NPASS Compound

Structure

NPC475899 OpenBabel07101718292D 85 94 0 0 1 0 0 0 0 0999 V2000 -9.5490 -0.6728 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0981 -4.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0981 -4.3660 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 3.0981 2.3660 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 -0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -2.0000 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 0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -2.0000 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 -1.7321 -3.0000 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 6.0622 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1677 2.2944 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6160 3.9674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0981 2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.6995 0.9282 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.0589 1.9936 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.8419 -1.3799 0.0000 C 0 0 1 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 -2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.3231 4.6745 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1962 4.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.4265 1.3284 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 2 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 -9.1007 -2.3458 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.2890 4.4157 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3301 4.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.3936 -3.0529 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4641 4.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.5478 3.4497 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.4277 -2.7941 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.3924 1.0696 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.6512 0.1037 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9441 -0.6034 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -9.3120 0.3955 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.8407 2.7426 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.1689 -1.8282 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3301 2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.9782 -0.3446 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.3243 0.5520 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3052 -0.7929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -9.7660 1.2865 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.0622 5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2018 2.5532 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 3.2321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.4767 1.5575 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0643 5.6404 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.0667 -2.6046 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.9961 5.1228 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6525 -4.0188 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.5137 3.1909 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7206 -3.5012 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.7660 -0.4955 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0464 0.1730 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.5431 1.9159 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8748 3.0015 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.1678 1.5397 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.8760 -1.1211 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7194 0.6213 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.0995 1.7767 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6172 -0.1551 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.2030 -1.5694 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 -4.2711 -1.0517 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 52 1 0 0 0 0 3 52 1 0 0 0 0 6 55 1 0 0 0 0 8 9 1 0 0 0 0 8 25 2 0 0 0 0 9 32 1 0 0 0 0 10 11 1 0 0 0 0 10 31 1 0 0 0 0 11 56 1 0 0 0 0 12 14 1 0 0 0 0 12 52 1 0 0 0 0 13 15 1 0 0 0 0 13 55 1 0 0 0 0 14 57 1 0 0 0 0 15 57 1 0 0 0 0 16 26 1 0 0 0 0 16 52 1 0 0 0 0 17 27 1 0 0 0 0 17 53 1 0 0 0 0 18 59 1 0 0 0 0 19 60 1 0 0 0 0 20 28 1 0 0 0 0 20 76 1 0 0 0 0 21 54 1 0 0 0 0 21 61 1 0 0 0 0 22 58 1 0 0 0 0 22 62 1 0 0 0 0 23 58 1 0 0 0 0 23 77 1 0 0 0 0 24 1 1 6 0 0 0 24 33 1 0 0 0 0 24 78 1 0 0 0 0 25 26 1 0 0 0 0 25 55 1 0 0 0 0 26 57 1 6 0 0 0 27 45 1 0 0 0 0 27 63 1 1 0 0 0 28 34 1 0 0 0 0 28 64 1 6 0 0 0 29 18 1 1 0 0 0 29 35 1 0 0 0 0 29 79 1 0 0 0 0 30 19 1 1 0 0 0 30 41 1 0 0 0 0 30 80 1 0 0 0 0 31 53 1 1 0 0 0 31 54 1 0 0 0 0 32 53 1 1 0 0 0 32 56 1 0 0 0 0 33 36 1 0 0 0 0 33 65 1 1 0 0 0 34 38 1 0 0 0 0 34 66 1 1 0 0 0 35 37 1 0 0 0 0 35 67 1 6 0 0 0 36 39 1 0 0 0 0 36 68 1 6 0 0 0 37 40 1 0 0 0 0 37 69 1 1 0 0 0 38 46 1 0 0 0 0 38 70 1 6 0 0 0 39 47 1 0 0 0 0 39 71 1 6 0 0 0 40 48 1 0 0 0 0 40 72 1 6 0 0 0 41 42 1 0 0 0 0 41 81 1 6 0 0 0 42 43 1 0 0 0 0 42 82 1 1 0 0 0 43 49 1 0 0 0 0 43 83 1 6 0 0 0 44 50 1 0 0 0 0 44 58 1 6 0 0 0 44 73 1 0 0 0 0 45 54 1 1 0 0 0 45 84 1 0 0 0 0 46 76 1 0 0 0 0 46 81 1 1 0 0 0 47 78 1 0 0 0 0 47 83 1 1 0 0 0 48 79 1 0 0 0 0 48 84 1 1 0 0 0 49 80 1 0 0 0 0 49 85 1 1 0 0 0 50 77 1 0 0 0 0 50 82 1 1 0 0 0 51 74 2 0 0 0 0 51 85 1 0 0 0 0 53 4 1 1 0 0 0 54 5 1 6 0 0 0 55 56 1 1 0 0 0 56 7 1 1 0 0 0 57 51 1 1 0 0 0 58 75 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	1222.6
Volume:	1158.222
LogP:	1.234
LogD:	0.749
LogS:	-3.001
# Rotatable Bonds:	15
TPSA:	433.05
# H-Bond Aceptor:	27
# H-Bond Donor:	16
# Rings:	10
# Heavy Atoms:	27

