NPASS Compound

Structure

CID60186 OpenBabel06191715392D 25 28 0 0 0 0 0 0 0 0999 V2000 -4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -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 -0.0000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 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 -3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 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 -2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 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 -0.8660 -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 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 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 -0.0000 -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 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 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 3.4641 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 21 1 0 0 0 0 2 24 1 0 0 0 0 3 25 1 0 0 0 0 4 5 2 0 0 0 0 4 11 1 0 0 0 0 5 13 1 0 0 0 0 6 7 1 0 0 0 0 6 12 1 0 0 0 0 7 21 1 0 0 0 0 8 11 2 0 0 0 0 8 16 1 0 0 0 0 9 14 2 0 0 0 0 9 17 1 0 0 0 0 10 15 1 0 0 0 0 10 21 1 0 0 0 0 11 14 1 0 0 0 0 12 13 2 0 0 0 0 12 15 1 0 0 0 0 13 18 1 0 0 0 0 14 18 1 0 0 0 0 15 19 2 0 0 0 0 16 17 2 0 0 0 0 16 22 1 0 0 0 0 17 24 1 0 0 0 0 18 20 2 0 0 0 0 19 20 1 0 0 0 0 19 23 1 0 0 0 0 20 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	342.15
Volume:	354.303
LogP:	3.767
LogD:	3.431
LogS:	-5.884
# Rotatable Bonds:	7
TPSA:	61.06
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.702
Synthetic Accessibility Score:	2.198
Fsp3:	0.3
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.731
MDCK Permeability:	3.3428543247282505e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.191
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.011
30% Bioavailability (F30%):	0.014

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.767
Plasma Protein Binding (PPB):	86.94779968261719%
Volume Distribution (VD):	0.768
Pgp-substrate:	8.768146514892578%

ADMET: Metabolism

CYP1A2-inhibitor:	0.966
CYP1A2-substrate:	0.947
CYP2C19-inhibitor:	0.765
CYP2C19-substrate:	0.391
CYP2C9-inhibitor:	0.716
CYP2C9-substrate:	0.89
CYP2D6-inhibitor:	0.192
CYP2D6-substrate:	0.935
CYP3A4-inhibitor:	0.871
CYP3A4-substrate:	0.458

ADMET: Excretion

Clearance (CL):	10.185
Half-life (T1/2):	0.699

ADMET: Toxicity

hERG Blockers:	0.033
Human Hepatotoxicity (H-HT):	0.262
Drug-inuced Liver Injury (DILI):	0.921
AMES Toxicity:	0.206
Rat Oral Acute Toxicity:	0.037
Maximum Recommended Daily Dose:	0.59
Skin Sensitization:	0.302
Carcinogencity:	0.186
Eye Corrosion:	0.003
Eye Irritation:	0.013
Respiratory Toxicity:	0.059

Download Data

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

Natural Product: NPC60186

Natural Product ID:	NPC60186
*Common Name:**	Litebamine
IUPAC Name:	9,11-dimethoxy-2-methyl-3,4-dihydro-1H-naphtho[2,1-f]isoquinoline-8,12-diol
Synonyms:	Litebamine
Standard InCHIKey:	QOWFEPGZJDCIKG-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C20H21NO4/c1-21-7-6-12-13-5-4-11-8-16(22)17(24-2)9-14(11)18(13)20(25-3)19(23)15(12)10-21/h4-5,8-9,22-23H,6-7,10H2,1-3H3
SMILES:	COc1c(O)c2CN(C)CCc2c2c1c1cc(OC)c(cc1cc2)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL453173
PubChem CID:	196885
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000025] Phenanthrenes and derivatives [CHEMONTID:0003007] Phenanthrols

