0.8473	Intermediate Similarity	NPC476872
0.8473	Intermediate Similarity	NPC180006
0.8467	Intermediate Similarity	NPC121376
0.8462	Intermediate Similarity	NPC478239
0.8462	Intermediate Similarity	NPC138212
0.8462	Intermediate Similarity	NPC281356
0.8462	Intermediate Similarity	NPC298796
0.8456	Intermediate Similarity	NPC168710
0.8456	Intermediate Similarity	NPC253595
0.8451	Intermediate Similarity	NPC210192
0.8451	Intermediate Similarity	NPC108674
0.8444	Intermediate Similarity	NPC288416
0.844	Intermediate Similarity	NPC471072
0.844	Intermediate Similarity	NPC164148
0.844	Intermediate Similarity	NPC471070
0.844	Intermediate Similarity	NPC100389
0.844	Intermediate Similarity	NPC43500
0.844	Intermediate Similarity	NPC471071
0.8435	Intermediate Similarity	NPC21184
0.8435	Intermediate Similarity	NPC120426
0.8435	Intermediate Similarity	NPC205727
0.8435	Intermediate Similarity	NPC294522
0.8433	Intermediate Similarity	NPC126991
0.8433	Intermediate Similarity	NPC83218
0.8433	Intermediate Similarity	NPC470510
0.8429	Intermediate Similarity	NPC160727
0.8429	Intermediate Similarity	NPC128529
0.8429	Intermediate Similarity	NPC55615
0.8429	Intermediate Similarity	NPC177281
0.8429	Intermediate Similarity	NPC476455
0.8429	Intermediate Similarity	NPC471630
0.8429	Intermediate Similarity	NPC283019
0.8429	Intermediate Similarity	NPC149320
0.8417	Intermediate Similarity	NPC471029
0.8417	Intermediate Similarity	NPC34456
0.8417	Intermediate Similarity	NPC309953
0.8417	Intermediate Similarity	NPC188555
0.8417	Intermediate Similarity	NPC130496
0.8414	Intermediate Similarity	NPC205361
0.8411	Intermediate Similarity	NPC43638
0.8406	Intermediate Similarity	NPC162093
0.8406	Intermediate Similarity	NPC299144
0.8403	Intermediate Similarity	NPC471028
0.8403	Intermediate Similarity	NPC297342
0.8397	Intermediate Similarity	NPC247553
0.8392	Intermediate Similarity	NPC472353
0.8392	Intermediate Similarity	NPC475084

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 NPC103409 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	347
0.1-0.2	875
0.2-0.3	1877
0.3-0.4	2697
0.4-0.5	1914
0.5-0.6	976
0.6-0.7	312
0.7-0.8	116
0.8-0.85	33
0.85-0.9	2
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9149	High Similarity	NPD1653	Approved
0.8714	High Similarity	NPD1652	Phase 2
0.8692	High Similarity	NPD1091	Approved
0.8289	Intermediate Similarity	NPD4381	Clinical (unspecified phase)
0.8271	Intermediate Similarity	NPD422	Phase 1
0.8214	Intermediate Similarity	NPD5124	Phase 1
0.8214	Intermediate Similarity	NPD5123	Clinical (unspecified phase)
0.7887	Intermediate Similarity	NPD1612	Clinical (unspecified phase)
0.7887	Intermediate Similarity	NPD1613	Approved
0.7836	Intermediate Similarity	NPD1548	Phase 1
0.7815	Intermediate Similarity	NPD5403	Approved
0.7808	Intermediate Similarity	NPD7266	Discontinued
0.78	Intermediate Similarity	NPD5401	Approved
0.7764	Intermediate Similarity	NPD3818	Discontinued
0.7746	Intermediate Similarity	NPD6859	Clinical (unspecified phase)
0.7744	Intermediate Similarity	NPD4338	Clinical (unspecified phase)
0.7742	Intermediate Similarity	NPD8455	Phase 2
