NPASS Compound

Structure

CID113836 OpenBabel06191715472D 44 48 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 0.8660 -1.5000 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 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 C 0 0 2 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 -0.8660 -1.5000 0.0000 C 0 0 2 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 -1.0000 0.0000 C 0 0 1 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 0.8660 -2.5000 0.0000 O 0 0 0 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 -6.9282 2.0000 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 0.8660 0.5000 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 -3.4641 -1.0000 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 0.0000 0.0000 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 -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 17 2 0 0 0 0 8 29 1 0 0 0 0 9 24 1 0 0 0 0 10 27 1 0 0 0 0 11 30 1 0 0 0 0 12 13 2 0 0 0 0 12 31 1 0 0 0 0 13 32 1 0 0 0 0 14 19 2 0 0 0 0 14 33 1 0 0 0 0 15 20 2 0 0 0 0 15 34 1 0 0 0 0 16 20 1 0 0 0 0 16 35 1 0 0 0 0 17 19 1 0 0 0 0 17 41 1 0 0 0 0 18 8 1 6 0 0 0 18 21 1 0 0 0 0 18 42 1 0 0 0 0 19 22 1 0 0 0 0 20 36 1 0 0 0 0 21 23 1 0 0 0 0 21 37 1 1 0 0 0 22 25 1 0 0 0 0 22 38 2 0 0 0 0 23 26 1 0 0 0 0 23 39 1 6 0 0 0 24 25 2 0 0 0 0 24 41 1 0 0 0 0 25 44 1 0 0 0 0 26 28 1 0 0 0 0 26 43 1 1 0 0 0 27 40 2 0 0 0 0 27 43 1 0 0 0 0 28 42 1 0 0 0 0 28 44 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	616.11
Volume:	559.068
LogP:	1.297
LogD:	0.331
LogS:	-4.676
# Rotatable Bonds:	7
TPSA:	277.27
# H-Bond Aceptor:	16
# H-Bond Donor:	10
# Rings:	5
# Heavy Atoms:	16

MedChem Properties

QED Drug-Likeness Score:	0.104
Synthetic Accessibility Score:	4.372
Fsp3:	0.214
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:	-6.539
MDCK Permeability:	6.6008465182676446e-06
Pgp-inhibitor:	0.069
Pgp-substrate:	0.011
Human Intestinal Absorption (HIA):	0.783
20% Bioavailability (F20%):	0.274
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.007
Plasma Protein Binding (PPB):	87.69371795654297%
Volume Distribution (VD):	0.653
Pgp-substrate:	17.656391143798828%

ADMET: Metabolism

CYP1A2-inhibitor:	0.545
CYP1A2-substrate:	0.024
CYP2C19-inhibitor:	0.017
CYP2C19-substrate:	0.031
CYP2C9-inhibitor:	0.377
CYP2C9-substrate:	0.081
CYP2D6-inhibitor:	0.028
CYP2D6-substrate:	0.13
CYP3A4-inhibitor:	0.088
CYP3A4-substrate:	0.006

ADMET: Excretion

Clearance (CL):	7.65
Half-life (T1/2):	0.967

ADMET: Toxicity

hERG Blockers:	0.275
Human Hepatotoxicity (H-HT):	0.172
Drug-inuced Liver Injury (DILI):	0.987
AMES Toxicity:	0.508
Rat Oral Acute Toxicity:	0.006
Maximum Recommended Daily Dose:	0.008
Skin Sensitization:	0.94
Carcinogencity:	0.03
Eye Corrosion:	0.003
Eye Irritation:	0.91
Respiratory Toxicity:	0.009

Download Data

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

Natural Product: NPC113836

Natural Product ID:	NPC113836
*Common Name:**	Isoquercitin 2''-O-Gallate
IUPAC Name:	[(2S,3R,4S,5S,6R)-2-[2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxochromen-3-yl]oxy-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl] 3,4,5-trihydroxybenzoate
Synonyms:
Standard InCHIKey:	PXGWEUQZDRUMRE-KQOASZHBSA-N
Standard InCHI:	InChI=1S/C28H24O16/c29-8-18-21(37)23(39)26(43-27(40)10-4-15(34)20(36)16(35)5-10)28(42-18)44-25-22(38)19-14(33)6-11(30)7-17(19)41-24(25)9-1-2-12(31)13(32)3-9/h1-7,18,21,23,26,28-37,39H,8H2/t18-,21-,23+,26-,28+/m1/s1
SMILES:	c1cc(c(cc1c1c(c(=O)c2c(cc(cc2o1)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)OC(=O)c1cc(c(c(c1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL459260
PubChem CID:	5480249
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
NPO29554	Diospyros kaki	Species	Ebenaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[3430165]
NPO18996	Tamarix aphylla	Species	Tamaricaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31532650]
NPO29401	Bupleurum chinense	Species	Apiaceae	Eukaryota	roots	n.a.	n.a.	PMID[26259802]
NPO13691	Caenorhabditis elegans	Species	Rhabditidae	Eukaryota	n.a.	n.a.	n.a.	PMID[24453122]
NPO13691	Caenorhabditis elegans	Species	Rhabditidae	Eukaryota	n.a.	n.a.	n.a.	PMID[24411940]
NPO13691	Caenorhabditis elegans	Species	Rhabditidae	Eukaryota	n.a.	n.a.	n.a.	PMID[23894595]
NPO13691	Caenorhabditis elegans	Species	Rhabditidae	Eukaryota	n.a.	n.a.	n.a.	PMID[23475189]
NPO13691	Caenorhabditis elegans	Species	Rhabditidae	Eukaryota	n.a.	n.a.	n.a.	PMID[23163760]
NPO13691	Caenorhabditis elegans	Species	Rhabditidae	Eukaryota	n.a.	n.a.	n.a.	PMID[22239548]
NPO13691	Caenorhabditis elegans	Species	Rhabditidae	Eukaryota	n.a.	n.a.	n.a.	PMID[222395484]

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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	2
Others	11

Activity Type	# Activity
Cell Line	2
Individual Protein	10
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT35	Others	n.a.		Activity	<	35.0	%	PMID[490571]
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	=	16400.0	nM	PMID[490570]
NPT113	Cell Line	RAW264.7	Mus musculus	Inhibition	=	21.5	%	PMID[490570]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	Inhibition	>	40.0	%	PMID[490570]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	18050.0	nM	PMID[490570]
NPT1310	Individual Protein	Xanthine dehydrogenase	Bos taurus	Inhibition	=	21.0	%	PMID[490568]
NPT3539	Individual Protein	Angiotensin-converting enzyme	Rattus norvegicus	Inhibition	=	39.0	%	PMID[490567]
NPT3539	Individual Protein	Angiotensin-converting enzyme	Rattus norvegicus	Inhibition	=	18.0	%	PMID[490567]
NPT3539	Individual Protein	Angiotensin-converting enzyme	Rattus norvegicus	Inhibition	=	12.0	%	PMID[490567]
NPT3539	Individual Protein	Angiotensin-converting enzyme	Rattus norvegicus	Inhibition	=	10.0	%	PMID[490567]

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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 NPC113836 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	NPC253521
1.0	High Similarity	NPC37668
0.9939	High Similarity	NPC61904
0.9939	High Similarity	NPC144097
0.9879	High Similarity	NPC267680

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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 NPC113836 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
0.9521	High Similarity	NPD4338	Clinical (unspecified phase)
0.9518	High Similarity	NPD6797	Phase 2
0.9461	High Similarity	NPD7251	Discontinued
0.929	High Similarity	NPD7808	Phase 3
0.9226	High Similarity	NPD7472	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