NPASS Compound

Structure

CID87662 OpenBabel06191715422D 45 50 0 0 1 0 0 0 0 0999 V2000 -1.4103 -3.6127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3329 -2.7560 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7366 -0.5235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9291 2.0108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1406 -2.6255 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3736 -1.1579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5933 0.3190 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3109 -0.9569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3953 -2.6067 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5188 -1.7672 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7625 -2.2539 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0064 -1.5107 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6083 -0.6870 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4922 -2.2727 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.4871 -1.1770 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.5021 -2.1830 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.6384 -2.6990 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2161 -0.4587 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.0172 -2.2351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8062 -1.4450 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1189 -1.1767 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3170 -0.9569 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2845 0.0649 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7296 -2.1319 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7597 -2.2091 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8576 0.5360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7517 -1.5295 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5031 -1.5483 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0061 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.4570 0.8350 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4681 -1.4339 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8701 -0.9947 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3508 -0.6609 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3809 -2.6730 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6535 -3.7050 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1730 -0.1478 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0690 1.0069 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5821 -2.6663 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7475 0.0667 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8191 1.5414 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 2.7555 -1.1117 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7446 -1.2031 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1448 -2.5002 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8960 -2.7251 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 9 1 0 0 0 0 2 10 1 0 0 0 0 4 40 1 0 0 0 0 5 11 1 0 0 0 0 5 14 1 0 0 0 0 6 12 1 0 0 0 0 6 27 1 0 0 0 0 7 30 1 0 0 0 0 8 41 1 0 0 0 0 9 11 1 0 0 0 0 9 19 2 0 0 0 0 10 31 2 0 0 0 0 10 42 1 0 0 0 0 11 27 1 1 0 0 0 12 19 1 0 0 0 0 12 32 2 0 0 0 0 13 7 1 1 0 0 0 13 15 1 0 0 0 0 13 43 1 0 0 0 0 14 28 1 6 0 0 0 14 44 1 0 0 0 0 15 16 1 0 0 0 0 15 33 1 6 0 0 0 16 17 1 0 0 0 0 16 34 1 1 0 0 0 17 25 1 0 0 0 0 17 35 1 6 0 0 0 18 21 1 0 0 0 0 18 23 1 0 0 0 0 18 36 1 1 0 0 0 19 45 1 0 0 0 0 20 22 1 0 0 0 0 20 24 1 0 0 0 0 20 42 1 1 0 0 0 21 27 1 1 0 0 0 21 28 1 0 0 0 0 22 28 1 6 0 0 0 22 29 1 0 0 0 0 23 29 1 6 0 0 0 23 37 1 0 0 0 0 24 38 2 0 0 0 0 24 44 1 0 0 0 0 25 43 1 0 0 0 0 25 45 1 1 0 0 0 26 39 2 0 0 0 0 26 40 1 0 0 0 0 27 3 1 1 0 0 0 28 8 1 1 0 0 0 29 26 1 6 0 0 0 29 41 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	642.22
Volume:	586.263
LogP:	-0.509
LogD:	-0.669
LogS:	-2.99
# Rotatable Bonds:	7
TPSA:	245.04
# H-Bond Aceptor:	16
# H-Bond Donor:	6
# Rings:	6
# Heavy Atoms:	16

MedChem Properties

QED Drug-Likeness Score:	0.097
Synthetic Accessibility Score:	6.95
Fsp3:	0.793
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.146
MDCK Permeability:	0.00015046604676172137
Pgp-inhibitor:	0.615
Pgp-substrate:	1.0
Human Intestinal Absorption (HIA):	0.952
20% Bioavailability (F20%):	0.906
30% Bioavailability (F30%):	0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.116
Plasma Protein Binding (PPB):	51.22518539428711%
Volume Distribution (VD):	0.428
Pgp-substrate:	40.306514739990234%

ADMET: Metabolism

CYP1A2-inhibitor:	0.001
CYP1A2-substrate:	0.242
CYP2C19-inhibitor:	0.005
CYP2C19-substrate:	0.129
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.016
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.087
CYP3A4-inhibitor:	0.042
CYP3A4-substrate:	0.051