MedChem Properties

QED Drug-Likeness Score:	0.045
Synthetic Accessibility Score:	7.358
Fsp3:	0.948
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.533
MDCK Permeability:	0.00017428913270123303
Pgp-inhibitor:	0.002
Pgp-substrate:	0.993
Human Intestinal Absorption (HIA):	0.999
20% Bioavailability (F20%):	0.668
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.199
Plasma Protein Binding (PPB):	51.29925537109375%
Volume Distribution (VD):	-0.105
Pgp-substrate:	20.58550453186035%

ADMET: Metabolism

CYP1A2-inhibitor:	0.0
CYP1A2-substrate:	0.32
CYP2C19-inhibitor:	0.0
CYP2C19-substrate:	0.068
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.001
CYP2D6-inhibitor:	0.0
CYP2D6-substrate:	0.02
CYP3A4-inhibitor:	0.085
CYP3A4-substrate:	0.004

ADMET: Excretion

Clearance (CL):	0.077
Half-life (T1/2):	0.787

ADMET: Toxicity

hERG Blockers:	0.253
Human Hepatotoxicity (H-HT):	0.176
Drug-inuced Liver Injury (DILI):	0.025
AMES Toxicity:	0.075
Rat Oral Acute Toxicity:	0.061
Maximum Recommended Daily Dose:	0.003
Skin Sensitization:	0.019
Carcinogencity:	0.014
Eye Corrosion:	0.003
Eye Irritation:	0.005
Respiratory Toxicity:	0.417

Download Data

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

Natural Product: NPC475899

Natural Product ID:	NPC475899
*Common Name:**	Polygalasaponin V
IUPAC Name:	[(2S,3R,4S,5R,6R)-4-[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy-6-(hydroxymethyl)-3-[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy-5-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxyoxan-2-yl] (4aS,6aR,6aS,6bR,8aR,9S,10R,11S,12aR,14bS)-11-hydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-10-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-1,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-4a-carboxylate
Synonyms:	Polygalasaponin V
Standard InCHIKey:	LCVQAJAGNRLCRZ-LSXSQVAQSA-N
Standard InCHI:	InChI=1S/C58H94O27/c1-24-33(65)36(68)39(71)47(78-24)83-43-42(82-50-44(73)58(75,22-62)23-77-50)41(81-46-38(70)34(66)28(64)20-76-46)30(19-60)80-49(43)85-51(74)57-14-12-52(2,3)16-26(57)25-8-9-32-53(4)17-27(63)45(84-48-40(72)37(69)35(67)29(18-59)79-48)54(5,21-61)31(53)10-11-56(32,7)55(25,6)13-15-57/h8,24,26-50,59-73,75H,9-23H2,1-7H3/t24-,26-,27-,28+,29+,30+,31+,32+,33-,34-,35+,36+,37-,38+,39+,40+,41+,42-,43+,44-,45-,46-,47-,48-,49-,50-,53-,54+,55+,56+,57-,58+/m0/s1
SMILES:	CC1C(C(C(C(O1)OC2C(C(C(OC2OC(=O)C34CCC(CC3C5=CCC6C(C5(CC4)C)(CCC7C6(CC(C(C7(C)CO)OC8C(C(C(C(O8)CO)O)O)O)O)C)C)(C)C)CO)OC9C(C(C(CO9)O)O)O)OC1C(C(CO1)(CO)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL518138
PubChem CID:	44575293
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

