NPASS Compound

Structure

NPC203108 OpenBabel06302215182D 50 56 0 0 1 0 0 0 0 0999 V2000 5.1050 -0.9825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2542 -1.4737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4033 -0.9825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4033 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2542 0.4912 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1050 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5525 0.4912 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7017 -0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 0.8508 0.4912 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8508 1.4737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7017 1.9649 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7017 2.9474 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8508 3.4386 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.9474 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7017 3.9298 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7017 4.9123 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8508 5.4035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8508 6.3860 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7017 6.8772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5525 6.3860 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5525 5.4035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4033 4.9123 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4033 3.9298 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2542 3.4386 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1050 3.9298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9558 3.4386 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9558 2.4561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1050 1.9649 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2542 2.4561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1050 0.9825 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8067 1.9649 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5525 3.4386 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5525 2.4561 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7017 7.8596 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 4.9123 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.9649 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8508 1.4737 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8508 0.4912 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7017 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5525 0.4912 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4033 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4033 -0.9825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5525 -1.4737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7017 -0.9825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5525 -2.4561 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2542 -1.4737 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 -0.9825 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8508 4.4211 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5525 1.4737 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 7 1 0 0 0 0 5 6 1 0 0 0 0 7 8 1 0 0 0 0 9 8 1 6 0 0 0 9 10 1 0 0 0 0 9 47 1 0 0 0 0 10 36 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 50 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 49 1 0 0 0 0 14 36 1 0 0 0 0 15 14 1 6 0 0 0 15 16 1 0 0 0 0 15 32 1 0 0 0 0 16 21 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 35 1 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 19 34 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 1 0 0 0 23 32 1 0 0 0 0 24 29 2 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 31 1 0 0 0 0 28 29 1 0 0 0 0 28 30 1 0 0 0 0 32 33 1 1 0 0 0 36 37 1 0 0 0 0 37 38 1 0 0 0 0 38 39 1 1 0 0 0 38 47 1 0 0 0 0 39 44 2 0 0 0 0 39 40 1 0 0 0 0 40 41 2 0 0 0 0 41 42 1 0 0 0 0 42 43 2 0 0 0 0 42 46 1 0 0 0 0 43 44 1 0 0 0 0 43 45 1 0 0 0 0 47 48 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	700.16
Volume:	673.058
LogP:	4.354
LogD:	3.056
LogS:	-4.773
# Rotatable Bonds:	6
TPSA:	220.76
# H-Bond Aceptor:	12
# H-Bond Donor:	10
# Rings:	7
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.1
Synthetic Accessibility Score:	4.825
Fsp3:	0.189
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.876
MDCK Permeability:	3.6034923596162116e-06
Pgp-inhibitor:	0.04
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.985
20% Bioavailability (F20%):	0.998
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001
Plasma Protein Binding (PPB):	98.12342834472656%
Volume Distribution (VD):	0.281
Pgp-substrate:	3.2477803230285645%

ADMET: Metabolism

CYP1A2-inhibitor:	0.14
CYP1A2-substrate:	0.084
CYP2C19-inhibitor:	0.433
CYP2C19-substrate:	0.046
CYP2C9-inhibitor:	0.79
CYP2C9-substrate:	0.982
CYP2D6-inhibitor:	0.092
CYP2D6-substrate:	0.229
CYP3A4-inhibitor:	0.106
CYP3A4-substrate:	0.41

ADMET: Excretion

Clearance (CL):	12.339
Half-life (T1/2):	0.79

ADMET: Toxicity

hERG Blockers:	0.024
Human Hepatotoxicity (H-HT):	0.095
Drug-inuced Liver Injury (DILI):	0.979
AMES Toxicity:	0.366
Rat Oral Acute Toxicity:	0.664
Maximum Recommended Daily Dose:	0.711
Skin Sensitization:	0.964
Carcinogencity:	0.041
Eye Corrosion:	0.003
Eye Irritation:	0.912
Respiratory Toxicity:	0.02

Download Data

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

Natural Product: NPC203108

Natural Product ID:	NPC203108
*Common Name:**	OKJLVCMLZQNHPB-JYBJKFQYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	OKJLVCMLZQNHPB-JYBJKFQYSA-N
Standard InCHI:	InChI=1S/C37H32O12S/c38-19-12-24(43)28-27(13-19)48-34(17-6-8-20(39)22(41)10-17)32(46)31(28)29-25(44)14-26(45)30-36(29)49-35(18-7-9-21(40)23(42)11-18)33(47)37(30)50-15-16-4-2-1-3-5-16/h1-14,31-35,37-47H,15H2/t31-,32-,33+,34-,35-,37+/m1/s1
SMILES:	c1ccc(cc1)CS[C@H]1c2c(cc(c([C@H]3c4c(cc(cc4O[C@H](c4ccc(c(c4)O)O)[C@@H]3O)O)O)c2O[C@H](c2ccc(c(c2)O)O)[C@@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10372558
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001586] Biflavonoids and polyflavonoids

*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
NPO12068	Firmiana simplex	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16124753]
NPO2669	Bowdichia virgilioides	Species	Fabaceae	Eukaryota	n.a.	xylem	n.a.	PMID[16286304]
NPO2669	Bowdichia virgilioides	Species	Fabaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[29182338]
NPO12068	Firmiana simplex	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2905	Tinospora hainanensis	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2905	Tinospora hainanensis	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9947	Teucrium scorodonia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12068	Firmiana simplex	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12068	Firmiana simplex	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8443	Uvaria microcarpa	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8140	Nauclea parva	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5365	Tetradenia glauca	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6937	Xylaria hypoxylon	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1406	Centaurea zuccariniana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9947	Teucrium scorodonia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8962	Cousinia canescens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1255	Waitzia acuminata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21689	Titanotrichum oldhamii	Species	Gesneriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5752	Pholas dactylus	Species	Pholadidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2905	Tinospora hainanensis	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4037	Veronica anagallis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3463	Wrightia tinctoria	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12068	Firmiana simplex	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4844	Acacia simplicifolia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2669	Bowdichia virgilioides	Species	Fabaceae	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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC203108 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	550
0.1-0.2	1983
0.2-0.3	5923
0.3-0.4	12365
0.4-0.5	5168
0.5-0.6	5321
0.6-0.7	7934
0.7-0.8	2958
0.8-0.85	400
0.85-0.9	66
0.9-0.95	29
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID

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 NPC203108 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	434
0.1-0.2	936
0.2-0.3	2065
0.3-0.4	2805
0.4-0.5	1518
0.5-0.6	936
0.6-0.7	408
0.7-0.8	44
0.8-0.85	4
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

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