ADMET: Excretion

Clearance (CL):	1.189
Half-life (T1/2):	0.836

ADMET: Toxicity

hERG Blockers:	0.058
Human Hepatotoxicity (H-HT):	0.357
Drug-inuced Liver Injury (DILI):	0.935
AMES Toxicity:	0.118
Rat Oral Acute Toxicity:	0.17
Maximum Recommended Daily Dose:	0.017
Skin Sensitization:	0.072
Carcinogencity:	0.039
Eye Corrosion:	0.003
Eye Irritation:	0.008
Respiratory Toxicity:	0.026

Download Data

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

Natural Product: NPC87662

Natural Product ID:	NPC87662
*Common Name:**	Yadanzioside I
IUPAC Name:	n.a.
Synonyms:	Yadanzioside I
Standard InCHIKey:	QVXFIBXCQCYPLP-WQZWDNGFSA-N
Standard InCHI:	InChI=1S/C29H38O16/c1-9-11-5-14-28-8-41-29(26(39)40-4,22(28)20(24(38)44-14)42-10(2)31)23(37)18(36)21(28)27(11,3)6-12(32)19(9)45-25-17(35)16(34)15(33)13(7-30)43-25/h11,13-18,20-23,25,30,33-37H,5-8H2,1-4H3/t11-,13+,14+,15+,16-,17+,18+,20+,21+,22+,23-,25-,27-,28+,29+/m0/s1
SMILES:	OC[C@H]1O[C@@H](OC2=C(C)[C@H]3[C@@](CC2=O)(C)[C@H]2[C@@H](O)[C@H](O)[C@]4([C@H]5[C@@]2([C@@H](C3)OC(=O)[C@@H]5OC(=O)C)CO4)C(=O)OC)[C@@H]([C@H]([C@@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL506706
PubChem CID:	10484290
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0002119] Quassinoids

*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
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	seed	n.a.	DOI[10.1016/0031-9422(96)00258-0]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	fruit	n.a.	DOI[10.1016/S1383-5769(99)00023-9]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10086989]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1512598]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[15165151]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	fruit	Indonesia	n.a.	PMID[17896817]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	Vietnam	n.a.	PMID[19026551]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	seeds	n.a.	n.a.	PMID[20050684]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[22506620]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6481366]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7561896]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14948	Brucea javanica	Species	Simaroubaceae	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	2
Others	5

Activity Type	# Activity
Organism	7

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT485	Organism	Plasmodium falciparum (isolate K1 / Thailand)	Plasmodium falciparum K1	IC50	=	22.04	ug.mL-1	PMID[470490]
NPT786	Organism	Tobacco mosaic virus	Tobacco mosaic virus	IC50	=	4220.0	nM	PMID[470491]
NPT786	Organism	Tobacco mosaic virus	Tobacco mosaic virus	Inhibition	=	67.9	%	PMID[470491]
NPT786	Organism	Tobacco mosaic virus	Tobacco mosaic virus	Inhibition	=	54.9	%	PMID[470491]
NPT786	Organism	Tobacco mosaic virus	Tobacco mosaic virus	Inhibition	=	35.4	%	PMID[470491]
NPT786	Organism	Tobacco mosaic virus	Tobacco mosaic virus	Inhibition	=	26.1	%	PMID[470491]
NPT786	Organism	Tobacco mosaic virus	Tobacco mosaic virus	Inhibition	=	81.5	%	PMID[470491]

☑ 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 NPC87662 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	329
0.1-0.2	2104
0.2-0.3	5776
0.3-0.4	9021
0.4-0.5	11163
0.5-0.6	7428
0.6-0.7	4343
0.7-0.8	1958
0.8-0.85	421
0.85-0.9	123
0.9-0.95	25
0.95-1	6