*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
NPO11905	Polygala japonica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16643032]
NPO11905	Polygala japonica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11905	Polygala japonica	Species	Polygalaceae	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
Others	2

Activity Type	# Activity
Organism	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	16.8	%	PMID[486129]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	16.6	%	PMID[486129]

☑ 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 NPC475899 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	252
0.1-0.2	1641
0.2-0.3	5254
0.3-0.4	12135
0.4-0.5	9480
0.5-0.6	5934
0.6-0.7	4458
0.7-0.8	1993
0.8-0.85	803
0.85-0.9	392
0.9-0.95	318
0.95-1	37

Similarity Score	Similarity Level	Natural Product ID
0.9908	High Similarity	NPC477464
0.9818	High Similarity	NPC37860
0.9818	High Similarity	NPC142151
0.9818	High Similarity	NPC144644
0.9818	High Similarity	NPC267694
0.9818	High Similarity	NPC153673
0.9818	High Similarity	NPC110385
0.973	High Similarity	NPC51099
0.973	High Similarity	NPC293031
0.973	High Similarity	NPC477463
0.973	High Similarity	NPC68767
0.973	High Similarity	NPC275225
0.964	High Similarity	NPC473645
0.963	High Similarity	NPC473826
0.963	High Similarity	NPC73318
0.963	High Similarity	NPC295823
0.963	High Similarity	NPC151543
0.963	High Similarity	NPC114304
0.963	High Similarity	NPC114287
0.963	High Similarity	NPC192600
0.963	High Similarity	NPC251263
0.963	High Similarity	NPC219180
0.963	High Similarity	NPC96641
0.963	High Similarity	NPC155410
0.963	High Similarity	NPC473343
0.963	High Similarity	NPC46665
0.963	High Similarity	NPC241909
0.963	High Similarity	NPC163183
0.963	High Similarity	NPC475287
0.963	High Similarity	NPC174720
0.963	High Similarity	NPC323341
0.963	High Similarity	NPC475467
0.963	High Similarity	NPC150400
0.963	High Similarity	NPC133818
0.963	High Similarity	NPC309714
0.963	High Similarity	NPC134835
0.963	High Similarity	NPC166422
0.955	High Similarity	NPC471577
0.955	High Similarity	NPC207738
0.9545	High Similarity	NPC68175
0.9541	High Similarity	NPC294453
0.9541	High Similarity	NPC204414
0.9541	High Similarity	NPC293330
0.9541	High Similarity	NPC475140
0.9541	High Similarity	NPC475160
0.9541	High Similarity	NPC76972
0.9541	High Similarity	NPC469782
0.9541	High Similarity	NPC123199
0.9541	High Similarity	NPC100639
0.9541	High Similarity	NPC67857
0.9541	High Similarity	NPC65105
0.9541	High Similarity	NPC473714
0.9541	High Similarity	NPC54636
0.9541	High Similarity	NPC4328
0.9541	High Similarity	NPC261506
0.9541	High Similarity	NPC41061
0.9541	High Similarity	NPC70809
0.9541	High Similarity	NPC161717
0.9541	High Similarity	NPC471385
0.9541	High Similarity	NPC119592
0.9541	High Similarity	NPC298034
0.9541	High Similarity	NPC202828
0.9541	High Similarity	NPC476068
0.9541	High Similarity	NPC43550
0.9541	High Similarity	NPC60557
0.9541	High Similarity	NPC79643
0.9541	High Similarity	NPC224381
0.9541	High Similarity	NPC305981
0.9541	High Similarity	NPC236638
0.9541	High Similarity	NPC227551
0.9541	High Similarity	NPC471550
0.9541	High Similarity	NPC71065
0.9541	High Similarity	NPC309907
0.9541	High Similarity	NPC57484
0.9541	High Similarity	NPC250247
0.9537	High Similarity	NPC292677
0.9537	High Similarity	NPC257468
0.9537	High Similarity	NPC475504
0.9537	High Similarity	NPC101744
0.9537	High Similarity	NPC473373
0.9537	High Similarity	NPC471383
0.9537	High Similarity	NPC104071
0.9537	High Similarity	NPC102439
0.9537	High Similarity	NPC109079
0.9537	High Similarity	NPC10320
0.9537	High Similarity	NPC79718
0.9537	High Similarity	NPC473383
0.9537	High Similarity	NPC139044
