NPASS Compound

Structure

NPC474434 OpenBabel07101718182D 33 36 0 0 1 0 0 0 0 0999 V2000 -6.0622 -1.5000 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 -3.4641 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 C 0 0 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 -3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -4.0000 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 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 2 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 -2.5981 -2.5000 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 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 2 0 0 0 0 0 0 0 0 0 -4.3301 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 0.0000 C 0 0 0 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 -3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -4.5000 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 -1.7321 -3.0000 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 2.5981 -1.5000 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 -6.0622 -2.5000 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 -0.8660 -1.5000 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 -4.3301 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 29 1 0 0 0 0 2 30 1 0 0 0 0 3 4 2 0 0 0 0 3 7 1 0 0 0 0 4 8 1 0 0 0 0 5 9 2 0 0 0 0 5 10 1 0 0 0 0 6 22 1 0 0 0 0 7 13 1 0 0 0 0 7 17 2 0 0 0 0 8 18 2 0 0 0 0 8 23 1 0 0 0 0 9 19 1 0 0 0 0 9 24 1 0 0 0 0 10 12 2 0 0 0 0 10 31 1 0 0 0 0 11 6 1 6 0 0 0 11 14 1 0 0 0 0 11 32 1 0 0 0 0 12 13 1 0 0 0 0 12 20 1 0 0 0 0 13 25 2 0 0 0 0 14 15 1 0 0 0 0 14 26 1 1 0 0 0 15 16 1 0 0 0 0 15 27 1 6 0 0 0 16 21 1 0 0 0 0 16 28 1 1 0 0 0 17 18 1 0 0 0 0 17 33 1 0 0 0 0 18 29 1 0 0 0 0 19 20 2 0 0 0 0 19 30 1 0 0 0 0 20 33 1 0 0 0 0 21 31 1 0 0 0 0 21 32 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	466.11
Volume:	424.574
LogP:	-0.075
LogD:	0.348
LogS:	-3.77
# Rotatable Bonds:	5
TPSA:	188.51
# H-Bond Aceptor:	12
# H-Bond Donor:	6
# Rings:	4
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.266
Synthetic Accessibility Score:	4.134
Fsp3:	0.381
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.257
MDCK Permeability:	2.6827976398635656e-05
Pgp-inhibitor:	0.014
Pgp-substrate:	0.959
Human Intestinal Absorption (HIA):	0.62
20% Bioavailability (F20%):	0.011
30% Bioavailability (F30%):	0.774

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.102
Plasma Protein Binding (PPB):	74.40045928955078%
Volume Distribution (VD):	0.903
Pgp-substrate:	31.01803970336914%

ADMET: Metabolism

CYP1A2-inhibitor:	0.074
CYP1A2-substrate:	0.919
CYP2C19-inhibitor:	0.015
CYP2C19-substrate:	0.177
CYP2C9-inhibitor:	0.009
CYP2C9-substrate:	0.226
CYP2D6-inhibitor:	0.018
CYP2D6-substrate:	0.163
CYP3A4-inhibitor:	0.043
CYP3A4-substrate:	0.022

ADMET: Excretion

Clearance (CL):	5.055
Half-life (T1/2):	0.865

ADMET: Toxicity

hERG Blockers:	0.019
Human Hepatotoxicity (H-HT):	0.29
Drug-inuced Liver Injury (DILI):	0.981
AMES Toxicity:	0.792
Rat Oral Acute Toxicity:	0.06
Maximum Recommended Daily Dose:	0.004
Skin Sensitization:	0.22
Carcinogencity:	0.111
Eye Corrosion:	0.003
Eye Irritation:	0.071
Respiratory Toxicity:	0.04

Download Data

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

Natural Product: NPC474434

Natural Product ID:	NPC474434
*Common Name:**	Corymbiferin 1-O-Glucoside
IUPAC Name:	3,6-dihydroxy-4,5-dimethoxy-1-[(3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyxanthen-9-one
Synonyms:	Corymbiferin 1-O-Glucoside
Standard InCHIKey:	STWLEHSEFAYLCI-HIALJPTESA-N
Standard InCHI:	InChI=1S/C21H22O12/c1-29-18-8(23)4-3-7-13(25)12-10(5-9(24)19(30-2)20(12)33-17(7)18)31-21-16(28)15(27)14(26)11(6-22)32-21/h3-5,11,14-16,21-24,26-28H,6H2,1-2H3/t11-,14-,15+,16-,21?/m1/s1
SMILES:	OC[C@H]1OC(Oc2cc(O)c(c3c2c(=O)c2c(o3)c(OC)c(cc2)O)OC)[C@@H]([C@H]([C@@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL468395
PubChem CID:	44577223
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0002817] Dibenzopyrans [CHEMONTID:0000200] Xanthenes [CHEMONTID:0000204] Xanthones

*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
NPO32688	gentianella amarella ssp. acuta	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18336006]

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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
Others	3

Activity Type	# Activity
Individual Protein	3

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT204	Individual Protein	Acetylcholinesterase	Homo sapiens	Inhibition	=	1.5	%	PMID[572479]
NPT261	Individual Protein	Monoamine oxidase A	Homo sapiens	Inhibition	=	15.0	%	PMID[572479]
NPT582	Individual Protein	Monoamine oxidase B	Homo sapiens	Inhibition	=	70.5	%	PMID[572479]

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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 NPC474434 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	450
0.1-0.2	1821
0.2-0.3	4338
0.3-0.4	10018
0.4-0.5	8129
0.5-0.6	4271
0.6-0.7	5282
0.7-0.8	5204
0.8-0.85	1510
0.85-0.9	1094
0.9-0.95	424
0.95-1	156

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Similarity Score	Similarity Level	Natural Product ID
0.9937	High Similarity	NPC210042
0.9937	High Similarity	NPC183036
0.9937	High Similarity	NPC95855
0.9875	High Similarity	NPC21190
0.9875	High Similarity	NPC22195

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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 NPC474434 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	396
0.1-0.2	963
0.2-0.3	2051
0.3-0.4	2687
0.4-0.5	1749
0.5-0.6	869
0.6-0.7	284
0.7-0.8	112
0.8-0.85	17
0.85-0.9	14
0.9-0.95	7
0.95-1	1

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9509	High Similarity	NPD7074	Phase 3
0.9448	High Similarity	NPD7054	Approved
0.939	High Similarity	NPD7472	Approved
0.9387	High Similarity	NPD3818	Discontinued
0.9337	High Similarity	NPD4338	Clinical (unspecified phase)

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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