Similarity Score	Similarity Level	Natural Product ID
0.9661	High Similarity	NPC295220
0.9661	High Similarity	NPC475636
0.958	High Similarity	NPC309096
0.958	High Similarity	NPC54614
0.935	High Similarity	NPC262813
0.9322	High Similarity	NPC227397
0.9274	High Similarity	NPC471089
0.9274	High Similarity	NPC190065
0.9274	High Similarity	NPC141215
0.9274	High Similarity	NPC251998
0.9217	High Similarity	NPC173686
0.9217	High Similarity	NPC16081
0.92	High Similarity	NPC140045
0.92	High Similarity	NPC596
0.92	High Similarity	NPC295885
0.9153	High Similarity	NPC275675
0.913	High Similarity	NPC323821
0.913	High Similarity	NPC143268
0.913	High Similarity	NPC268238
0.913	High Similarity	NPC45218
0.9008	High Similarity	NPC285091
0.8983	High Similarity	NPC279143
0.8983	High Similarity	NPC127530
0.8983	High Similarity	NPC473920
0.8843	High Similarity	NPC14617
0.8843	High Similarity	NPC471961
0.8843	High Similarity	NPC471964
0.8843	High Similarity	NPC202666
0.8843	High Similarity	NPC262199
0.8833	High Similarity	NPC169727
0.8833	High Similarity	NPC412
0.8833	High Similarity	NPC278163
0.8833	High Similarity	NPC241310
0.8833	High Similarity	NPC258789
0.8833	High Similarity	NPC258815
0.8833	High Similarity	NPC194310
0.8833	High Similarity	NPC187950
0.8833	High Similarity	NPC131841
0.8833	High Similarity	NPC47567
0.8824	High Similarity	NPC470777
0.877	High Similarity	NPC247315
0.877	High Similarity	NPC30188
0.877	High Similarity	NPC471962
0.877	High Similarity	NPC471963
0.877	High Similarity	NPC177820
0.876	High Similarity	NPC40775
0.876	High Similarity	NPC471965
0.876	High Similarity	NPC235438
0.876	High Similarity	NPC249848
0.876	High Similarity	NPC107966
0.8739	High Similarity	NPC297179
0.8739	High Similarity	NPC17772
0.8689	High Similarity	NPC235405
0.8689	High Similarity	NPC281148
0.8689	High Similarity	NPC30735
0.8689	High Similarity	NPC105926
0.8689	High Similarity	NPC91693
0.8689	High Similarity	NPC18945
0.8689	High Similarity	NPC265557
0.8689	High Similarity	NPC478066
0.8667	High Similarity	NPC258592
0.8667	High Similarity	NPC178548
0.8655	High Similarity	NPC309433
0.8651	High Similarity	NPC478154
0.8629	High Similarity	NPC470780
0.8618	High Similarity	NPC470477
0.8618	High Similarity	NPC6615
0.8618	High Similarity	NPC469842
0.8618	High Similarity	NPC7850
0.8618	High Similarity	NPC476729
0.8618	High Similarity	NPC469841
0.8607	High Similarity	NPC213952
0.8607	High Similarity	NPC312833
0.8607	High Similarity	NPC162574
0.8583	High Similarity	NPC204552
0.8583	High Similarity	NPC188667
0.8583	High Similarity	NPC176005
0.8583	High Similarity	NPC478151
0.8571	High Similarity	NPC172374
0.8571	High Similarity	NPC476074
0.8571	High Similarity	NPC134914
0.8571	High Similarity	NPC329993
0.8571	High Similarity	NPC478155
0.8571	High Similarity	NPC40632
0.8571	High Similarity	NPC475377
0.8571	High Similarity	NPC152199
0.8571	High Similarity	NPC251236
0.8571	High Similarity	NPC45346
0.8571	High Similarity	NPC96312
0.8571	High Similarity	NPC235539
0.8571	High Similarity	NPC25998
0.8571	High Similarity	NPC173435
0.8571	High Similarity	NPC478065
0.8571	High Similarity	NPC264566
0.8571	High Similarity	NPC301639
0.8571	High Similarity	NPC475167
0.8571	High Similarity	NPC134869
0.8571	High Similarity	NPC478064
0.8571	High Similarity	NPC328374
0.8571	High Similarity	NPC262796
0.8548	High Similarity	NPC181066
0.8548	High Similarity	NPC470218
0.8548	High Similarity	NPC469947
0.8537	High Similarity	NPC257211
0.8525	High Similarity	NPC31838
0.8525	High Similarity	NPC86222
