NPASS Compound

Structure

CID144097 OpenBabel06191715502D 42 46 0 0 1 0 0 0 0 0999 V2000 -1.7321 3.0000 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 -0.8660 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 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 3.5000 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 -0.8660 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 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 -2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 1 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 1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 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 0.0000 3.0000 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 -1.7321 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 0.0000 C 0 0 0 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 4.3301 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 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 -6.9282 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -1.0000 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 0.8660 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 1 9 1 0 0 0 0 2 12 1 0 0 0 0 3 9 2 0 0 0 0 3 13 1 0 0 0 0 4 10 2 0 0 0 0 4 15 1 0 0 0 0 5 10 1 0 0 0 0 5 16 2 0 0 0 0 6 11 2 0 0 0 0 6 14 1 0 0 0 0 7 11 1 0 0 0 0 7 18 2 0 0 0 0 8 17 1 0 0 0 0 8 39 1 0 0 0 0 9 23 1 0 0 0 0 10 26 1 0 0 0 0 11 28 1 0 0 0 0 12 13 2 0 0 0 0 12 29 1 0 0 0 0 13 30 1 0 0 0 0 14 19 2 0 0 0 0 14 31 1 0 0 0 0 15 20 2 0 0 0 0 15 32 1 0 0 0 0 16 20 1 0 0 0 0 16 33 1 0 0 0 0 17 21 1 0 0 0 0 17 34 1 6 0 0 0 18 19 1 0 0 0 0 18 40 1 0 0 0 0 19 22 1 0 0 0 0 20 35 1 0 0 0 0 21 25 1 0 0 0 0 21 36 1 6 0 0 0 22 24 1 0 0 0 0 22 37 2 0 0 0 0 23 24 2 0 0 0 0 23 40 1 0 0 0 0 24 42 1 0 0 0 0 25 27 1 0 0 0 0 25 41 1 1 0 0 0 26 38 2 0 0 0 0 26 41 1 0 0 0 0 27 39 1 0 0 0 0 27 42 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	586.1
Volume:	532.982
LogP:	1.7
LogD:	0.716
LogS:	-4.829
# Rotatable Bonds:	6
TPSA:	257.04
# H-Bond Aceptor:	15
# H-Bond Donor:	9
# Rings:	5
# Heavy Atoms:	15

MedChem Properties

QED Drug-Likeness Score:	0.117
Synthetic Accessibility Score:	4.269
Fsp3:	0.185
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:	-6.355
MDCK Permeability:	8.525584235030692e-06
Pgp-inhibitor:	0.05
Pgp-substrate:	0.012
Human Intestinal Absorption (HIA):	0.7
20% Bioavailability (F20%):	0.241
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.009
Plasma Protein Binding (PPB):	88.48787689208984%
Volume Distribution (VD):	0.646
Pgp-substrate:	17.01404571533203%

ADMET: Metabolism

CYP1A2-inhibitor:	0.587
CYP1A2-substrate:	0.034
CYP2C19-inhibitor:	0.023
CYP2C19-substrate:	0.03
CYP2C9-inhibitor:	0.492
CYP2C9-substrate:	0.11
CYP2D6-inhibitor:	0.052
CYP2D6-substrate:	0.128
CYP3A4-inhibitor:	0.091
CYP3A4-substrate:	0.007

ADMET: Excretion

Clearance (CL):	8.163
Half-life (T1/2):	0.956

ADMET: Toxicity

hERG Blockers:	0.165
Human Hepatotoxicity (H-HT):	0.161
Drug-inuced Liver Injury (DILI):	0.986
AMES Toxicity:	0.526
Rat Oral Acute Toxicity:	0.009
Maximum Recommended Daily Dose:	0.023
Skin Sensitization:	0.946
Carcinogencity:	0.038
Eye Corrosion:	0.003
Eye Irritation:	0.915
Respiratory Toxicity:	0.012

Download Data

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

Natural Product: NPC144097

Natural Product ID:	NPC144097
*Common Name:**	Quercetin -3-O-(2''-Galloyl)-Alpha-L-Arabinopyranoside
IUPAC Name:	[(2S,3R,4S,5S)-2-[2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxochromen-3-yl]oxy-4,5-dihydroxyoxan-3-yl] 3,4,5-trihydroxybenzoate
Synonyms:
Standard InCHIKey:	XLHGECRFSYAHQI-LEYCRWIUSA-N
Standard InCHI:	InChI=1S/C27H22O15/c28-11-6-14(31)19-18(7-11)40-23(9-1-2-12(29)13(30)3-9)24(22(19)37)42-27-25(21(36)17(34)8-39-27)41-26(38)10-4-15(32)20(35)16(33)5-10/h1-7,17,21,25,27-36H,8H2/t17-,21-,25+,27-/m0/s1
SMILES:	Oc1cc(O)c2c(c1)oc(c(c2=O)O[C@@H]1OC[C@@H]([C@@H]([C@H]1OC(=O)c1cc(O)c(c(c1)O)O)O)O)c1ccc(c(c1)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL501837
PubChem CID:	9985767
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003531] Flavonoid-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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO12148.2	Acer pictum subsp. okamotoanum	Subspecies	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9461665]
NPO17247	Actinoplanes friuliensis	Species	Micromonosporaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO19521	Inella verrucosa	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO18680	Larix decidua	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19095	Strophanthus preussii	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2359	Cynoglossum germanicum	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12148.2	Acer pictum subsp. okamotoanum	Subspecies	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13823	Hypericum mysorense	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18537	Leontopodium nanum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18775	Cratena peregrina	Species	Facelinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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	1

Activity Type	# Activity
Individual Protein	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT12	Individual Protein	Human immunodeficiency virus type 1 integrase	Human immunodeficiency virus 1	IC50	=	18.1	ug.mL-1	PMID[512689]

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☑ 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 NPC144097 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	447
0.1-0.2	1939
0.2-0.3	4513
0.3-0.4	9714
0.4-0.5	8099
0.5-0.6	4405
0.6-0.7	5466
0.7-0.8	5151
0.8-0.85	1605
0.85-0.9	784
0.9-0.95	420
0.95-1	154

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC61904
0.9939	High Similarity	NPC34267
0.9939	High Similarity	NPC253521
0.9939	High Similarity	NPC35167
0.9939	High Similarity	NPC37668

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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 NPC144097 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	410
0.1-0.2	961
0.2-0.3	2086
0.3-0.4	2652
0.4-0.5	1770
0.5-0.6	852
0.6-0.7	263
0.7-0.8	115
0.8-0.85	20
0.85-0.9	13
0.9-0.95	7
0.95-1	1

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9578	High Similarity	NPD4338	Clinical (unspecified phase)
0.9458	High Similarity	NPD6797	Phase 2
0.9401	High Similarity	NPD7251	Discontinued
0.9231	High Similarity	NPD7808	Phase 3
0.9222	High Similarity	NPD7054	Approved

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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