NPASS Compound

Structure

CID183407 OpenBabel06191715562D 41 48 0 0 1 0 0 0 0 0999 V2000 5.2812 1.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7579 -0.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7318 -0.7231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4152 1.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4679 4.7069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5544 5.1137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6701 1.4343 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5724 3.7124 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7454 4.5259 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8611 0.8465 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4067 -2.5316 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4013 -2.6361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3280 1.3870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 -1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4791 0.8465 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0190 0.4359 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 2.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 1.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 1.1910 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.6831 1.6910 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.7634 3.1246 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.6180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6589 2.1301 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 -1.3090 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -2.8499 3.5314 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1701 -0.1045 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3717 0.9711 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8171 0.1910 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9890 -1.8271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5823 -0.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6808 1.9222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 -0.3090 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.5878 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1808 2.7882 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.1701 -0.1045 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.0409 0.2280 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 -0.3090 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 -2.9836 -1.9316 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 4 1 0 0 0 0 2 38 1 0 0 0 0 3 39 1 0 0 0 0 5 6 2 0 0 0 0 5 8 1 0 0 0 0 6 9 1 0 0 0 0 7 10 1 0 0 0 0 7 15 1 0 0 0 0 8 23 2 0 0 0 0 9 27 2 0 0 0 0 10 28 1 0 0 0 0 11 12 2 0 0 0 0 11 24 1 0 0 0 0 12 31 1 0 0 0 0 13 16 1 0 0 0 0 13 25 1 0 0 0 0 14 17 1 0 0 0 0 14 26 1 0 0 0 0 15 38 1 0 0 0 0 16 39 1 0 0 0 0 17 40 1 0 0 0 0 19 22 1 0 0 0 0 19 30 1 0 0 0 0 20 21 1 0 0 0 0 20 40 1 0 0 0 0 21 4 1 1 0 0 0 21 22 1 0 0 0 0 22 18 1 6 0 0 0 23 25 1 0 0 0 0 23 27 1 0 0 0 0 24 26 1 0 0 0 0 24 35 2 0 0 0 0 25 33 2 0 0 0 0 26 34 1 0 0 0 0 27 36 1 0 0 0 0 28 32 1 1 0 0 0 28 38 1 0 0 0 0 29 18 1 6 0 0 0 29 33 1 0 0 0 0 29 39 1 0 0 0 0 30 34 1 0 0 0 0 30 40 1 6 0 0 0 31 32 2 0 0 0 0 31 41 1 0 0 0 0 32 35 1 0 0 0 0 33 36 1 0 0 0 0 34 37 1 0 0 0 0 35 37 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	553.38
Volume:	590.783
LogP:	5.507
LogD:	4.649
LogS:	-3.96
# Rotatable Bonds:	4
TPSA:	57.77
# H-Bond Aceptor:	6
# H-Bond Donor:	3
# Rings:	8
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.356
Synthetic Accessibility Score:	4.878
Fsp3:	0.6
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.506
MDCK Permeability:	8.279307621705811e-06
Pgp-inhibitor:	0.789
Pgp-substrate:	0.996
Human Intestinal Absorption (HIA):	0.056
20% Bioavailability (F20%):	0.94
30% Bioavailability (F30%):	0.01

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.531
Plasma Protein Binding (PPB):	89.84196472167969%
Volume Distribution (VD):	2.814
Pgp-substrate:	8.064675331115723%

ADMET: Metabolism

CYP1A2-inhibitor:	0.025
CYP1A2-substrate:	0.846
CYP2C19-inhibitor:	0.092
CYP2C19-substrate:	0.977
CYP2C9-inhibitor:	0.021
CYP2C9-substrate:	0.244
CYP2D6-inhibitor:	0.435
CYP2D6-substrate:	0.934
CYP3A4-inhibitor:	0.078
CYP3A4-substrate:	0.937