0.8525	High Similarity	NPC11242
0.8525	High Similarity	NPC223301
0.8525	High Similarity	NPC297263
0.8525	High Similarity	NPC114484
0.8525	High Similarity	NPC301449
0.8525	High Similarity	NPC104372
0.8525	High Similarity	NPC22956
0.8525	High Similarity	NPC64715
0.8525	High Similarity	NPC62725
0.8525	High Similarity	NPC222580
0.8525	High Similarity	NPC159309
0.8525	High Similarity	NPC477046
0.8525	High Similarity	NPC102822
0.8525	High Similarity	NPC171544
0.8525	High Similarity	NPC75417
0.8512	High Similarity	NPC475171
0.8512	High Similarity	NPC473884
0.8512	High Similarity	NPC214484
0.8512	High Similarity	NPC39211
0.8512	High Similarity	NPC180550
0.8512	High Similarity	NPC472949
0.8512	High Similarity	NPC35405
0.8512	High Similarity	NPC309780
0.8512	High Similarity	NPC6377
0.8512	High Similarity	NPC114441
0.8512	High Similarity	NPC208381
0.8512	High Similarity	NPC469945
0.8512	High Similarity	NPC11551
0.8512	High Similarity	NPC157868
0.8504	High Similarity	NPC478150
0.8504	High Similarity	NPC478153
0.8504	High Similarity	NPC478152
0.85	High Similarity	NPC287343
0.85	High Similarity	NPC470854
0.85	High Similarity	NPC122033
0.85	High Similarity	NPC97908
0.85	High Similarity	NPC474654
0.85	High Similarity	NPC477252
0.8492	Intermediate Similarity	NPC477196
0.8487	Intermediate Similarity	NPC473798
0.8487	Intermediate Similarity	NPC18547
0.8487	Intermediate Similarity	NPC474906
0.8468	Intermediate Similarity	NPC33068
0.8468	Intermediate Similarity	NPC23275
0.8468	Intermediate Similarity	NPC24651
0.8455	Intermediate Similarity	NPC4749
0.8455	Intermediate Similarity	NPC236870
0.8455	Intermediate Similarity	NPC10607
0.8455	Intermediate Similarity	NPC21691
0.8455	Intermediate Similarity	NPC187290
0.8455	Intermediate Similarity	NPC80986
0.8455	Intermediate Similarity	NPC475591
0.8448	Intermediate Similarity	NPC94942
0.8443	Intermediate Similarity	NPC236657
0.8443	Intermediate Similarity	NPC118440
0.8443	Intermediate Similarity	NPC112038
0.8443	Intermediate Similarity	NPC473645
0.843	Intermediate Similarity	NPC286347
0.8425	Intermediate Similarity	NPC477197
0.8413	Intermediate Similarity	NPC475281
0.8413	Intermediate Similarity	NPC477193
0.8413	Intermediate Similarity	NPC477078
0.8413	Intermediate Similarity	NPC188291
0.8413	Intermediate Similarity	NPC477192
0.8413	Intermediate Similarity	NPC477075
0.8413	Intermediate Similarity	NPC329923
0.8413	Intermediate Similarity	NPC477191
0.8413	Intermediate Similarity	NPC477194
0.8403	Intermediate Similarity	NPC198539
0.8403	Intermediate Similarity	NPC49451
0.84	Intermediate Similarity	NPC284449
0.84	Intermediate Similarity	NPC104427
0.84	Intermediate Similarity	NPC477745
0.8387	Intermediate Similarity	NPC302543
0.8387	Intermediate Similarity	NPC283417
0.8387	Intermediate Similarity	NPC67251
0.8387	Intermediate Similarity	NPC44716
0.8387	Intermediate Similarity	NPC200049
0.8387	Intermediate Similarity	NPC2370
0.8387	Intermediate Similarity	NPC258617
0.8374	Intermediate Similarity	NPC242840
0.8374	Intermediate Similarity	NPC302887
0.8374	Intermediate Similarity	NPC187618
0.8374	Intermediate Similarity	NPC470779
0.8374	Intermediate Similarity	NPC31193
0.8372	Intermediate Similarity	NPC478069
0.8362	Intermediate Similarity	NPC202524
0.8361	Intermediate Similarity	NPC192791
0.8361	Intermediate Similarity	NPC469488
0.8361	Intermediate Similarity	NPC319570
0.8361	Intermediate Similarity	NPC473401
0.8359	Intermediate Similarity	NPC100390
0.8359	Intermediate Similarity	NPC254614
0.8359	Intermediate Similarity	NPC476776