0.9537	High Similarity	NPC139894
0.9537	High Similarity	NPC475516
0.9537	High Similarity	NPC324875
0.9537	High Similarity	NPC469946
0.9537	High Similarity	NPC104400
0.9537	High Similarity	NPC276093
0.9459	High Similarity	NPC36831
0.9459	High Similarity	NPC105800
0.9459	High Similarity	NPC232237
0.9459	High Similarity	NPC237191
0.9455	High Similarity	NPC305267
0.9455	High Similarity	NPC471384
0.9455	High Similarity	NPC26626
0.9455	High Similarity	NPC288205
0.9455	High Similarity	NPC75287
0.9455	High Similarity	NPC160415
0.9455	High Similarity	NPC161674
0.9455	High Similarity	NPC58448
0.9455	High Similarity	NPC51465
0.9455	High Similarity	NPC476992
0.945	High Similarity	NPC258885
0.945	High Similarity	NPC124296
0.9444	High Similarity	NPC179434
0.9444	High Similarity	NPC164419
0.9375	High Similarity	NPC135849
0.9375	High Similarity	NPC51564
0.9375	High Similarity	NPC25663
0.9369	High Similarity	NPC148417
0.9369	High Similarity	NPC300419
0.9369	High Similarity	NPC136768
0.9369	High Similarity	NPC191827
0.9369	High Similarity	NPC102505
0.9369	High Similarity	NPC471547
0.9369	High Similarity	NPC220160
0.9369	High Similarity	NPC123522
0.9369	High Similarity	NPC104137
0.9369	High Similarity	NPC473824
0.9369	High Similarity	NPC33012
0.9369	High Similarity	NPC85154
0.9369	High Similarity	NPC309223
0.9369	High Similarity	NPC185466
0.9369	High Similarity	NPC470876
0.9369	High Similarity	NPC475209
0.9369	High Similarity	NPC69811
0.9369	High Similarity	NPC286457
0.9369	High Similarity	NPC110633
0.9369	High Similarity	NPC475119
0.9369	High Similarity	NPC473452
0.9369	High Similarity	NPC8524
0.9369	High Similarity	NPC475514
0.9364	High Similarity	NPC475486
0.9364	High Similarity	NPC164389
0.9352	High Similarity	NPC164194
0.9352	High Similarity	NPC59804
0.9352	High Similarity	NPC110139
0.9352	High Similarity	NPC174679
0.9352	High Similarity	NPC127056
0.9352	High Similarity	NPC75747
0.9352	High Similarity	NPC475296
0.9352	High Similarity	NPC270667
0.9352	High Similarity	NPC68419
0.9352	High Similarity	NPC474589
0.9352	High Similarity	NPC136877
0.9352	High Similarity	NPC199457
0.9352	High Similarity	NPC29069
0.9352	High Similarity	NPC108709
0.9352	High Similarity	NPC279554
0.9352	High Similarity	NPC7870
0.9352	High Similarity	NPC56713
0.9352	High Similarity	NPC102914
0.9352	High Similarity	NPC90856
0.9292	High Similarity	NPC476991
0.9292	High Similarity	NPC268184
0.9286	High Similarity	NPC473459
0.9286	High Similarity	NPC471548
0.9279	High Similarity	NPC37134
0.9279	High Similarity	NPC291903
0.9273	High Similarity	NPC238935
0.9273	High Similarity	NPC138334
0.9273	High Similarity	NPC475208
0.9273	High Similarity	NPC47063
0.9273	High Similarity	NPC269315
0.9273	High Similarity	NPC271138
0.9273	High Similarity	NPC204458
0.9273	High Similarity	NPC189884
0.9266	High Similarity	NPC30397
0.9266	High Similarity	NPC297208
0.9266	High Similarity	NPC108748
0.9266	High Similarity	NPC473481
0.9266	High Similarity	NPC235841
0.9266	High Similarity	NPC211798
0.9259	High Similarity	NPC127853
0.9259	High Similarity	NPC167383
0.9259	High Similarity	NPC204407
0.9259	High Similarity	NPC237503
0.9259	High Similarity	NPC306746
0.9259	High Similarity	NPC57362
0.9204	High Similarity	NPC473401
0.9204	High Similarity	NPC473386
0.9196	High Similarity	NPC323359
0.9196	High Similarity	NPC473405
0.9196	High Similarity	NPC471580
0.9182	High Similarity	NPC128925
0.9182	High Similarity	NPC1046
0.9182	High Similarity	NPC48249
0.9182	High Similarity	NPC80843
0.9182	High Similarity	NPC256798
0.9182	High Similarity	NPC46388
0.9182	High Similarity	NPC116794
0.9182	High Similarity	NPC37739
0.9174	High Similarity	NPC476883
0.9174	High Similarity	NPC476885