ADMET: Excretion

Clearance (CL):	9.212
Half-life (T1/2):	0.128

ADMET: Toxicity

hERG Blockers:	0.878
Human Hepatotoxicity (H-HT):	0.951
Drug-inuced Liver Injury (DILI):	0.833
AMES Toxicity:	0.342
Rat Oral Acute Toxicity:	0.543
Maximum Recommended Daily Dose:	0.987
Skin Sensitization:	0.518
Carcinogencity:	0.19
Eye Corrosion:	0.003
Eye Irritation:	0.005
Respiratory Toxicity:	0.895

Download Data

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

Natural Product: NPC183407

Natural Product ID:	NPC183407
*Common Name:**	Isostrychnopentamine
IUPAC Name:	(2R,3R,12bS)-3-ethyl-11-[(2S)-1-methylpyrrolidin-2-yl]-2-[[(1S)-2-methyl-1,3,4,9-tetrahydropyrido[3,4-b]indol-1-yl]methyl]-1,2,3,4,6,7,7a,12,12a,12b-decahydroindolo[2,3-a]quinolizin-10-ol
Synonyms:	Isostrychnopentamine
Standard InCHIKey:	MHIOYLXTHAIJLU-FVHQJPTNSA-N
Standard InCHI:	InChI=1S/C35H47N5O/c1-4-21-20-40-17-14-26-24-11-12-31(41)32(28-10-7-15-38(28)2)35(24)37-34(26)30(40)19-22(21)18-29-33-25(13-16-39(29)3)23-8-5-6-9-27(23)36-33/h5-6,8-9,11-12,21-22,26,28-30,34,36-37,41H,4,7,10,13-20H2,1-3H3/t21-,22-,26?,28-,29-,30-,34?/m0/s1
SMILES:	CC[C@H]1CN2CCC3C([C@@H]2C[C@@H]1C[C@@H]1N(C)CCc2c1[nH]c1c2cccc1)Nc1c3ccc(c1[C@@H]1CCCN1C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL496076
PubChem CID:	44559861
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0001140] Harmala alkaloids

*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
NPO18713	Strychnos usambarensis	Species	Loganiaceae	Eukaryota	roots	n.a.	n.a.	PMID[10217724]
NPO18713	Strychnos usambarensis	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12398531]
NPO18713	Strychnos usambarensis	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO18713	Strychnos usambarensis	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18713	Strychnos usambarensis	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18713	Strychnos usambarensis	Species	Loganiaceae	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	6
Others	6

Activity Type	# Activity
Cell Line	1
Organism	8
Others	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT393	Cell Line	HCT-116	Homo sapiens	IC50	=	7470.0	nM	PMID[564937]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	104.0	nM	PMID[564937]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	120.0	nM	PMID[564937]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	152.0	nM	PMID[564937]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC90	=	386.0	nM	PMID[564937]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC90	=	450.0	nM	PMID[564937]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC90	=	628.0	nM	PMID[564937]
NPT2	Others	Unspecified		Ratio IC50	=	49.1	n.a.	PMID[564937]
NPT2	Others	Unspecified		Ratio IC50	=	62.3	n.a.	PMID[564937]
NPT2	Others	Unspecified		Ratio IC50	=	71.8	n.a.	PMID[564937]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	0.0	nM	PMID[564938]
NPT992	Organism	Entamoeba histolytica	Entamoeba histolytica	IC50	=	10.39	ug.mL-1	PMID[564939]