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 NPC87662 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	315
0.1-0.2	2421
0.2-0.3	3874
0.3-0.4	1562
0.4-0.5	513
0.5-0.6	280
0.6-0.7	132
0.7-0.8	50
0.8-0.85	2
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8843	High Similarity	NPD8328	Phase 3
0.8655	High Similarity	NPD8295	Clinical (unspecified phase)
0.822	Intermediate Similarity	NPD8132	Clinical (unspecified phase)
0.7984	Intermediate Similarity	NPD7736	Approved
0.7907	Intermediate Similarity	NPD8293	Discontinued
0.7874	Intermediate Similarity	NPD6370	Approved
0.7752	Intermediate Similarity	NPD7492	Approved
0.7717	Intermediate Similarity	NPD6054	Approved
0.7717	Intermediate Similarity	NPD6059	Approved
0.7692	Intermediate Similarity	NPD6616	Approved
0.7652	Intermediate Similarity	NPD7319	Approved
0.7634	Intermediate Similarity	NPD7078	Approved
0.7578	Intermediate Similarity	NPD6319	Approved
0.7541	Intermediate Similarity	NPD5345	Clinical (unspecified phase)
0.7519	Intermediate Similarity	NPD6015	Approved
0.7519	Intermediate Similarity	NPD6016	Approved
0.7462	Intermediate Similarity	NPD5988	Approved
0.7459	Intermediate Similarity	NPD6412	Phase 2
0.744	Intermediate Similarity	NPD6882	Approved
0.7424	Intermediate Similarity	NPD7507	Approved
0.7385	Intermediate Similarity	NPD8517	Approved
0.7385	Intermediate Similarity	NPD8515	Approved
0.7385	Intermediate Similarity	NPD8513	Phase 3
0.7385	Intermediate Similarity	NPD8516	Approved
0.7381	Intermediate Similarity	NPD8133	Approved
0.7344	Intermediate Similarity	NPD6009	Approved
0.7339	Intermediate Similarity	NPD6373	Approved
0.7339	Intermediate Similarity	NPD6372	Approved
0.7302	Intermediate Similarity	NPD8297	Approved
0.7258	Intermediate Similarity	NPD6686	Approved
0.7236	Intermediate Similarity	NPD5739	Approved
0.7236	Intermediate Similarity	NPD6402	Approved
0.7236	Intermediate Similarity	NPD7128	Approved
0.7236	Intermediate Similarity	NPD6675	Approved
0.7222	Intermediate Similarity	NPD6649	Approved
0.7222	Intermediate Similarity	NPD6650	Approved
0.72	Intermediate Similarity	NPD4061	Clinical (unspecified phase)
0.7185	Intermediate Similarity	NPD6033	Approved
0.7143	Intermediate Similarity	NPD5955	Clinical (unspecified phase)
0.7121	Intermediate Similarity	NPD8378	Approved
0.7121	Intermediate Similarity	NPD8335	Approved
0.7121	Intermediate Similarity	NPD8380	Approved
0.7121	Intermediate Similarity	NPD8296	Approved
0.7121	Intermediate Similarity	NPD7503	Approved
0.7121	Intermediate Similarity	NPD8379	Approved
0.712	Intermediate Similarity	NPD6899	Approved
0.712	Intermediate Similarity	NPD7320	Approved
0.712	Intermediate Similarity	NPD6881	Approved
0.7109	Intermediate Similarity	NPD4632	Approved
0.7099	Intermediate Similarity	NPD7516	Approved
0.7068	Intermediate Similarity	NPD8080	Discontinued
0.7045	Intermediate Similarity	NPD8294	Approved
0.7045	Intermediate Similarity	NPD8377	Approved
0.704	Intermediate Similarity	NPD5701	Approved
0.704	Intermediate Similarity	NPD5697	Approved
0.7023	Intermediate Similarity	NPD7327	Approved
0.7023	Intermediate Similarity	NPD7328	Approved
0.7016	Intermediate Similarity	NPD8170	Clinical (unspecified phase)
0.7008	Intermediate Similarity	NPD7102	Approved