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 NPC475899 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	222
0.1-0.2	1930
0.2-0.3	4028
0.3-0.4	1936
0.4-0.5	549
0.5-0.6	280
0.6-0.7	161
0.7-0.8	30
0.8-0.85	12
0.85-0.9	2
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8596	High Similarity	NPD8133	Approved
0.8571	High Similarity	NPD8132	Clinical (unspecified phase)
0.8571	High Similarity	NPD8328	Phase 3
0.8376	Intermediate Similarity	NPD8295	Clinical (unspecified phase)
0.8017	Intermediate Similarity	NPD8377	Approved
0.8017	Intermediate Similarity	NPD8294	Approved
0.7951	Intermediate Similarity	NPD8379	Approved
0.7951	Intermediate Similarity	NPD8517	Approved
0.7951	Intermediate Similarity	NPD8296	Approved
0.7951	Intermediate Similarity	NPD8335	Approved
0.7951	Intermediate Similarity	NPD8515	Approved
0.7951	Intermediate Similarity	NPD8378	Approved
0.7951	Intermediate Similarity	NPD8380	Approved
0.7951	Intermediate Similarity	NPD8516	Approved
0.7913	Intermediate Similarity	NPD6412	Phase 2
0.7845	Intermediate Similarity	NPD6686	Approved
0.784	Intermediate Similarity	NPD7507	Approved
0.7805	Intermediate Similarity	NPD8513	Phase 3
0.7805	Intermediate Similarity	NPD8033	Approved
0.7717	Intermediate Similarity	NPD7736	Approved
0.7656	Intermediate Similarity	NPD7319	Approved
0.7642	Intermediate Similarity	NPD7516	Approved
0.7568	Intermediate Similarity	NPD7748	Approved
0.7561	Intermediate Similarity	NPD7327	Approved
0.7561	Intermediate Similarity	NPD7328	Approved
0.7522	Intermediate Similarity	NPD7902	Approved
0.75	Intermediate Similarity	NPD8413	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD8293	Discontinued
0.7436	Intermediate Similarity	NPD8170	Clinical (unspecified phase)
0.7387	Intermediate Similarity	NPD7515	Phase 2
0.7381	Intermediate Similarity	NPD7503	Approved
0.7323	Intermediate Similarity	NPD6370	Approved
0.7257	Intermediate Similarity	NPD7900	Approved
0.7257	Intermediate Similarity	NPD7901	Clinical (unspecified phase)
0.7209	Intermediate Similarity	NPD7492	Approved
0.719	Intermediate Similarity	NPD4061	Clinical (unspecified phase)
0.7165	Intermediate Similarity	NPD6059	Approved
0.7165	Intermediate Similarity	NPD6054	Approved
0.7154	Intermediate Similarity	NPD6616	Approved
0.7154	Intermediate Similarity	NPD6882	Approved
0.7154	Intermediate Similarity	NPD8297	Approved
0.7099	Intermediate Similarity	NPD7078	Approved
0.708	Intermediate Similarity	NPD8035	Phase 2
0.708	Intermediate Similarity	NPD8034	Phase 2
0.7063	Intermediate Similarity	NPD6009	Approved
0.7031	Intermediate Similarity	NPD6319	Approved
0.7018	Intermediate Similarity	NPD8171	Discontinued
0.7009	Intermediate Similarity	NPD7638	Approved
0.7	Intermediate Similarity	NPD6067	Discontinued
0.6992	Remote Similarity	NPD5955	Clinical (unspecified phase)
0.6977	Remote Similarity	NPD6016	Approved
0.6977	Remote Similarity	NPD6015	Approved
0.6967	Remote Similarity	NPD5345	Clinical (unspecified phase)
0.696	Remote Similarity	NPD4632	Approved
0.6949	Remote Similarity	NPD7639	Approved
0.6949	Remote Similarity	NPD7640	Approved
0.6942	Remote Similarity	NPD6402	Approved
0.6942	Remote Similarity	NPD5739	Approved