☑ 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 NPC183407 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	599
0.1-0.2	2881
0.2-0.3	13485
0.3-0.4	13483
0.4-0.5	6994
0.5-0.6	3093
0.6-0.7	1653
0.7-0.8	479
0.8-0.85	28
0.85-0.9	0
0.9-0.95	1
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9303	High Similarity	NPC162748
0.8873	High Similarity	NPC477861
0.8614	High Similarity	NPC476116
0.8416	Intermediate Similarity	NPC469734
0.8404	Intermediate Similarity	NPC470126
0.84	Intermediate Similarity	NPC249040
0.8394	Intermediate Similarity	NPC94943
0.8364	Intermediate Similarity	NPC253580
0.8342	Intermediate Similarity	NPC190007
0.8325	Intermediate Similarity	NPC476041
0.8325	Intermediate Similarity	NPC304926
0.829	Intermediate Similarity	NPC212535
0.8213	Intermediate Similarity	NPC475422
0.8204	Intermediate Similarity	NPC87755
0.8182	Intermediate Similarity	NPC469592
0.8182	Intermediate Similarity	NPC471080
0.8135	Intermediate Similarity	NPC72980
0.8131	Intermediate Similarity	NPC280272
0.8116	Intermediate Similarity	NPC475910
0.8102	Intermediate Similarity	NPC2497
0.8061	Intermediate Similarity	NPC472294
0.8039	Intermediate Similarity	NPC329747
0.8028	Intermediate Similarity	NPC469594
0.8021	Intermediate Similarity	NPC474409
0.798	Intermediate Similarity	NPC70956
0.798	Intermediate Similarity	NPC153042
0.798	Intermediate Similarity	NPC243834
0.7965	Intermediate Similarity	NPC81939
0.7962	Intermediate Similarity	NPC294620
0.7934	Intermediate Similarity	NPC330009
0.793	Intermediate Similarity	NPC475666
0.7917	Intermediate Similarity	NPC477532
0.79	Intermediate Similarity	NPC6215
0.7885	Intermediate Similarity	NPC475070
0.7874	Intermediate Similarity	NPC475085
0.7874	Intermediate Similarity	NPC291535
0.7874	Intermediate Similarity	NPC475112
0.7867	Intermediate Similarity	NPC126066
0.785	Intermediate Similarity	NPC46580
0.7848	Intermediate Similarity	NPC325976
0.7835	Intermediate Similarity	NPC472123
0.7824	Intermediate Similarity	NPC193267
0.7824	Intermediate Similarity	NPC213530
0.782	Intermediate Similarity	NPC469589
0.7818	Intermediate Similarity	NPC473185
0.7804	Intermediate Similarity	NPC470549
0.7783	Intermediate Similarity	NPC324149
0.7772	Intermediate Similarity	NPC106833
0.7772	Intermediate Similarity	NPC469497
0.7767	Intermediate Similarity	NPC170114
0.7748	Intermediate Similarity	NPC326363
0.7742	Intermediate Similarity	NPC473179
0.7731	Intermediate Similarity	NPC305984
0.7723	Intermediate Similarity	NPC246700
0.7723	Intermediate Similarity	NPC128751
0.7713	Intermediate Similarity	NPC476451
0.7706	Intermediate Similarity	NPC477533
0.77	Intermediate Similarity	NPC11464
0.77	Intermediate Similarity	NPC167860
0.77	Intermediate Similarity	NPC123976
0.7696	Intermediate Similarity	NPC99666
0.7689	Intermediate Similarity	NPC470931