0.7008	Intermediate Similarity	NPD6883	Approved
0.7008	Intermediate Similarity	NPD7290	Approved
0.6992	Remote Similarity	NPD8033	Approved
0.6992	Remote Similarity	NPD6921	Approved
0.6953	Remote Similarity	NPD8130	Phase 1
0.6953	Remote Similarity	NPD6869	Approved
0.6953	Remote Similarity	NPD6847	Approved
0.6953	Remote Similarity	NPD6617	Approved
0.6929	Remote Similarity	NPD6014	Approved
0.6929	Remote Similarity	NPD6012	Approved
0.6929	Remote Similarity	NPD6013	Approved
0.6905	Remote Similarity	NPD5954	Clinical (unspecified phase)
0.6889	Remote Similarity	NPD7604	Phase 2
0.6875	Remote Similarity	NPD4634	Approved
0.6866	Remote Similarity	NPD5983	Phase 2
0.6866	Remote Similarity	NPD8274	Clinical (unspecified phase)
0.685	Remote Similarity	NPD6011	Approved
0.6822	Remote Similarity	NPD6401	Clinical (unspecified phase)
0.6818	Remote Similarity	NPD7115	Discovery
0.6803	Remote Similarity	NPD7902	Approved
0.6788	Remote Similarity	NPD6336	Discontinued
0.6694	Remote Similarity	NPD7748	Approved
0.6693	Remote Similarity	NPD6008	Approved
0.6692	Remote Similarity	NPD8413	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD6084	Phase 2
0.6667	Remote Similarity	NPD6083	Phase 2
0.6667	Remote Similarity	NPD4755	Approved
0.6667	Remote Similarity	NPD7515	Phase 2
0.6642	Remote Similarity	NPD6067	Discontinued
0.6619	Remote Similarity	NPD8074	Phase 3
0.6617	Remote Similarity	NPD6274	Approved
0.6613	Remote Similarity	NPD5696	Approved
0.6593	Remote Similarity	NPD7101	Approved
0.6593	Remote Similarity	NPD7100	Approved
0.6567	Remote Similarity	NPD8137	Clinical (unspecified phase)
0.656	Remote Similarity	NPD5286	Approved
0.656	Remote Similarity	NPD4696	Approved
0.656	Remote Similarity	NPD4700	Approved
0.656	Remote Similarity	NPD5285	Approved
0.6557	Remote Similarity	NPD7900	Approved
0.6557	Remote Similarity	NPD5282	Discontinued
0.6557	Remote Similarity	NPD7901	Clinical (unspecified phase)
0.6519	Remote Similarity	NPD6335	Approved
0.6496	Remote Similarity	NPD6909	Approved
0.6496	Remote Similarity	NPD6908	Approved
0.648	Remote Similarity	NPD4225	Approved
0.6479	Remote Similarity	NPD5956	Approved
0.6457	Remote Similarity	NPD5211	Phase 2
0.6457	Remote Similarity	NPD5226	Approved
0.6457	Remote Similarity	NPD4633	Approved
0.6457	Remote Similarity	NPD5224	Approved
0.6457	Remote Similarity	NPD5225	Approved
0.6452	Remote Similarity	NPD4697	Phase 3
0.6444	Remote Similarity	NPD6317	Approved
0.6434	Remote Similarity	NPD4767	Approved
0.6434	Remote Similarity	NPD4768	Approved
0.6406	Remote Similarity	NPD5175	Approved
0.6406	Remote Similarity	NPD5174	Approved
0.6397	Remote Similarity	NPD6313	Approved
0.6397	Remote Similarity	NPD6314	Approved
0.6389	Remote Similarity	NPD6845	Suspended
0.6378	Remote Similarity	NPD5223	Approved
0.6378	Remote Similarity	NPD1700	Approved
0.6377	Remote Similarity	NPD6291	Clinical (unspecified phase)
0.6371	Remote Similarity	NPD5695	Phase 3
0.637	Remote Similarity	NPD6868	Approved
0.6364	Remote Similarity	NPD5328	Approved
0.6357	Remote Similarity	NPD5141	Approved
0.6349	Remote Similarity	NPD7638	Approved
0.6341	Remote Similarity	NPD6399	Phase 3
0.6336	Remote Similarity	NPD4730	Approved
0.6336	Remote Similarity	NPD4729	Approved