0.7716	Intermediate Similarity	NPD7804	Clinical (unspecified phase)
0.7716	Intermediate Similarity	NPD7054	Approved
0.7683	Intermediate Similarity	NPD6559	Discontinued
0.7677	Intermediate Similarity	NPD6801	Discontinued
0.7669	Intermediate Similarity	NPD7472	Approved
0.7662	Intermediate Similarity	NPD4380	Phase 2
0.7643	Intermediate Similarity	NPD4868	Clinical (unspecified phase)
0.7628	Intermediate Similarity	NPD7096	Clinical (unspecified phase)
0.7622	Intermediate Similarity	NPD6797	Phase 2
0.7616	Intermediate Similarity	NPD6799	Approved
0.7609	Intermediate Similarity	NPD1610	Phase 2
0.7606	Intermediate Similarity	NPD1529	Clinical (unspecified phase)
0.7606	Intermediate Similarity	NPD1008	Clinical (unspecified phase)
0.7595	Intermediate Similarity	NPD7075	Discontinued
0.758	Intermediate Similarity	NPD5402	Approved
0.7576	Intermediate Similarity	NPD7251	Discontinued
0.7571	Intermediate Similarity	NPD3225	Approved
0.7561	Intermediate Similarity	NPD7074	Phase 3
0.7538	Intermediate Similarity	NPD290	Approved
0.7538	Intermediate Similarity	NPD1358	Approved
0.7535	Intermediate Similarity	NPD1530	Clinical (unspecified phase)
0.753	Intermediate Similarity	NPD7808	Phase 3
0.7519	Intermediate Similarity	NPD9697	Approved
0.7517	Intermediate Similarity	NPD1549	Phase 2
0.75	Intermediate Similarity	NPD1296	Phase 2
0.7483	Intermediate Similarity	NPD7097	Phase 1
0.7483	Intermediate Similarity	NPD4908	Phase 1
0.7468	Intermediate Similarity	NPD3817	Phase 2
0.7466	Intermediate Similarity	NPD4340	Discontinued
0.7453	Intermediate Similarity	NPD7199	Phase 2
0.745	Intermediate Similarity	NPD1552	Clinical (unspecified phase)
0.745	Intermediate Similarity	NPD1550	Clinical (unspecified phase)
0.7417	Intermediate Similarity	NPD3750	Approved
0.7417	Intermediate Similarity	NPD1878	Clinical (unspecified phase)
0.7389	Intermediate Similarity	NPD7411	Suspended
0.7383	Intermediate Similarity	NPD1551	Phase 2
0.7379	Intermediate Similarity	NPD4907	Clinical (unspecified phase)
0.7379	Intermediate Similarity	NPD6798	Discontinued
0.7342	Intermediate Similarity	NPD37	Approved
0.7329	Intermediate Similarity	NPD6233	Phase 2
0.7325	Intermediate Similarity	NPD6599	Discontinued
0.7315	Intermediate Similarity	NPD3748	Approved
0.7312	Intermediate Similarity	NPD4966	Approved
0.7312	Intermediate Similarity	NPD4967	Phase 2
0.7312	Intermediate Similarity	NPD4965	Approved
0.731	Intermediate Similarity	NPD3027	Phase 3
0.7303	Intermediate Similarity	NPD4628	Phase 3
0.7296	Intermediate Similarity	NPD7819	Suspended
0.7289	Intermediate Similarity	NPD5844	Phase 1
0.7285	Intermediate Similarity	NPD2424	Discontinued
0.7273	Intermediate Similarity	NPD2797	Approved
0.7267	Intermediate Similarity	NPD2796	Approved
0.7259	Intermediate Similarity	NPD7843	Approved
0.7256	Intermediate Similarity	NPD7184	Clinical (unspecified phase)
0.7237	Intermediate Similarity	NPD6674	Discontinued
0.7233	Intermediate Similarity	NPD1934	Approved
0.723	Intermediate Similarity	NPD1933	Approved
0.7229	Intermediate Similarity	NPD7228	Approved
0.7222	Intermediate Similarity	NPD6234	Discontinued
0.7218	Intermediate Similarity	NPD2684	Approved