0.7677	Intermediate Similarity	NPC88363
0.7675	Intermediate Similarity	NPC81175
0.767	Intermediate Similarity	NPC242209
0.767	Intermediate Similarity	NPC70259
0.7668	Intermediate Similarity	NPC209174
0.7662	Intermediate Similarity	NPC471891
0.7656	Intermediate Similarity	NPC267423
0.7656	Intermediate Similarity	NPC476044
0.7655	Intermediate Similarity	NPC295228
0.7644	Intermediate Similarity	NPC474880
0.7644	Intermediate Similarity	NPC221786
0.7642	Intermediate Similarity	NPC193777
0.7634	Intermediate Similarity	NPC477531
0.763	Intermediate Similarity	NPC285558
0.7626	Intermediate Similarity	NPC96890
0.7623	Intermediate Similarity	NPC252251
0.7623	Intermediate Similarity	NPC314954
0.7621	Intermediate Similarity	NPC205934
0.7621	Intermediate Similarity	NPC43787
0.7613	Intermediate Similarity	NPC214980
0.7608	Intermediate Similarity	NPC329793
0.7596	Intermediate Similarity	NPC72211
0.7596	Intermediate Similarity	NPC306376
0.7594	Intermediate Similarity	NPC476106
0.7593	Intermediate Similarity	NPC478074
0.759	Intermediate Similarity	NPC317430
0.7588	Intermediate Similarity	NPC232340
0.7588	Intermediate Similarity	NPC41679
0.7583	Intermediate Similarity	NPC223427
0.7565	Intermediate Similarity	NPC478082
0.7565	Intermediate Similarity	NPC477067
0.7562	Intermediate Similarity	NPC472108
0.7562	Intermediate Similarity	NPC139291
0.7556	Intermediate Similarity	NPC475253
0.7548	Intermediate Similarity	NPC77555
0.7546	Intermediate Similarity	NPC48353
0.7544	Intermediate Similarity	NPC473183
0.7537	Intermediate Similarity	NPC171171
0.7534	Intermediate Similarity	NPC303658
0.7534	Intermediate Similarity	NPC264285
0.7534	Intermediate Similarity	NPC319232
0.7534	Intermediate Similarity	NPC24370
0.7533	Intermediate Similarity	NPC473184
0.7525	Intermediate Similarity	NPC84478
0.7523	Intermediate Similarity	NPC152768
0.7523	Intermediate Similarity	NPC469928
0.7523	Intermediate Similarity	NPC148183
0.7513	Intermediate Similarity	NPC229173
0.75	Intermediate Similarity	NPC23294
0.7489	Intermediate Similarity	NPC478081
0.7488	Intermediate Similarity	NPC106937
0.7488	Intermediate Similarity	NPC232727
0.7477	Intermediate Similarity	NPC220851
0.7477	Intermediate Similarity	NPC473362
0.7477	Intermediate Similarity	NPC166492
0.7467	Intermediate Similarity	NPC477608
0.7467	Intermediate Similarity	NPC477607
0.7465	Intermediate Similarity	NPC470500
0.7462	Intermediate Similarity	NPC474897
0.7461	Intermediate Similarity	NPC475990
0.7455	Intermediate Similarity	NPC214142
0.7455	Intermediate Similarity	NPC473041
0.7454	Intermediate Similarity	NPC5145
0.7454	Intermediate Similarity	NPC303951
0.7452	Intermediate Similarity	NPC131017
0.7446	Intermediate Similarity	NPC477066
0.7443	Intermediate Similarity	NPC74969
0.7441	Intermediate Similarity	NPC11017
0.7438	Intermediate Similarity	NPC204717