*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
NPO27883	Bursera simaruba	Species	Burseraceae	Eukaryota	Resin	n.a.	n.a.	PMID[1294696]
NPO28935	Ericameria laricifolia	Species	Asteraceae	Eukaryota	n.a.	Sonoran Desert	n.a.	PMID[15043404]
NPO29110	Litsea cubeba	Species	Lauraceae	Eukaryota	n.a.	aerial part	n.a.	PMID[18991207]
NPO27883	Bursera simaruba	Species	Burseraceae	Eukaryota	n.a.	bark	n.a.	PMID[19329133]
NPO29110	Litsea cubeba	Species	Lauraceae	Eukaryota	essential oil	Tibet	n.a.	PMID[20944522]
NPO29110	Litsea cubeba	Species	Lauraceae	Eukaryota	Twigs	n.a.	n.a.	PMID[28541690]
NPO27903	Delphinium denudatum	Species	Ranunculaceae	Eukaryota	n.a.	root	n.a.	PMID[9170290]
NPO29110	Litsea cubeba	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26851	Eupatorium rebaudianum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27903	Delphinium denudatum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27724	Polygala senega	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1079	Vachellia karroo	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26851	Eupatorium rebaudianum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18780	Diplacus aurantiacus	Species	Phrymaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27724	Polygala senega	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29110	Litsea cubeba	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27903	Delphinium denudatum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27724	Polygala senega	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27724	Polygala senega	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29110	Litsea cubeba	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29307	Loranthus longiflorus	Species	Loranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27724	Polygala senega	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16079	Cephalaria leucantha	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27883	Bursera simaruba	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29411	Streptomyces nigrescens	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO26851	Eupatorium rebaudianum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26549	Polanisia trachysperma	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1079	Vachellia karroo	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28959	Cissus quadrangularis	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18780	Diplacus aurantiacus	Species	Phrymaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29377	Callistemon speciosus	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28549	Mentha incana	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29218	Ramalina farinacea	Species	Ramalinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27256	Solanum boerhaavii	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29144	Ormosia fordiana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27562	Coleus wulfenioides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28935	Ericameria laricifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27903	Delphinium denudatum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29110	Litsea cubeba	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO862	Podocarpus elatus	Species	Podocarpaceae	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	1

Activity Type	# Activity
Individual Protein	1
NON-MOLECULAR	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT66	Individual Protein	Acetylcholinesterase	Electrophorus electricus	IC50	=	22000.0	nM	PMID[531264]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Inhibition	=	77.0	%	PMID[531264]