0.6333	Remote Similarity	NPD3573	Approved
0.6327	Remote Similarity	NPD7966	Clinical (unspecified phase)
0.632	Remote Similarity	NPD5221	Approved
0.632	Remote Similarity	NPD5222	Approved
0.632	Remote Similarity	NPD5220	Clinical (unspecified phase)
0.6319	Remote Similarity	NPD7260	Phase 2
0.6299	Remote Similarity	NPD7639	Approved
0.6299	Remote Similarity	NPD7640	Approved
0.6281	Remote Similarity	NPD6672	Approved
0.6281	Remote Similarity	NPD5737	Approved
0.6279	Remote Similarity	NPD4754	Approved
0.6276	Remote Similarity	NPD8338	Approved
0.627	Remote Similarity	NPD5173	Approved
0.626	Remote Similarity	NPD6079	Approved
0.626	Remote Similarity	NPD6411	Approved
0.625	Remote Similarity	NPD3618	Phase 1
0.6241	Remote Similarity	NPD5248	Approved
0.6241	Remote Similarity	NPD5251	Approved
0.6241	Remote Similarity	NPD5250	Approved
0.6241	Remote Similarity	NPD5247	Approved
0.6241	Remote Similarity	NPD5249	Phase 3
0.6231	Remote Similarity	NPD4056	Clinical (unspecified phase)
0.6231	Remote Similarity	NPD4057	Clinical (unspecified phase)
0.623	Remote Similarity	NPD7285	Clinical (unspecified phase)
0.6224	Remote Similarity	NPD8336	Approved
0.6224	Remote Similarity	NPD8337	Approved
0.6212	Remote Similarity	NPD5128	Approved
0.621	Remote Similarity	NPD8171	Discontinued
0.6202	Remote Similarity	NPD7632	Discontinued
0.619	Remote Similarity	NPD7799	Discontinued
0.6148	Remote Similarity	NPD6053	Discontinued
0.6136	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.6134	Remote Similarity	NPD3669	Approved
0.6134	Remote Similarity	NPD3670	Clinical (unspecified phase)
0.6129	Remote Similarity	NPD8035	Phase 2
0.6129	Remote Similarity	NPD8034	Phase 2
0.6127	Remote Similarity	NPD8407	Phase 2
0.6116	Remote Similarity	NPD3574	Clinical (unspecified phase)
0.6111	Remote Similarity	NPD5210	Approved
0.6111	Remote Similarity	NPD4629	Approved
0.6111	Remote Similarity	NPD6356	Clinical (unspecified phase)
0.6102	Remote Similarity	NPD1779	Approved
0.6102	Remote Similarity	NPD1780	Approved
0.6098	Remote Similarity	NPD6101	Approved
0.6098	Remote Similarity	NPD6904	Approved
0.6098	Remote Similarity	NPD6080	Approved
0.6098	Remote Similarity	NPD6673	Approved
0.6098	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.6098	Remote Similarity	NPD4753	Phase 2
0.608	Remote Similarity	NPD4202	Approved
0.6074	Remote Similarity	NPD5215	Approved
0.6074	Remote Similarity	NPD5216	Approved
0.6074	Remote Similarity	NPD5217	Approved
0.6068	Remote Similarity	NPD7329	Approved
0.6067	Remote Similarity	NPD6334	Approved
0.6067	Remote Similarity	NPD6333	Approved
0.6047	Remote Similarity	NPD8368	Discontinued
0.604	Remote Similarity	NPD8387	Clinical (unspecified phase)
0.6027	Remote Similarity	NPD6914	Discontinued
0.6016	Remote Similarity	NPD7513	Clinical (unspecified phase)
0.6	Remote Similarity	NPD5135	Approved
0.6	Remote Similarity	NPD6371	Approved
0.6	Remote Similarity	NPD5169	Approved
0.6	Remote Similarity	NPD5134	Clinical (unspecified phase)
0.5984	Remote Similarity	NPD5330	Approved
0.5984	Remote Similarity	NPD7521	Approved
0.5984	Remote Similarity	NPD6684	Approved
0.5984	Remote Similarity	NPD6409	Approved
0.5984	Remote Similarity	NPD7146	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