NPASS Compound

Structure

NPC44558 OpenBabel07101718292D 32 35 0 0 1 0 0 0 0 0999 V2000 6.0622 -4.5000 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 2.5981 1.5000 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 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -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 1.7321 1.0000 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 3.4641 -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 5.1962 -3.0000 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 3.4641 -2.0000 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 -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 5.1962 -2.0000 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 -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 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -3.5000 0.0000 O 0 0 0 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 -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 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -1.5000 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 4.3301 -0.5000 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 1 28 1 0 0 0 0 2 29 1 0 0 0 0 3 4 2 0 0 0 0 3 8 1 0 0 0 0 4 11 1 0 0 0 0 5 8 2 0 0 0 0 5 9 1 0 0 0 0 6 10 2 0 0 0 0 6 12 1 0 0 0 0 7 22 1 0 0 0 0 8 30 1 0 0 0 0 9 11 2 0 0 0 0 9 15 1 0 0 0 0 10 14 1 0 0 0 0 10 23 1 0 0 0 0 11 31 1 0 0 0 0 12 19 2 0 0 0 0 12 28 1 0 0 0 0 13 7 1 6 0 0 0 13 16 1 0 0 0 0 13 32 1 0 0 0 0 14 15 1 0 0 0 0 14 20 2 0 0 0 0 15 24 2 0 0 0 0 16 17 1 0 0 0 0 16 25 1 1 0 0 0 17 18 1 0 0 0 0 17 26 1 6 0 0 0 18 21 1 0 0 0 0 18 27 1 1 0 0 0 19 20 1 0 0 0 0 19 29 1 0 0 0 0 20 31 1 0 0 0 0 21 30 1 6 0 0 0 21 32 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	450.12
Volume:	415.784
LogP:	0.752
LogD:	0.894
LogS:	-3.857
# Rotatable Bonds:	5
TPSA:	168.28
# H-Bond Aceptor:	11
# H-Bond Donor:	5
# Rings:	4
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.328
Synthetic Accessibility Score:	3.853
Fsp3:	0.381
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.076
MDCK Permeability:	2.742114338616375e-05
Pgp-inhibitor:	0.013
Pgp-substrate:	0.793
Human Intestinal Absorption (HIA):	0.302
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.792

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.135
Plasma Protein Binding (PPB):	73.07906341552734%
Volume Distribution (VD):	1.0
Pgp-substrate:	23.20404815673828%

ADMET: Metabolism

CYP1A2-inhibitor:	0.095
CYP1A2-substrate:	0.942
CYP2C19-inhibitor:	0.018
CYP2C19-substrate:	0.502
CYP2C9-inhibitor:	0.011
CYP2C9-substrate:	0.498
CYP2D6-inhibitor:	0.049
CYP2D6-substrate:	0.249
CYP3A4-inhibitor:	0.037
CYP3A4-substrate:	0.054

ADMET: Excretion

Clearance (CL):	4.066
Half-life (T1/2):	0.563

ADMET: Toxicity

hERG Blockers:	0.083
Human Hepatotoxicity (H-HT):	0.323
Drug-inuced Liver Injury (DILI):	0.966
AMES Toxicity:	0.794
Rat Oral Acute Toxicity:	0.027
Maximum Recommended Daily Dose:	0.01
Skin Sensitization:	0.177
Carcinogencity:	0.437
Eye Corrosion:	0.003
Eye Irritation:	0.031
Respiratory Toxicity:	0.036

Download Data

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

Natural Product: NPC44558

Natural Product ID:	NPC44558
*Common Name:**	Veratriloside
IUPAC Name:	1-hydroxy-3,4-dimethoxy-7-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyxanthen-9-one
Synonyms:	Veratriloside
Standard InCHIKey:	AVZPRERNBNKYMD-GUFUGUNKSA-N
Standard InCHI:	InChI=1S/C21H22O11/c1-28-12-6-10(23)14-15(24)9-5-8(3-4-11(9)31-20(14)19(12)29-2)30-21-18(27)17(26)16(25)13(7-22)32-21/h3-6,13,16-18,21-23,25-27H,7H2,1-2H3/t13-,16-,17+,18-,21-/m1/s1
SMILES:	OC[C@H]1O[C@@H](Oc2ccc3c(c2)c(=O)c2c(o3)c(OC)c(cc2O)OC)[C@@H]([C@H]([C@@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL468010
PubChem CID:	5490799
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	=	28.2	%	PMID[507382]
NPT261	Individual Protein	Monoamine oxidase A	Homo sapiens	Inhibition	=	19.4	%	PMID[507382]
NPT582	Individual Protein	Monoamine oxidase B	Homo sapiens	Inhibition	=	56.0	%	PMID[507382]

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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 NPC44558 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	442
0.1-0.2	1756
0.2-0.3	4086
0.3-0.4	9620
0.4-0.5	8500
0.5-0.6	4309
0.6-0.7	5263
0.7-0.8	5311
0.8-0.85	1646
0.85-0.9	1137
0.9-0.95	457
0.95-1	170

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Similarity Score	Similarity Level	Natural Product ID
0.9937	High Similarity	NPC472381
0.9937	High Similarity	NPC472383
0.9875	High Similarity	NPC474434
0.9875	High Similarity	NPC22195
0.9875	High Similarity	NPC471416

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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 NPC44558 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	392
0.1-0.2	936
0.2-0.3	1957
0.3-0.4	2678
0.4-0.5	1812
0.5-0.6	905
0.6-0.7	304
0.7-0.8	123
0.8-0.85	20
0.85-0.9	14
0.9-0.95	8
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