☑ 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 NPC60186 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	339
0.1-0.2	1708
0.2-0.3	7304
0.3-0.4	10811
0.4-0.5	5014
0.5-0.6	9811
0.6-0.7	6080
0.7-0.8	1207
0.8-0.85	274
0.85-0.9	128
0.9-0.95	20
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9363	High Similarity	NPC81218
0.9363	High Similarity	NPC474931
0.9363	High Similarity	NPC145832
0.9363	High Similarity	NPC117188
0.9363	High Similarity	NPC306555
0.9363	High Similarity	NPC205421
0.9363	High Similarity	NPC158376
0.9363	High Similarity	NPC12053
0.9359	High Similarity	NPC96603
0.9359	High Similarity	NPC306843
0.9359	High Similarity	NPC477563
0.9359	High Similarity	NPC136508
0.9359	High Similarity	NPC253043
0.9359	High Similarity	NPC212794
0.9359	High Similarity	NPC78222
0.9359	High Similarity	NPC13504
0.9359	High Similarity	NPC196447
0.9295	High Similarity	NPC324144
0.9172	High Similarity	NPC1229
0.9167	High Similarity	NPC27410
0.9167	High Similarity	NPC166014
0.9097	High Similarity	NPC186063
0.9079	High Similarity	NPC103379
0.9079	High Similarity	NPC477565
0.9068	High Similarity	NPC239775
0.9032	High Similarity	NPC276588
0.9032	High Similarity	NPC110416
0.9032	High Similarity	NPC207757
0.9032	High Similarity	NPC204828
0.9032	High Similarity	NPC295691
0.9032	High Similarity	NPC39701
0.9032	High Similarity	NPC172765
0.9032	High Similarity	NPC189266
0.9032	High Similarity	NPC278799
0.9032	High Similarity	NPC127674
0.9032	High Similarity	NPC54379
0.9032	High Similarity	NPC2413
0.9032	High Similarity	NPC244112
0.9032	High Similarity	NPC469817
0.9032	High Similarity	NPC184026
0.9032	High Similarity	NPC5238
0.9032	High Similarity	NPC249797
0.9032	High Similarity	NPC193949
0.9012	High Similarity	NPC477020
0.9012	High Similarity	NPC66341
0.9012	High Similarity	NPC192135
0.9006	High Similarity	NPC118274
0.9006	High Similarity	NPC69712
0.9006	High Similarity	NPC168753
0.9006	High Similarity	NPC26240
0.9006	High Similarity	NPC477562
0.9	High Similarity	NPC210140
0.9	High Similarity	NPC150879
0.8963	High Similarity	NPC114364
0.8963	High Similarity	NPC320223
0.8957	High Similarity	NPC128560
0.8957	High Similarity	NPC199465
0.8957	High Similarity	NPC229166
0.8947	High Similarity	NPC476151
0.8938	High Similarity	NPC13916
0.8938	High Similarity	NPC264850
0.8924	High Similarity	NPC205255
0.8924	High Similarity	NPC119649
0.8924	High Similarity	NPC230956
0.8924	High Similarity	NPC235143
0.8924	High Similarity	NPC271388
0.8917	High Similarity	NPC476572
0.891	High Similarity	NPC99659
0.891	High Similarity	NPC325871
0.8903	High Similarity	NPC26601
0.8889	High Similarity	NPC246587
0.8889	High Similarity	NPC428
0.8889	High Similarity	NPC24233
0.8889	High Similarity	NPC135538
0.8889	High Similarity	NPC476571
0.8889	High Similarity	NPC147390
0.8875	High Similarity	NPC24465
0.8875	High Similarity	NPC134858
0.8875	High Similarity	NPC169743
0.8868	High Similarity	NPC79402
0.8868	High Similarity	NPC80759
0.8861	High Similarity	NPC221864
0.8824	High Similarity	NPC191376
0.8824	High Similarity	NPC321505
0.8824	High Similarity	NPC179825
0.882	High Similarity	NPC476573
0.882	High Similarity	NPC35627
0.882	High Similarity	NPC81247
0.8812	High Similarity	NPC233650
0.8795	High Similarity	NPC474507
0.8795	High Similarity	NPC32154
0.8774	High Similarity	NPC151895
0.8774	High Similarity	NPC192768
0.8774	High Similarity	NPC88249
0.8774	High Similarity	NPC97221
0.8774	High Similarity	NPC220858