0.7437	Intermediate Similarity	NPC329688
0.7437	Intermediate Similarity	NPC189812
0.7436	Intermediate Similarity	NPC17437
0.7435	Intermediate Similarity	NPC470784
0.7432	Intermediate Similarity	NPC310118
0.7431	Intermediate Similarity	NPC477610
0.7427	Intermediate Similarity	NPC469501
0.7427	Intermediate Similarity	NPC469470
0.7422	Intermediate Similarity	NPC304307
0.7422	Intermediate Similarity	NPC34580
0.7422	Intermediate Similarity	NPC124920
0.7422	Intermediate Similarity	NPC261251
0.7422	Intermediate Similarity	NPC118559
0.7418	Intermediate Similarity	NPC476098
0.7418	Intermediate Similarity	NPC162484
0.7416	Intermediate Similarity	NPC472193
0.7414	Intermediate Similarity	NPC473312
0.7411	Intermediate Similarity	NPC21638
0.7402	Intermediate Similarity	NPC314002
0.7391	Intermediate Similarity	NPC184680
0.7389	Intermediate Similarity	NPC472109
0.7389	Intermediate Similarity	NPC100547
0.7389	Intermediate Similarity	NPC19679
0.7389	Intermediate Similarity	NPC220765
0.7389	Intermediate Similarity	NPC472110
0.7387	Intermediate Similarity	NPC259545
0.7387	Intermediate Similarity	NPC471294
0.7384	Intermediate Similarity	NPC153400
0.7381	Intermediate Similarity	NPC232130
0.7378	Intermediate Similarity	NPC202503
0.7361	Intermediate Similarity	NPC210828
0.7361	Intermediate Similarity	NPC86834
0.7359	Intermediate Similarity	NPC470785
0.7357	Intermediate Similarity	NPC95240
0.7357	Intermediate Similarity	NPC223409
0.7357	Intermediate Similarity	NPC322135
0.7352	Intermediate Similarity	NPC475602
0.7349	Intermediate Similarity	NPC472111
0.7346	Intermediate Similarity	NPC265576
0.7336	Intermediate Similarity	NPC473105
0.7336	Intermediate Similarity	NPC473182
0.7336	Intermediate Similarity	NPC323752
0.7336	Intermediate Similarity	NPC53144
0.7327	Intermediate Similarity	NPC201697
0.7327	Intermediate Similarity	NPC209769
0.7325	Intermediate Similarity	NPC14288
0.7322	Intermediate Similarity	NPC478080
0.7321	Intermediate Similarity	NPC16352
0.7317	Intermediate Similarity	NPC15102
0.7313	Intermediate Similarity	NPC33949
0.7311	Intermediate Similarity	NPC476167
0.7309	Intermediate Similarity	NPC195788
0.7309	Intermediate Similarity	NPC237901
0.7309	Intermediate Similarity	NPC132642
0.7297	Intermediate Similarity	NPC477609
0.7293	Intermediate Similarity	NPC54803
0.7293	Intermediate Similarity	NPC321592
0.729	Intermediate Similarity	NPC135887
0.729	Intermediate Similarity	NPC199277
0.7289	Intermediate Similarity	NPC211416
0.7286	Intermediate Similarity	NPC195314
0.7286	Intermediate Similarity	NPC326634
0.7281	Intermediate Similarity	NPC39679
0.7277	Intermediate Similarity	NPC473317
0.7277	Intermediate Similarity	NPC471506
0.7273	Intermediate Similarity	NPC473187
0.7273	Intermediate Similarity	NPC473757
0.7269	Intermediate Similarity	NPC476492
0.7269	Intermediate Similarity	NPC110151

