NPASS Compound

Structure

NPC232080 OpenBabel06302215142D 34 37 0 0 1 0 0 0 0 0999 V2000 5.6962 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8301 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -0.5000 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 1.3660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -8.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 -7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 -6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -5.0000 0.0000 O 0 3 0 0 0 0 0 0 0 0 0 0 0.5000 -8.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -8.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8301 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6962 -5.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 6.5622 -4.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 7.4282 -5.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 7.4282 -6.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 6.5622 -6.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 6.5622 -7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6962 -8.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6962 -6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.2942 -6.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.2942 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.5622 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 11 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 10 1 0 0 0 0 8 9 1 0 0 0 0 11 20 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 23 1 0 0 0 0 13 14 1 0 0 0 0 14 19 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 15 22 1 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 21 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 24 31 1 0 0 0 0 25 26 1 0 0 0 0 25 34 1 0 0 0 0 26 27 1 0 0 0 0 26 33 1 0 0 0 0 27 28 1 0 0 0 0 27 32 1 0 0 0 0 28 29 1 0 0 0 0 28 31 1 0 0 0 0 29 30 1 0 0 0 0 M CHG 2 9 -1 20 1 M END $$$$

Physi-Chem Properties

Molecular Weight:	478.11
Volume:	439.233
LogP:	0.205
LogD:	0.279
LogS:	-2.807
# Rotatable Bonds:	5
TPSA:	203.66
# H-Bond Aceptor:	12
# H-Bond Donor:	7
# Rings:	4
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.237
Synthetic Accessibility Score:	4.617
Fsp3:	0.318
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.389
MDCK Permeability:	1.0873665814870037e-05
Pgp-inhibitor:	0.072
Pgp-substrate:	0.919
Human Intestinal Absorption (HIA):	0.471
20% Bioavailability (F20%):	0.01
30% Bioavailability (F30%):	0.984

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.025
Plasma Protein Binding (PPB):	88.40567016601562%
Volume Distribution (VD):	0.814
Pgp-substrate:	14.873676300048828%

ADMET: Metabolism

CYP1A2-inhibitor:	0.122
CYP1A2-substrate:	0.086
CYP2C19-inhibitor:	0.012
CYP2C19-substrate:	0.06
CYP2C9-inhibitor:	0.007
CYP2C9-substrate:	0.148
CYP2D6-inhibitor:	0.023
CYP2D6-substrate:	0.178
CYP3A4-inhibitor:	0.009
CYP3A4-substrate:	0.016

ADMET: Excretion

Clearance (CL):	8.334
Half-life (T1/2):	0.935

ADMET: Toxicity

hERG Blockers:	0.137
Human Hepatotoxicity (H-HT):	0.596
Drug-inuced Liver Injury (DILI):	0.954
AMES Toxicity:	0.73
Rat Oral Acute Toxicity:	0.055
Maximum Recommended Daily Dose:	0.277
Skin Sensitization:	0.844
Carcinogencity:	0.046
Eye Corrosion:	0.003
Eye Irritation:	0.264
Respiratory Toxicity:	0.079

Download Data

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

Natural Product: NPC232080

Natural Product ID:	NPC232080
*Common Name:**	HBKZHMZCXXQMOX-YATQZQGFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HBKZHMZCXXQMOX-YATQZQGFSA-N
Standard InCHI:	InChI=1S/C22H22O12.ClH/c1-31-14-3-8(2-12(26)17(14)27)21-15(6-10-11(25)4-9(24)5-13(10)32-21)33-22-20(30)19(29)18(28)16(7-23)34-22;/h2-6,16,18-20,22-23,28-30H,7H2,1H3,(H3-,24,25,26,27);1H/t16-,18-,19+,20-,22-;/m1./s1
SMILES:	COc1cc(cc(c1[O-])O)c1c(cc2c(cc(cc2[o+]1)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O.Cl
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	176449
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0001361] Anthocyanins [CHEMONTID:0002996] Anthocyanidin-3-O-glycosides

*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
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1002/hlca.19270100148]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1007/s11746-997-0093-1]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	Wrocław, Poland	2004–2005	DOI[10.1016/J.FOODCHEM.2006.08.014]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	n.a.	retail stores, supermarkets and market stalls in Forssa and in the Helsinki area	2003–2005	DOI[10.1016/j.jfca.2006.05.007]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	retail stores, supermarkets and market stalls in Forssa and in the Helsinki area	2003–2005	DOI[10.1016/j.jfca.2006.05.007]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1021/jf950732o]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1021/jf980687v]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10775096]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	Petals	n.a.	n.a.	PMID[15043425]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	root	n.a.	PMID[1622242]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16659156]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16668466]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18460139]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20963508]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22537213]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24338885]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	Seeds	Tekirdag, Turkey		PMID[24499198]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25053043]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25070365]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	seed	n.a.	PMID[25369450]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25369450]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	Hypocotyl	n.a.	n.a.	Database[FooDB]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	Stem	n.a.	n.a.	Database[FooDB]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	Testa	n.a.	n.a.	Database[FooDB]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	Oil	n.a.	n.a.	Database[FooDB]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	Pericarp	n.a.	n.a.	Database[FooDB]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	Silk Stigma Style	n.a.	n.a.	Database[FooDB]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	Sprout Seedling	n.a.	n.a.	Database[FooDB]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	Sprout Seedling	n.a.	n.a.	Database[FooDB]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	Cotyledon	n.a.	n.a.	Database[FooDB]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24559.1	Cotinus coggygria var. cinerea	Varieties	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4593	Lagerstroemia indica	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	seed	n.a.	Database[MetaboLights]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	Seeds	n.a.		Database[Phenol-Explorer]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4593	Lagerstroemia indica	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24559.1	Cotinus coggygria var. cinerea	Varieties	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4593	Lagerstroemia indica	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4593	Lagerstroemia indica	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4934	Phaseolus vulgaris	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7635	Glycine max	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 NPC232080 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	436
0.1-0.2	1829
0.2-0.3	4155
0.3-0.4	9691
0.4-0.5	8415
0.5-0.6	4258
0.6-0.7	5156
0.7-0.8	5352
0.8-0.85	1652
0.85-0.9	1150
0.9-0.95	443
0.95-1	160

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 NPC232080 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	400
0.1-0.2	953
0.2-0.3	2020
0.3-0.4	2652
0.4-0.5	1771
0.5-0.6	899
0.6-0.7	289
0.7-0.8	128
0.8-0.85	12
0.85-0.9	15
0.9-0.95	10
0.95-1	1

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