0.8726	High Similarity	NPC477564
0.8726	High Similarity	NPC2295
0.8718	High Similarity	NPC81733
0.8718	High Similarity	NPC326316
0.8712	High Similarity	NPC204908
0.8712	High Similarity	NPC83198
0.871	High Similarity	NPC219162
0.871	High Similarity	NPC92541
0.8706	High Similarity	NPC275680
0.8706	High Similarity	NPC22115
0.8693	High Similarity	NPC185838
0.869	High Similarity	NPC116284
0.8675	High Similarity	NPC241704
0.8675	High Similarity	NPC173416
0.8675	High Similarity	NPC148709
0.8675	High Similarity	NPC476577
0.865	High Similarity	NPC298979
0.8647	High Similarity	NPC320088
0.8645	High Similarity	NPC130941
0.8642	High Similarity	NPC232514
0.8642	High Similarity	NPC276944
0.8642	High Similarity	NPC238530
0.8639	High Similarity	NPC135772
0.8631	High Similarity	NPC312918
0.8631	High Similarity	NPC477561
0.8631	High Similarity	NPC155442
0.8631	High Similarity	NPC476574
0.8589	High Similarity	NPC24264
0.8589	High Similarity	NPC223077
0.8589	High Similarity	NPC476432
0.8589	High Similarity	NPC193853
0.8589	High Similarity	NPC56887
0.8588	High Similarity	NPC302245
0.8588	High Similarity	NPC16357
0.8588	High Similarity	NPC95426
0.8581	High Similarity	NPC210437
0.8581	High Similarity	NPC106295
0.8581	High Similarity	NPC16107
0.8581	High Similarity	NPC253883
0.8581	High Similarity	NPC95075
0.8581	High Similarity	NPC476144
0.8581	High Similarity	NPC144863
0.8581	High Similarity	NPC51957
0.8581	High Similarity	NPC90844
0.858	High Similarity	NPC229373
0.858	High Similarity	NPC258657
0.858	High Similarity	NPC217748
0.858	High Similarity	NPC285931
0.858	High Similarity	NPC223690
0.858	High Similarity	NPC239824
0.858	High Similarity	NPC49075
0.858	High Similarity	NPC279228
0.858	High Similarity	NPC104196
0.858	High Similarity	NPC8836
0.858	High Similarity	NPC251735
0.858	High Similarity	NPC90998
0.858	High Similarity	NPC290005
0.858	High Similarity	NPC328155
0.858	High Similarity	NPC311973
0.858	High Similarity	NPC54654
0.858	High Similarity	NPC15414
0.858	High Similarity	NPC185639
0.858	High Similarity	NPC182052
0.858	High Similarity	NPC222661
0.858	High Similarity	NPC271013
0.858	High Similarity	NPC42663
0.858	High Similarity	NPC290582
0.858	High Similarity	NPC181796
0.858	High Similarity	NPC7715
0.8555	High Similarity	NPC478093
0.8554	High Similarity	NPC190783
0.8554	High Similarity	NPC232386
0.8554	High Similarity	NPC152680
0.8553	High Similarity	NPC123323
0.8547	High Similarity	NPC206900
0.8538	High Similarity	NPC65312
0.8538	High Similarity	NPC139783
0.8537	High Similarity	NPC247389
0.8533	High Similarity	NPC131204
0.8533	High Similarity	NPC301050
0.8529	High Similarity	NPC33902
0.8529	High Similarity	NPC254441
0.8529	High Similarity	NPC274716
0.8529	High Similarity	NPC167116
0.8529	High Similarity	NPC276674
0.8528	High Similarity	NPC225774
0.8528	High Similarity	NPC209377
0.8528	High Similarity	NPC16805
0.8528	High Similarity	NPC167546
0.8528	High Similarity	NPC302527
0.8526	High Similarity	NPC7467
0.8521	High Similarity	NPC286119
0.8506	High Similarity	NPC478092
0.8506	High Similarity	NPC30182
0.8506	High Similarity	NPC473589
0.8506	High Similarity	NPC478091
0.8481	Intermediate Similarity	NPC277669
0.8481	Intermediate Similarity	NPC76213
0.8481	Intermediate Similarity	NPC52475
0.8476	Intermediate Similarity	NPC256012
0.8476	Intermediate Similarity	NPC195392
0.8476	Intermediate Similarity	NPC317272
0.8476	Intermediate Similarity	NPC268503
0.8476	Intermediate Similarity	NPC240841