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 NPC183407 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	296
0.1-0.2	578
0.2-0.3	854
0.3-0.4	1480
0.4-0.5	2699
0.5-0.6	2332
0.6-0.7	790
0.7-0.8	120
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.798	Intermediate Similarity	NPD7948	Phase 1
0.7902	Intermediate Similarity	NPD8396	Approved
0.7902	Intermediate Similarity	NPD8395	Approved
0.7839	Intermediate Similarity	NPD6344	Clinical (unspecified phase)
0.7826	Intermediate Similarity	NPD4511	Phase 1
0.7773	Intermediate Similarity	NPD2916	Discontinued
0.7731	Intermediate Similarity	NPD7823	Clinical (unspecified phase)
0.7696	Intermediate Similarity	NPD8405	Clinical (unspecified phase)
0.7689	Intermediate Similarity	NPD5658	Approved
0.7659	Intermediate Similarity	NPD5575	Clinical (unspecified phase)
0.765	Intermediate Similarity	NPD5522	Clinical (unspecified phase)
0.7644	Intermediate Similarity	NPD3814	Phase 1
0.7641	Intermediate Similarity	NPD1326	Approved
0.7641	Intermediate Similarity	NPD1325	Approved
0.7596	Intermediate Similarity	NPD7889	Clinical (unspecified phase)
0.756	Intermediate Similarity	NPD4118	Clinical (unspecified phase)
0.7557	Intermediate Similarity	NPD7221	Approved
0.7557	Intermediate Similarity	NPD7219	Approved
0.755	Intermediate Similarity	NPD8464	Clinical (unspecified phase)
0.7525	Intermediate Similarity	NPD5065	Approved
0.7523	Intermediate Similarity	NPD7112	Discontinued
0.7512	Intermediate Similarity	NPD3003	Approved
0.75	Intermediate Similarity	NPD7194	Discontinued
0.749	Intermediate Similarity	NPD8363	Approved
0.749	Intermediate Similarity	NPD8364	Approved
0.7488	Intermediate Similarity	NPD6610	Clinical (unspecified phase)
0.7488	Intermediate Similarity	NPD802	Phase 2
0.7452	Intermediate Similarity	NPD6861	Clinical (unspecified phase)
0.7436	Intermediate Similarity	NPD8358	Approved
0.7429	Intermediate Similarity	NPD8365	Clinical (unspecified phase)
0.7412	Intermediate Similarity	NPD7558	Phase 2
0.7382	Intermediate Similarity	NPD2882	Phase 1
0.7376	Intermediate Similarity	NPD8109	Clinical (unspecified phase)
0.7354	Intermediate Similarity	NPD7726	Phase 1
0.7349	Intermediate Similarity	NPD3932	Clinical (unspecified phase)
0.7349	Intermediate Similarity	NPD8403	Phase 1
0.7315	Intermediate Similarity	NPD3930	Clinical (unspecified phase)
0.7309	Intermediate Similarity	NPD8466	Approved
0.7309	Intermediate Similarity	NPD8465	Approved
0.7309	Intermediate Similarity	NPD8467	Approved
0.7306	Intermediate Similarity	NPD3330	Phase 1
0.7301	Intermediate Similarity	NPD7603	Discontinued
0.726	Intermediate Similarity	NPD5936	Approved
0.726	Intermediate Similarity	NPD5939	Approved
0.7251	Intermediate Similarity	NPD6449	Clinical (unspecified phase)
0.724	Intermediate Similarity	NPD5903	Approved
0.724	Intermediate Similarity	NPD5902	Approved
0.7235	Intermediate Similarity	NPD6838	Clinical (unspecified phase)
0.7235	Intermediate Similarity	NPD7222	Phase 2
0.723	Intermediate Similarity	NPD1768	Approved
0.7207	Intermediate Similarity	NPD6803	Clinical (unspecified phase)
0.7196	Intermediate Similarity	NPD4601	Approved
0.7196	Intermediate Similarity	NPD4600	Approved
0.7194	Intermediate Similarity	NPD8460	Approved
0.7194	Intermediate Similarity	NPD8426	Approved
0.7194	Intermediate Similarity	NPD8459	Approved
0.7194	Intermediate Similarity	NPD8425	Approved
0.7192	Intermediate Similarity	NPD6159	Phase 2
0.719	Intermediate Similarity	NPD3404	Approved
0.7189	Intermediate Similarity	NPD5530	Phase 1