0.7208	Intermediate Similarity	NPD5058	Phase 3
0.7202	Intermediate Similarity	NPD7993	Clinical (unspecified phase)
0.72	Intermediate Similarity	NPD1510	Phase 2
0.72	Intermediate Similarity	NPD7033	Discontinued
0.7197	Intermediate Similarity	NPD3134	Approved
0.719	Intermediate Similarity	NPD6398	Clinical (unspecified phase)
0.7188	Intermediate Similarity	NPD2393	Clinical (unspecified phase)
0.7188	Intermediate Similarity	NPD1465	Phase 2
0.7185	Intermediate Similarity	NPD969	Suspended
0.7183	Intermediate Similarity	NPD9717	Approved
0.717	Intermediate Similarity	NPD7615	Clinical (unspecified phase)
0.7163	Intermediate Similarity	NPD3496	Discontinued
0.7161	Intermediate Similarity	NPD1511	Approved
0.7153	Intermediate Similarity	NPD1203	Approved
0.7143	Intermediate Similarity	NPD3268	Approved
0.7134	Intermediate Similarity	NPD6980	Clinical (unspecified phase)
0.7133	Intermediate Similarity	NPD4978	Clinical (unspecified phase)
0.7132	Intermediate Similarity	NPD5535	Approved
0.7126	Intermediate Similarity	NPD3751	Discontinued
0.7124	Intermediate Similarity	NPD7421	Clinical (unspecified phase)
0.7123	Intermediate Similarity	NPD6832	Phase 2
0.7115	Intermediate Similarity	NPD4378	Clinical (unspecified phase)
0.7114	Intermediate Similarity	NPD6355	Discontinued
0.711	Intermediate Similarity	NPD6841	Approved
0.711	Intermediate Similarity	NPD6843	Phase 3
0.711	Intermediate Similarity	NPD6842	Approved
0.7108	Intermediate Similarity	NPD6167	Clinical (unspecified phase)
0.7108	Intermediate Similarity	NPD6168	Clinical (unspecified phase)
0.7108	Intermediate Similarity	NPD6166	Phase 2
0.7101	Intermediate Similarity	NPD7157	Approved
0.7092	Intermediate Similarity	NPD1778	Approved
0.7091	Intermediate Similarity	NPD3787	Discontinued
0.7083	Intermediate Similarity	NPD8651	Approved
0.7081	Intermediate Similarity	NPD2801	Approved
0.7076	Intermediate Similarity	NPD8312	Approved
0.7076	Intermediate Similarity	NPD8313	Approved
0.707	Intermediate Similarity	NPD1512	Approved
0.7059	Intermediate Similarity	NPD970	Clinical (unspecified phase)
0.7059	Intermediate Similarity	NPD7240	Approved
0.7059	Intermediate Similarity	NPD7685	Pre-registration
0.7055	Intermediate Similarity	NPD2861	Phase 2
0.7049	Intermediate Similarity	NPD7583	Approved
0.7047	Intermediate Similarity	NPD4060	Phase 1
0.7044	Intermediate Similarity	NPD8158	Clinical (unspecified phase)
0.7032	Intermediate Similarity	NPD6190	Approved
0.7027	Intermediate Similarity	NPD1048	Approved
0.7027	Intermediate Similarity	NPD6410	Clinical (unspecified phase)
0.7025	Intermediate Similarity	NPD920	Approved
0.702	Intermediate Similarity	NPD4538	Approved
0.702	Intermediate Similarity	NPD4536	Approved
0.702	Intermediate Similarity	NPD4537	Clinical (unspecified phase)
0.7018	Intermediate Similarity	NPD7549	Discontinued
0.7014	Intermediate Similarity	NPD4749	Approved
0.7013	Intermediate Similarity	NPD5698	Clinical (unspecified phase)
0.7011	Intermediate Similarity	NPD7585	Approved
0.7006	Intermediate Similarity	NPD642	Clinical (unspecified phase)
0.7006	Intermediate Similarity	NPD7410	Clinical (unspecified phase)