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 NPC60186 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	208
0.1-0.2	823
0.2-0.3	1033
0.3-0.4	2061
0.4-0.5	2513
0.5-0.6	1610
0.6-0.7	720
0.7-0.8	165
0.8-0.85	17
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8581	High Similarity	NPD4584	Approved
0.858	High Similarity	NPD8053	Approved
0.858	High Similarity	NPD8054	Approved
0.8431	Intermediate Similarity	NPD4664	Clinical (unspecified phase)
0.8397	Intermediate Similarity	NPD2420	Approved
0.8397	Intermediate Similarity	NPD2421	Approved
0.8272	Intermediate Similarity	NPD6818	Clinical (unspecified phase)
0.8242	Intermediate Similarity	NPD7201	Clinical (unspecified phase)
0.8232	Intermediate Similarity	NPD7831	Phase 2
0.8232	Intermediate Similarity	NPD7833	Phase 2
0.8232	Intermediate Similarity	NPD7832	Clinical (unspecified phase)
0.8171	Intermediate Similarity	NPD6788	Approved
0.8166	Intermediate Similarity	NPD8252	Approved
0.8166	Intermediate Similarity	NPD8251	Approved
0.8166	Intermediate Similarity	NPD8099	Discontinued
0.8155	Intermediate Similarity	NPD2489	Approved
0.8155	Intermediate Similarity	NPD27	Approved
0.8155	Intermediate Similarity	NPD2898	Approved
0.8144	Intermediate Similarity	NPD3051	Approved
0.8118	Intermediate Similarity	NPD8156	Discontinued
0.8101	Intermediate Similarity	NPD3845	Phase 1
0.8095	Intermediate Similarity	NPD2970	Approved
0.8095	Intermediate Similarity	NPD2969	Approved
0.8061	Intermediate Similarity	NPD4581	Clinical (unspecified phase)
0.8036	Intermediate Similarity	NPD4010	Discontinued
0.8036	Intermediate Similarity	NPD6071	Discontinued
0.8011	Intermediate Similarity	NPD7906	Approved
0.8	Intermediate Similarity	NPD2560	Approved
0.8	Intermediate Similarity	NPD2563	Approved
0.7949	Intermediate Similarity	NPD1632	Clinical (unspecified phase)
0.7931	Intermediate Similarity	NPD8453	Clinical (unspecified phase)
0.7886	Intermediate Similarity	NPD7313	Approved
0.7886	Intermediate Similarity	NPD4578	Approved
0.7886	Intermediate Similarity	NPD7310	Approved
0.7886	Intermediate Similarity	NPD7312	Approved
0.7886	Intermediate Similarity	NPD7311	Approved
0.7886	Intermediate Similarity	NPD4577	Approved
0.7885	Intermediate Similarity	NPD6029	Clinical (unspecified phase)
0.7885	Intermediate Similarity	NPD6028	Clinical (unspecified phase)
0.7853	Intermediate Similarity	NPD4663	Approved
0.7841	Intermediate Similarity	NPD7309	Approved
0.784	Intermediate Similarity	NPD6090	Discontinued
0.7818	Intermediate Similarity	NPD4773	Phase 2
0.7818	Intermediate Similarity	NPD4772	Phase 2
0.7812	Intermediate Similarity	NPD5241	Discontinued
0.7805	Intermediate Similarity	NPD4017	Approved
0.7805	Intermediate Similarity	NPD7261	Clinical (unspecified phase)
0.7791	Intermediate Similarity	NPD6030	Approved
0.7791	Intermediate Similarity	NPD6031	Approved
0.7778	Intermediate Similarity	NPD1754	Clinical (unspecified phase)
0.7771	Intermediate Similarity	NPD7298	Approved
0.7765	Intermediate Similarity	NPD7802	Discontinued
0.7727	Intermediate Similarity	NPD5718	Phase 2
0.7707	Intermediate Similarity	NPD7718	Clinical (unspecified phase)
0.7702	Intermediate Similarity	NPD5084	Clinical (unspecified phase)
0.7688	Intermediate Similarity	NPD5177	Phase 3
0.7688	Intermediate Similarity	NPD3060	Approved
0.7677	Intermediate Similarity	NPD2674	Phase 3
0.7669	Intermediate Similarity	NPD1424	Approved
0.7654	Intermediate Similarity	NPD2422	Clinical (unspecified phase)
0.765	Intermediate Similarity	NPD7667	Clinical (unspecified phase)
0.763	Intermediate Similarity	NPD4481	Phase 3
0.7624	Intermediate Similarity	NPD2490	Approved