0.7181	Intermediate Similarity	NPD4401	Phase 2
0.7181	Intermediate Similarity	NPD4403	Phase 3
0.7176	Intermediate Similarity	NPD4886	Phase 2
0.7172	Intermediate Similarity	NPD5138	Approved
0.7172	Intermediate Similarity	NPD5140	Approved
0.7171	Intermediate Similarity	NPD8427	Approved
0.7171	Intermediate Similarity	NPD7867	Phase 1
0.7171	Intermediate Similarity	NPD8429	Approved
0.7171	Intermediate Similarity	NPD8428	Approved
0.7168	Intermediate Similarity	NPD6824	Clinical (unspecified phase)
0.7163	Intermediate Similarity	NPD6141	Clinical (unspecified phase)
0.7163	Intermediate Similarity	NPD2383	Phase 1
0.715	Intermediate Similarity	NPD2177	Approved
0.715	Intermediate Similarity	NPD2176	Approved
0.715	Intermediate Similarity	NPD2175	Phase 3
0.7143	Intermediate Similarity	NPD2380	Approved
0.7143	Intermediate Similarity	NPD2382	Approved
0.7143	Intermediate Similarity	NPD2381	Approved
0.7143	Intermediate Similarity	NPD4885	Approved
0.7136	Intermediate Similarity	NPD5744	Clinical (unspecified phase)
0.713	Intermediate Similarity	NPD6975	Discontinued
0.713	Intermediate Similarity	NPD5612	Discontinued
0.7123	Intermediate Similarity	NPD3324	Clinical (unspecified phase)
0.7123	Intermediate Similarity	NPD7947	Clinical (unspecified phase)
0.7121	Intermediate Similarity	NPD1685	Approved
0.7121	Intermediate Similarity	NPD1684	Approved
0.7118	Intermediate Similarity	NPD7731	Approved
0.7118	Intermediate Similarity	NPD7730	Approved
0.7113	Intermediate Similarity	NPD6158	Phase 2
0.7113	Intermediate Similarity	NPD6476	Clinical (unspecified phase)
0.7112	Intermediate Similarity	NPD7789	Approved
0.7112	Intermediate Similarity	NPD7951	Approved
0.7112	Intermediate Similarity	NPD7790	Approved
0.7112	Intermediate Similarity	NPD7952	Approved
0.7112	Intermediate Similarity	NPD7791	Approved
0.7112	Intermediate Similarity	NPD7950	Approved
0.7112	Intermediate Similarity	NPD7953	Approved
0.7108	Intermediate Similarity	NPD6203	Clinical (unspecified phase)
0.7105	Intermediate Similarity	NPD6976	Clinical (unspecified phase)
0.7105	Intermediate Similarity	NPD7271	Approved
0.7105	Intermediate Similarity	NPD7586	Clinical (unspecified phase)
0.709	Intermediate Similarity	NPD7955	Approved
0.709	Intermediate Similarity	NPD7956	Approved
0.7085	Intermediate Similarity	NPD8284	Discontinued
0.7081	Intermediate Similarity	NPD8431	Approved
0.7073	Intermediate Similarity	NPD8386	Phase 2
0.7067	Intermediate Similarity	NPD6985	Discontinued
0.7064	Intermediate Similarity	NPD4795	Phase 2
0.7056	Intermediate Similarity	NPD7824	Approved
0.7054	Intermediate Similarity	NPD6503	Clinical (unspecified phase)
0.7048	Intermediate Similarity	NPD6965	Clinical (unspecified phase)
0.7043	Intermediate Similarity	NPD6977	Clinical (unspecified phase)
0.7043	Intermediate Similarity	NPD6978	Phase 2
0.7039	Intermediate Similarity	NPD6595	Phase 3
0.7034	Intermediate Similarity	NPD8017	Clinical (unspecified phase)
0.7034	Intermediate Similarity	NPD8016	Phase 3
0.701	Intermediate Similarity	NPD6492	Phase 2
0.7009	Intermediate Similarity	NPD3127	Clinical (unspecified phase)
0.7	Intermediate Similarity	NPD1392	Approved
0.7	Intermediate Similarity	NPD7452	Approved
0.7	Intermediate Similarity	NPD7453	Approved
0.6996	Remote Similarity	NPD8093	Discontinued
0.6996	Remote Similarity	NPD2794	Discontinued
0.6995	Remote Similarity	NPD1038	Approved
0.6992	Remote Similarity	NPD7729	Clinical (unspecified phase)
0.6986	Remote Similarity	NPD5426	Phase 3
0.6981	Remote Similarity	NPD5913	Phase 3
