NPASS Compound

Structure

NPC215910 OpenBabel06302215342D 31 36 0 0 1 0 0 0 0 0999 V2000 2.6615 -3.1292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1819 -2.2981 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 2.1821 -1.3384 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.0132 -1.8182 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8439 -1.3387 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.6750 -1.8186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6750 -2.6745 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5058 -1.3391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5060 -0.3792 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.6754 0.1006 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.8441 -0.3789 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.1822 -0.3786 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.3511 0.1013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3512 0.9573 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5204 -0.3782 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3924 -0.0814 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9568 -0.8578 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.1069 -0.8460 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7607 -1.6111 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1421 -0.6995 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0136 -0.6209 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9131 -1.2563 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3927 -1.6345 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5202 -1.3381 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.3508 -1.8179 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3507 -2.6739 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6295 -2.3076 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6354 -0.1005 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 4.6755 0.9566 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.2474 0.0486 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 3 2 1 6 0 0 0 3 25 1 0 0 0 0 3 4 1 0 0 0 0 3 12 1 0 0 0 0 5 4 1 6 0 0 0 5 6 1 0 0 0 0 5 11 1 0 0 0 0 6 7 2 0 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 9 31 1 1 0 0 0 10 11 1 0 0 0 0 10 30 1 1 0 0 0 11 12 1 6 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 15 1 0 0 0 0 15 24 1 0 0 0 0 15 29 1 0 0 0 0 15 16 1 1 0 0 0 17 16 1 6 0 0 0 17 18 1 0 0 0 0 17 23 1 0 0 0 0 18 19 2 0 0 0 0 18 20 1 0 0 0 0 21 20 1 1 0 0 0 21 22 1 0 0 0 0 21 28 1 0 0 0 0 22 23 1 0 0 0 0 22 27 1 1 0 0 0 23 24 1 6 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 28 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	486.06
Volume:	414.348
LogP:	-0.177
LogD:	0.098
LogS:	-2.926
# Rotatable Bonds:	1
TPSA:	135.45
# H-Bond Aceptor:	9
# H-Bond Donor:	3
# Rings:	6
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.395
Synthetic Accessibility Score:	6.643
Fsp3:	0.789
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:	-5.382
MDCK Permeability:	5.925787718297215e-06
Pgp-inhibitor:	0.377
Pgp-substrate:	0.843
Human Intestinal Absorption (HIA):	0.618
20% Bioavailability (F20%):	0.01
30% Bioavailability (F30%):	0.276

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.01
Plasma Protein Binding (PPB):	56.813472747802734%
Volume Distribution (VD):	0.403
Pgp-substrate:	43.54380798339844%

ADMET: Metabolism

CYP1A2-inhibitor:	0.003
CYP1A2-substrate:	0.084
CYP2C19-inhibitor:	0.064
CYP2C19-substrate:	0.889
CYP2C9-inhibitor:	0.713
CYP2C9-substrate:	0.2
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.053
CYP3A4-inhibitor:	0.052
CYP3A4-substrate:	0.971

ADMET: Excretion

Clearance (CL):	6.368
Half-life (T1/2):	0.834

ADMET: Toxicity

hERG Blockers:	0.001
Human Hepatotoxicity (H-HT):	0.317
Drug-inuced Liver Injury (DILI):	0.994
AMES Toxicity:	0.006
Rat Oral Acute Toxicity:	0.913
Maximum Recommended Daily Dose:	0.025
Skin Sensitization:	0.336
Carcinogencity:	0.683
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.008

Download Data

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

Natural Product: NPC215910

Natural Product ID:	NPC215910
*Common Name:**	PWTRPOVBBGDOBW-KKRNIYGSSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PWTRPOVBBGDOBW-KKRNIYGSSA-N
Standard InCHI:	InChI=1S/C19H22N2O7S3/c1-29-18-4-6-8(22)2-10(24)14(25)12(6)20(18)17(28)19-5-7-9(23)3-11(30-31-19)15(26)13(7)21(19)16(18)27/h6-7,10-15,24-26H,2-5H2,1H3/t6-,7-,10-,11+,12-,13-,14-,15-,18+,19+/m0/s1
SMILES:	CS[C@]12C[C@H]3C(=O)C[C@@H]([C@@H]([C@H]3N2C(=O)[C@]23C[C@H]4C(=O)C[C@H]([C@@H]([C@H]4N2C1=O)O)SS3)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	46873061
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0000013] Amino acids, peptides, and analogues [CHEMONTID:0000347] Amino acids and derivatives [CHEMONTID:0000060] Alpha amino acids and derivatives

*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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO18557	Epicoccum nigrum	Species	Didymellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17711348]
NPO18557	Epicoccum nigrum	Species	Didymellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19919067]
NPO18557	Epicoccum nigrum	Species	Didymellaceae	Eukaryota	n.a.	The fungus is isolated from the leaves of L. rhodostegia, collected in June 2007 at Nanning, Guangxi Province, China	2007-JUN	PMID[20550196]
NPO28219	Euphorbia peplus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21612217]
NPO18557	Epicoccum nigrum	Species	Didymellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24328302]
NPO28219	Euphorbia peplus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27203291]
NPO18557	Epicoccum nigrum	Species	Didymellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Title]
NPO28129	Reticulitermes virginicus	Species	Termitoidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23676	Fleroya rubrostipulata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28219	Euphorbia peplus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18557	Epicoccum nigrum	Species	Didymellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28114	Peltophorum adnatum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23882	Cremastosperma microcarpum	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27974	Swertia leduci	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28310	Phacelocarpus labillardieri	Species	Phacelocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28982	Calliandra confusa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ 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

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ 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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC215910 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score	Similarity Level	Natural Product ID

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 NPC215910 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score	Similarity Level	Drug ID	Developmental Stage

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