0.7624	Intermediate Similarity	NPD2488	Approved
0.7584	Intermediate Similarity	NPD3534	Clinical (unspecified phase)
0.7576	Intermediate Similarity	NPD3639	Approved
0.7576	Intermediate Similarity	NPD3641	Approved
0.7576	Intermediate Similarity	NPD3640	Phase 3
0.7564	Intermediate Similarity	NPD4475	Approved
0.7564	Intermediate Similarity	NPD4474	Approved
0.7562	Intermediate Similarity	NPD2029	Clinical (unspecified phase)
0.7546	Intermediate Similarity	NPD6783	Clinical (unspecified phase)
0.7514	Intermediate Similarity	NPD6747	Phase 1
0.75	Intermediate Similarity	NPD3145	Approved
0.75	Intermediate Similarity	NPD3144	Approved
0.75	Intermediate Similarity	NPD6812	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD4873	Discontinued
0.7485	Intermediate Similarity	NPD4055	Discovery
0.7485	Intermediate Similarity	NPD5307	Clinical (unspecified phase)
0.7484	Intermediate Similarity	NPD6895	Approved
0.7484	Intermediate Similarity	NPD5752	Clinical (unspecified phase)
0.7484	Intermediate Similarity	NPD6896	Approved
0.7455	Intermediate Similarity	NPD4160	Clinical (unspecified phase)
0.7455	Intermediate Similarity	NPD4123	Phase 3
0.7455	Intermediate Similarity	NPD7447	Phase 1
0.7447	Intermediate Similarity	NPD3452	Approved
0.7447	Intermediate Similarity	NPD3450	Approved
0.7447	Intermediate Similarity	NPD2493	Approved
0.7447	Intermediate Similarity	NPD2494	Approved
0.7439	Intermediate Similarity	NPD7124	Phase 2
0.743	Intermediate Similarity	NPD7549	Discontinued
0.741	Intermediate Similarity	NPD5261	Clinical (unspecified phase)
0.7407	Intermediate Similarity	NPD7037	Approved
0.7405	Intermediate Similarity	NPD2238	Phase 2
0.7405	Intermediate Similarity	NPD3109	Approved
0.7405	Intermediate Similarity	NPD3110	Approved
0.7399	Intermediate Similarity	NPD4666	Phase 3
0.7394	Intermediate Similarity	NPD7212	Phase 2
0.7394	Intermediate Similarity	NPD7598	Phase 2
0.7394	Intermediate Similarity	NPD7213	Phase 3
0.7365	Intermediate Similarity	NPD5976	Discontinued
0.7362	Intermediate Similarity	NPD4236	Phase 3
0.7362	Intermediate Similarity	NPD4162	Approved
0.7362	Intermediate Similarity	NPD4237	Approved
0.736	Intermediate Similarity	NPD7479	Phase 2
0.7353	Intermediate Similarity	NPD7945	Clinical (unspecified phase)
0.7348	Intermediate Similarity	NPD7090	Clinical (unspecified phase)
0.7341	Intermediate Similarity	NPD5709	Phase 3
0.734	Intermediate Similarity	NPD8095	Phase 1
0.733	Intermediate Similarity	NPD4582	Approved
0.733	Intermediate Similarity	NPD4583	Approved
0.7325	Intermediate Similarity	NPD2669	Clinical (unspecified phase)
0.732	Intermediate Similarity	NPD2233	Approved
0.732	Intermediate Similarity	NPD2230	Approved
0.732	Intermediate Similarity	NPD2232	Approved
0.7318	Intermediate Similarity	NPD6297	Approved
0.7318	Intermediate Similarity	NPD6996	Clinical (unspecified phase)
0.7317	Intermediate Similarity	NPD6748	Discontinued
0.7312	Intermediate Similarity	NPD4579	Clinical (unspecified phase)
0.731	Intermediate Similarity	NPD2978	Approved
0.731	Intermediate Similarity	NPD2977	Approved
0.7293	Intermediate Similarity	NPD2971	Approved
0.7293	Intermediate Similarity	NPD2968	Approved
0.7288	Intermediate Similarity	NPD5602	Clinical (unspecified phase)
0.7285	Intermediate Similarity	NPD4093	Discontinued
0.7283	Intermediate Similarity	NPD5604	Discontinued
0.7278	Intermediate Similarity	NPD6523	Clinical (unspecified phase)
0.7277	Intermediate Similarity	NPD4004	Approved
0.7277	Intermediate Similarity	NPD4002	Approved
0.7273	Intermediate Similarity	NPD6687	Approved
0.7273	Intermediate Similarity	NPD6688	Approved