0.6942	Remote Similarity	NPD7128	Approved
0.6942	Remote Similarity	NPD6675	Approved
0.6923	Remote Similarity	NPD5988	Approved
0.6911	Remote Similarity	NPD6373	Approved
0.6911	Remote Similarity	NPD6372	Approved
0.687	Remote Similarity	NPD6399	Phase 3
0.6847	Remote Similarity	NPD7520	Clinical (unspecified phase)
0.6842	Remote Similarity	NPD8074	Phase 3
0.6829	Remote Similarity	NPD6881	Approved
0.6829	Remote Similarity	NPD6899	Approved
0.6829	Remote Similarity	NPD7320	Approved
0.68	Remote Similarity	NPD8130	Phase 1
0.68	Remote Similarity	NPD6649	Approved
0.68	Remote Similarity	NPD6650	Approved
0.6797	Remote Similarity	NPD7115	Discovery
0.6788	Remote Similarity	NPD8450	Suspended
0.6759	Remote Similarity	NPD7645	Phase 2
0.6748	Remote Similarity	NPD5697	Approved
0.6748	Remote Similarity	NPD5954	Clinical (unspecified phase)
0.6748	Remote Similarity	NPD5701	Approved
0.672	Remote Similarity	NPD6883	Approved
0.672	Remote Similarity	NPD7102	Approved
0.672	Remote Similarity	NPD7290	Approved
0.6715	Remote Similarity	NPD8449	Approved
0.6667	Remote Similarity	NPD6008	Approved
0.6667	Remote Similarity	NPD6033	Approved
0.6667	Remote Similarity	NPD6847	Approved
0.6667	Remote Similarity	NPD6617	Approved
0.6667	Remote Similarity	NPD6869	Approved
0.664	Remote Similarity	NPD6013	Approved
0.664	Remote Similarity	NPD6012	Approved
0.664	Remote Similarity	NPD6014	Approved
0.6639	Remote Similarity	NPD6083	Phase 2
0.6639	Remote Similarity	NPD6084	Phase 2
0.6617	Remote Similarity	NPD7604	Phase 2
0.6591	Remote Similarity	NPD5983	Phase 2
0.6583	Remote Similarity	NPD4225	Approved
0.656	Remote Similarity	NPD6011	Approved
0.6535	Remote Similarity	NPD6401	Clinical (unspecified phase)
0.6522	Remote Similarity	NPD7513	Clinical (unspecified phase)
0.6519	Remote Similarity	NPD6336	Discontinued
0.65	Remote Similarity	NPD4755	Approved
0.6496	Remote Similarity	NPD6411	Approved
0.6491	Remote Similarity	NPD3618	Phase 1
0.6466	Remote Similarity	NPD5328	Approved
0.6466	Remote Similarity	NPD6921	Approved
0.6463	Remote Similarity	NPD7625	Phase 1
0.646	Remote Similarity	NPD4786	Approved
0.6457	Remote Similarity	NPD4634	Approved
0.6441	Remote Similarity	NPD4202	Approved
0.6435	Remote Similarity	NPD3573	Approved
0.6429	Remote Similarity	NPD3667	Approved
0.6423	Remote Similarity	NPD7632	Discontinued
0.641	Remote Similarity	NPD6698	Approved
0.641	Remote Similarity	NPD46	Approved
0.6396	Remote Similarity	NPD7525	Registered
0.6393	Remote Similarity	NPD4700	Approved
0.6393	Remote Similarity	NPD5285	Approved
0.6393	Remote Similarity	NPD4696	Approved
0.6393	Remote Similarity	NPD5286	Approved
0.6372	Remote Similarity	NPD3669	Approved
0.6372	Remote Similarity	NPD3670	Clinical (unspecified phase)
0.6356	Remote Similarity	NPD6079	Approved
0.6348	Remote Similarity	NPD7334	Approved
0.6348	Remote Similarity	NPD7146	Approved
0.6348	Remote Similarity	NPD5330	Approved
0.6348	Remote Similarity	NPD6684	Approved
0.6348	Remote Similarity	NPD7521	Approved
0.6348	Remote Similarity	NPD6409	Approved
0.6336	Remote Similarity	NPD6940	Discontinued
0.6336	Remote Similarity	NPD6274	Approved
0.6333	Remote Similarity	NPD5695	Phase 3
