NPASS Compound

Structure

CID210042 OpenBabel06191716002D 33 36 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 3.4641 1.0000 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 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 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 1.7321 1.0000 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 -0.5000 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 -1.7321 -0.0000 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 -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 0.8660 -0.5000 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 1.7321 -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 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 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 1 29 1 0 0 0 0 2 30 1 0 0 0 0 3 4 2 0 0 0 0 3 8 1 0 0 0 0 4 9 1 0 0 0 0 5 7 2 0 0 0 0 5 10 1 0 0 0 0 6 22 1 0 0 0 0 7 12 1 0 0 0 0 7 23 1 0 0 0 0 8 13 2 0 0 0 0 8 31 1 0 0 0 0 9 14 2 0 0 0 0 9 32 1 0 0 0 0 10 19 2 0 0 0 0 10 29 1 0 0 0 0 11 6 1 6 0 0 0 11 15 1 0 0 0 0 11 33 1 0 0 0 0 12 16 1 0 0 0 0 12 20 2 0 0 0 0 13 14 1 0 0 0 0 13 16 1 0 0 0 0 14 24 1 0 0 0 0 15 17 1 0 0 0 0 15 25 1 1 0 0 0 16 26 2 0 0 0 0 17 18 1 0 0 0 0 17 27 1 6 0 0 0 18 21 1 0 0 0 0 18 28 1 1 0 0 0 19 20 1 0 0 0 0 19 30 1 0 0 0 0 20 31 1 0 0 0 0 21 32 1 6 0 0 0 21 33 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	466.11
Volume:	424.574
LogP:	0.342
LogD:	0.268
LogS:	-3.773
# 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:	4.039
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:	-6.157
MDCK Permeability:	2.296832280990202e-05
Pgp-inhibitor:	0.035
Pgp-substrate:	0.933
Human Intestinal Absorption (HIA):	0.612
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.618

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.072
Plasma Protein Binding (PPB):	73.34917449951172%
Volume Distribution (VD):	0.986
Pgp-substrate:	24.924036026000977%

ADMET: Metabolism

CYP1A2-inhibitor:	0.072
CYP1A2-substrate:	0.941
CYP2C19-inhibitor:	0.012
CYP2C19-substrate:	0.222
CYP2C9-inhibitor:	0.012
CYP2C9-substrate:	0.332
CYP2D6-inhibitor:	0.033
CYP2D6-substrate:	0.189
CYP3A4-inhibitor:	0.039
CYP3A4-substrate:	0.027

ADMET: Excretion

Clearance (CL):	3.44
Half-life (T1/2):	0.808

ADMET: Toxicity

hERG Blockers:	0.09
Human Hepatotoxicity (H-HT):	0.162
Drug-inuced Liver Injury (DILI):	0.968
AMES Toxicity:	0.773
Rat Oral Acute Toxicity:	0.015
Maximum Recommended Daily Dose:	0.004
Skin Sensitization:	0.217
Carcinogencity:	0.049
Eye Corrosion:	0.003
Eye Irritation:	0.041
Respiratory Toxicity:	0.025

Download Data

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

Natural Product: NPC210042

Natural Product ID:	NPC210042
*Common Name:**	Triptexanthoside C
IUPAC Name:	1,8-dihydroxy-5,6-dimethoxy-2-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyxanthen-9-one
Synonyms:	Triptexanthoside C
Standard InCHIKey:	MQLIUXPJHVQKKI-UVPJDIOGSA-N
Standard InCHI:	InChI=1S/C21H22O12/c1-29-10-5-7(23)12-16(26)13-8(31-20(12)19(10)30-2)3-4-9(14(13)24)32-21-18(28)17(27)15(25)11(6-22)33-21/h3-5,11,15,17-18,21-25,27-28H,6H2,1-2H3/t11-,15-,17+,18-,21-/m1/s1
SMILES:	OC[C@H]1O[C@@H](Oc2ccc3c(c2O)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:	CHEMBL466536
PubChem CID:	10552156
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
NPO26277	Euphorbia hirta	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32141299]
NPO22355	Flacourtia indica	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23354072]
NPO32688	gentianella amarella ssp. acuta	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18336006]
NPO10470	Pimpinella major	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19646	Cynthia papillosa	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO10942	Retama sphaerocarpa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14921	Anisothrix integra	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26277	Euphorbia hirta	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22355	Flacourtia indica	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22459	Impatiens capensis	Species	Balsaminaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Showing 1 to 10 of 18 entries

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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	=	43.7	%	PMID[558603]
NPT261	Individual Protein	Monoamine oxidase A	Homo sapiens	Inhibition	=	13.4	%	PMID[558603]
NPT582	Individual Protein	Monoamine oxidase B	Homo sapiens	Inhibition	=	38.8	%	PMID[558603]

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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 NPC210042 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
1.0	High Similarity	NPC95855
0.9937	High Similarity	NPC22195
0.9937	High Similarity	NPC93099
0.9937	High Similarity	NPC474434
0.9937	High Similarity	NPC21190

Showing 1 to 5 of 200 entries

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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 NPC210042 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
0.9568	High Similarity	NPD7074	Phase 3
0.9506	High Similarity	NPD7054	Approved
0.9448	High Similarity	NPD7472	Approved
0.9394	High Similarity	NPD4338	Clinical (unspecified phase)
0.9325	High Similarity	NPD3818	Discontinued

Showing 1 to 5 of 200 entries

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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