0.6981	Remote Similarity	NPD5912	Clinical (unspecified phase)
0.698	Remote Similarity	NPD7181	Phase 3
0.6972	Remote Similarity	NPD3931	Approved
0.6972	Remote Similarity	NPD3928	Approved
0.6971	Remote Similarity	NPD5596	Phase 2
0.6968	Remote Similarity	NPD7666	Phase 3
0.6968	Remote Similarity	NPD7665	Phase 2
0.6968	Remote Similarity	NPD6376	Discontinued
0.6967	Remote Similarity	NPD8110	Clinical (unspecified phase)
0.6966	Remote Similarity	NPD5040	Clinical (unspecified phase)
0.6964	Remote Similarity	NPD8094	Discontinued
0.696	Remote Similarity	NPD3402	Phase 1
0.6959	Remote Similarity	NPD484	Approved
0.6955	Remote Similarity	NPD7958	Clinical (unspecified phase)
0.6955	Remote Similarity	NPD7957	Phase 1
0.6951	Remote Similarity	NPD4502	Phase 2
0.6951	Remote Similarity	NPD6220	Phase 3
0.6948	Remote Similarity	NPD7803	Approved
0.693	Remote Similarity	NPD5930	Phase 3
0.6926	Remote Similarity	NPD7676	Clinical (unspecified phase)
0.6926	Remote Similarity	NPD7674	Phase 3
0.6926	Remote Similarity	NPD7675	Phase 3
0.6923	Remote Similarity	NPD6290	Phase 2
0.6923	Remote Similarity	NPD4204	Approved
0.6923	Remote Similarity	NPD8322	Phase 2
0.6923	Remote Similarity	NPD4203	Approved
0.6916	Remote Similarity	NPD1304	Clinical (unspecified phase)
0.691	Remote Similarity	NPD6968	Phase 2
0.691	Remote Similarity	NPD6969	Phase 2
0.6905	Remote Similarity	NPD2762	Phase 2
0.6905	Remote Similarity	NPD6227	Discontinued
0.6898	Remote Similarity	NPD7081	Clinical (unspecified phase)
0.6897	Remote Similarity	NPD1921	Clinical (unspecified phase)
0.6894	Remote Similarity	NPD8489	Phase 1
0.6893	Remote Similarity	NPD6375	Clinical (unspecified phase)
0.6892	Remote Similarity	NPD7671	Approved
0.6892	Remote Similarity	NPD7672	Approved
0.6889	Remote Similarity	NPD8488	Clinical (unspecified phase)
0.6888	Remote Similarity	NPD4463	Approved
0.6888	Remote Similarity	NPD4462	Approved
0.6883	Remote Similarity	NPD6246	Approved
0.6881	Remote Similarity	NPD1740	Approved
0.6881	Remote Similarity	NPD5497	Clinical (unspecified phase)
0.6881	Remote Similarity	NPD1739	Approved
0.6875	Remote Similarity	NPD7470	Discontinued
0.6872	Remote Similarity	NPD5164	Discontinued
0.687	Remote Similarity	NPD8244	Phase 2
0.6867	Remote Similarity	NPD7781	Approved
0.6867	Remote Similarity	NPD7780	Approved
0.6863	Remote Similarity	NPD4184	Clinical (unspecified phase)
0.6851	Remote Similarity	NPD7796	Approved
0.6851	Remote Similarity	NPD7797	Approved
0.6847	Remote Similarity	NPD8493	Clinical (unspecified phase)
0.6844	Remote Similarity	NPD8458	Clinical (unspecified phase)
0.6844	Remote Similarity	NPD7594	Clinical (unspecified phase)
0.6839	Remote Similarity	NPD4637	Clinical (unspecified phase)
0.6833	Remote Similarity	NPD31	Approved
0.6833	Remote Similarity	NPD4033	Approved
0.6833	Remote Similarity	NPD5901	Discontinued
0.6833	Remote Similarity	NPD32	Approved
0.6833	Remote Similarity	NPD4039	Approved
0.6833	Remote Similarity	NPD4122	Approved
0.6833	Remote Similarity	NPD4036	Approved
0.6833	Remote Similarity	NPD4037	Approved
0.6833	Remote Similarity	NPD4038	Approved
0.6833	Remote Similarity	NPD4034	Approved
0.6833	Remote Similarity	NPD4035	Approved
0.6824	Remote Similarity	NPD6327	Phase 1
0.682	Remote Similarity	NPD7025	Clinical (unspecified phase)
0.6806	Remote Similarity	NPD3017	Clinical (unspecified phase)
0.6806	Remote Similarity	NPD6491	Clinical (unspecified phase)
0.6804	Remote Similarity	NPD4500	Approved
0.6804	Remote Similarity	NPD4501	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