0.7	Intermediate Similarity	NPD230	Phase 1
0.7	Intermediate Similarity	NPD447	Suspended
0.6994	Remote Similarity	NPD7768	Phase 2
0.6993	Remote Similarity	NPD5763	Approved
0.6993	Remote Similarity	NPD5762	Approved
0.6987	Remote Similarity	NPD643	Clinical (unspecified phase)
0.6986	Remote Similarity	NPD1019	Discontinued
0.698	Remote Similarity	NPD4062	Phase 3
0.6974	Remote Similarity	NPD5960	Phase 3
0.6974	Remote Similarity	NPD5588	Approved
0.6962	Remote Similarity	NPD7314	Clinical (unspecified phase)
0.6943	Remote Similarity	NPD6143	Clinical (unspecified phase)
0.6943	Remote Similarity	NPD7212	Phase 2
0.6943	Remote Similarity	NPD7213	Phase 3
0.6939	Remote Similarity	NPD3018	Phase 2
0.6933	Remote Similarity	NPD8443	Clinical (unspecified phase)
0.6933	Remote Similarity	NPD1240	Approved
0.6933	Remote Similarity	NPD2415	Discontinued
0.6918	Remote Similarity	NPD3267	Approved
0.6918	Remote Similarity	NPD3266	Approved
0.6905	Remote Similarity	NPD7852	Clinical (unspecified phase)
0.6903	Remote Similarity	NPD1243	Approved
0.6901	Remote Similarity	NPD1357	Approved
0.6899	Remote Similarity	NPD7004	Clinical (unspecified phase)
0.6893	Remote Similarity	NPD7879	Clinical (unspecified phase)
0.689	Remote Similarity	NPD3882	Suspended
0.6875	Remote Similarity	NPD3705	Approved
0.6863	Remote Similarity	NPD4308	Phase 3
0.6853	Remote Similarity	NPD6516	Phase 2
0.6853	Remote Similarity	NPD5846	Approved
0.6848	Remote Similarity	NPD3749	Approved
0.6846	Remote Similarity	NPD4625	Phase 3
0.6846	Remote Similarity	NPD7095	Approved
0.6842	Remote Similarity	NPD1607	Approved
0.6842	Remote Similarity	NPD6653	Approved
0.6835	Remote Similarity	NPD1241	Discontinued
0.6831	Remote Similarity	NPD1894	Discontinued
0.6831	Remote Similarity	NPD9545	Approved
0.6826	Remote Similarity	NPD8127	Discontinued
0.6821	Remote Similarity	NPD4140	Approved
0.6815	Remote Similarity	NPD968	Approved
0.6807	Remote Similarity	NPD919	Approved
0.68	Remote Similarity	NPD2313	Discontinued
0.6792	Remote Similarity	NPD7447	Phase 1
0.6783	Remote Similarity	NPD5691	Approved
0.6781	Remote Similarity	NPD3685	Discontinued
0.6781	Remote Similarity	NPD2983	Phase 2
0.6781	Remote Similarity	NPD2982	Phase 2
0.6776	Remote Similarity	NPD1899	Clinical (unspecified phase)
0.6774	Remote Similarity	NPD6002	Phase 3
0.6774	Remote Similarity	NPD6004	Phase 3
0.6774	Remote Similarity	NPD6003	Clinical (unspecified phase)
0.6774	Remote Similarity	NPD6005	Phase 3
0.6774	Remote Similarity	NPD7584	Approved
0.6774	Remote Similarity	NPD6006	Clinical (unspecified phase)
0.6766	Remote Similarity	NPD5494	Approved
0.6759	Remote Similarity	NPD1547	Clinical (unspecified phase)
0.6759	Remote Similarity	NPD1535	Discovery
0.675	Remote Similarity	NPD1940	Clinical (unspecified phase)
0.6736	Remote Similarity	NPD4626	Approved
0.6733	Remote Similarity	NPD3180	Approved
0.6733	Remote Similarity	NPD3179	Approved
0.6728	Remote Similarity	NPD7458	Discontinued
0.6728	Remote Similarity	NPD5808	Clinical (unspecified phase)
0.6727	Remote Similarity	NPD4288	Approved
0.6712	Remote Similarity	NPD1481	Phase 2

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