0.6333	Remote Similarity	NPD6356	Clinical (unspecified phase)
0.6325	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.6325	Remote Similarity	NPD6101	Approved
0.6316	Remote Similarity	NPD7101	Approved
0.6316	Remote Similarity	NPD7100	Approved
0.6311	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.6311	Remote Similarity	NPD5696	Approved
0.629	Remote Similarity	NPD5225	Approved
0.629	Remote Similarity	NPD5224	Approved
0.629	Remote Similarity	NPD4633	Approved
0.629	Remote Similarity	NPD5211	Phase 2
0.629	Remote Similarity	NPD5226	Approved
0.6288	Remote Similarity	NPD8137	Clinical (unspecified phase)
0.627	Remote Similarity	NPD4767	Approved
0.627	Remote Similarity	NPD4768	Approved
0.6241	Remote Similarity	NPD6335	Approved
0.624	Remote Similarity	NPD5175	Approved
0.624	Remote Similarity	NPD5174	Approved
0.6239	Remote Similarity	NPD6903	Approved
0.6239	Remote Similarity	NPD6672	Approved
0.6239	Remote Similarity	NPD5737	Approved
0.6222	Remote Similarity	NPD6908	Approved
0.6222	Remote Similarity	NPD6909	Approved
0.6218	Remote Similarity	NPD7983	Approved
0.6216	Remote Similarity	NPD6118	Approved
0.6216	Remote Similarity	NPD6697	Approved
0.6216	Remote Similarity	NPD6114	Approved
0.6216	Remote Similarity	NPD6115	Approved
0.6214	Remote Similarity	NPD5956	Approved
0.621	Remote Similarity	NPD5344	Discontinued
0.621	Remote Similarity	NPD5223	Approved
0.6195	Remote Similarity	NPD1779	Approved
0.6195	Remote Similarity	NPD1780	Approved
0.619	Remote Similarity	NPD5141	Approved
0.6187	Remote Similarity	NPD8337	Approved
0.6187	Remote Similarity	NPD8336	Approved
0.6186	Remote Similarity	NPD7285	Clinical (unspecified phase)
0.6186	Remote Similarity	NPD4753	Phase 2
0.6174	Remote Similarity	NPD3133	Approved
0.6174	Remote Similarity	NPD3665	Phase 1
0.6174	Remote Similarity	NPD3666	Approved
0.6172	Remote Similarity	NPD4730	Approved
0.6172	Remote Similarity	NPD4729	Approved
0.6167	Remote Similarity	NPD5779	Approved
0.6167	Remote Similarity	NPD5778	Approved
0.6165	Remote Similarity	NPD6317	Approved
0.6154	Remote Similarity	NPD7524	Approved
0.6148	Remote Similarity	NPD5222	Approved
0.6148	Remote Similarity	NPD5221	Approved
0.6148	Remote Similarity	NPD4697	Phase 3
0.6148	Remote Similarity	NPD5220	Clinical (unspecified phase)
0.6127	Remote Similarity	NPD8338	Approved
0.6126	Remote Similarity	NPD6116	Phase 1
0.6119	Remote Similarity	NPD6314	Approved
0.6119	Remote Similarity	NPD6313	Approved
0.6115	Remote Similarity	NPD8448	Approved
0.6111	Remote Similarity	NPD4754	Approved
0.6107	Remote Similarity	NPD6053	Discontinued
0.6103	Remote Similarity	NPD6291	Clinical (unspecified phase)
0.6103	Remote Similarity	NPD8274	Clinical (unspecified phase)
0.6099	Remote Similarity	NPD8392	Approved
0.6099	Remote Similarity	NPD8391	Approved
0.6099	Remote Similarity	NPD8390	Approved
0.6098	Remote Similarity	NPD5173	Approved
0.6094	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.609	Remote Similarity	NPD6868	Approved
0.6087	Remote Similarity	NPD8299	Approved
0.6087	Remote Similarity	NPD8341	Approved
0.6087	Remote Similarity	NPD8340	Approved
0.6087	Remote Similarity	NPD8342	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