0.7273	Intermediate Similarity	NPD1669	Approved
0.7267	Intermediate Similarity	NPD5978	Approved
0.7267	Intermediate Similarity	NPD5977	Approved
0.7262	Intermediate Similarity	NPD1914	Approved
0.7262	Intermediate Similarity	NPD7427	Discontinued
0.7257	Intermediate Similarity	NPD6107	Approved
0.7247	Intermediate Similarity	NPD7177	Discontinued
0.7241	Intermediate Similarity	NPD7400	Phase 3
0.7239	Intermediate Similarity	NPD7030	Discontinued
0.7237	Intermediate Similarity	NPD2667	Approved
0.7237	Intermediate Similarity	NPD2668	Approved
0.7235	Intermediate Similarity	NPD4678	Approved
0.7235	Intermediate Similarity	NPD4675	Approved
0.7234	Intermediate Similarity	NPD2974	Approved
0.7234	Intermediate Similarity	NPD2973	Approved
0.7234	Intermediate Similarity	NPD2975	Approved
0.7229	Intermediate Similarity	NPD6666	Approved
0.7229	Intermediate Similarity	NPD6667	Approved
0.7226	Intermediate Similarity	NPD7258	Clinical (unspecified phase)
0.7215	Intermediate Similarity	NPD5155	Approved
0.7215	Intermediate Similarity	NPD5156	Approved
0.7212	Intermediate Similarity	NPD6331	Phase 2
0.72	Intermediate Similarity	NPD5677	Discontinued
0.7193	Intermediate Similarity	NPD7109	Clinical (unspecified phase)
0.7193	Intermediate Similarity	NPD6072	Discontinued
0.7193	Intermediate Similarity	NPD7110	Phase 1
0.7191	Intermediate Similarity	NPD5938	Phase 3
0.7186	Intermediate Similarity	NPD3124	Discontinued
0.7176	Intermediate Similarity	NPD4005	Discontinued
0.7176	Intermediate Similarity	NPD824	Approved
0.717	Intermediate Similarity	NPD2028	Clinical (unspecified phase)
0.7169	Intermediate Similarity	NPD2677	Approved
0.7158	Intermediate Similarity	NPD6851	Approved
0.7158	Intermediate Similarity	NPD6853	Approved
0.7152	Intermediate Similarity	NPD3594	Approved
0.7152	Intermediate Similarity	NPD3595	Approved
0.7152	Intermediate Similarity	NPD2605	Approved
0.7152	Intermediate Similarity	NPD2606	Approved
0.7151	Intermediate Similarity	NPD6656	Clinical (unspecified phase)
0.715	Intermediate Similarity	NPD4040	Phase 1
0.7143	Intermediate Similarity	NPD7019	Approved
0.7143	Intermediate Similarity	NPD7020	Approved
0.7136	Intermediate Similarity	NPD7047	Phase 3
0.7135	Intermediate Similarity	NPD6607	Clinical (unspecified phase)
0.7134	Intermediate Similarity	NPD4721	Approved
0.7134	Intermediate Similarity	NPD6584	Phase 3
0.7134	Intermediate Similarity	NPD4726	Approved
0.7134	Intermediate Similarity	NPD4725	Approved
0.7127	Intermediate Similarity	NPD6496	Clinical (unspecified phase)
0.712	Intermediate Similarity	NPD4580	Approved
0.7117	Intermediate Similarity	NPD1753	Discontinued
0.7111	Intermediate Similarity	NPD42	Phase 2
0.7111	Intermediate Similarity	NPD6042	Phase 2
0.711	Intermediate Similarity	NPD5773	Approved
0.711	Intermediate Similarity	NPD5772	Approved
0.7107	Intermediate Similarity	NPD4625	Phase 3
0.7107	Intermediate Similarity	NPD3027	Phase 3
0.7104	Intermediate Similarity	NPD5917	Clinical (unspecified phase)
0.7094	Intermediate Similarity	NPD6997	Phase 2
0.7091	Intermediate Similarity	NPD7045	Clinical (unspecified phase)
0.7089	Intermediate Similarity	NPD3635	Approved
0.7089	Intermediate Similarity	NPD3637	Approved
0.7089	Intermediate Similarity	NPD3636	Approved
0.7086	Intermediate Similarity	NPD8005	Clinical (unspecified phase)
0.7081	Intermediate Similarity	NPD3619	Clinical (unspecified phase)
0.7081	Intermediate Similarity	NPD3061	Approved
0.7081	Intermediate Similarity	NPD3620	Phase 2
0.7081	Intermediate Similarity	NPD3062	Approved
0.7081	Intermediate Similarity	NPD3059	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