NPASS Compound

Structure

NPC190917 OpenBabel06302215482D 21 24 0 0 0 0 0 0 0 0999 V2000 2.5415 1.6797 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6245 1.8748 0.0000 S 0 0 2 0 0 0 0 0 0 0 0 0 1.3349 2.7664 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8126 1.4061 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0004 1.8750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8115 1.4064 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6505 1.8909 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8117 0.4689 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.6241 0.0003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4362 0.4692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2481 0.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2483 -0.9373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4366 -1.4062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6242 -0.9377 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0002 -0.9380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8120 -1.4069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6239 -0.9383 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6241 -0.0003 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.8124 0.4686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8119 -2.3758 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 4 19 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 8 1 0 0 0 0 8 20 1 0 0 0 0 8 9 1 0 0 0 0 9 14 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 20 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 21 1 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	298.04
Volume:	279.552
LogP:	1.097
LogD:	1.106
LogS:	-3.731
# Rotatable Bonds:	1
TPSA:	77.66
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.544
Synthetic Accessibility Score:	3.869
Fsp3:	0.067
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.884
MDCK Permeability:	1.036935736919986e-05
Pgp-inhibitor:	0.01
Pgp-substrate:	0.994
Human Intestinal Absorption (HIA):	0.018
20% Bioavailability (F20%):	0.005
30% Bioavailability (F30%):	0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.351
Plasma Protein Binding (PPB):	95.07132720947266%
Volume Distribution (VD):	0.576
Pgp-substrate:	2.6576242446899414%

ADMET: Metabolism

CYP1A2-inhibitor:	0.981
CYP1A2-substrate:	0.579
CYP2C19-inhibitor:	0.045
CYP2C19-substrate:	0.626
CYP2C9-inhibitor:	0.403
CYP2C9-substrate:	0.856
CYP2D6-inhibitor:	0.025
CYP2D6-substrate:	0.243
CYP3A4-inhibitor:	0.161
CYP3A4-substrate:	0.34

ADMET: Excretion

Clearance (CL):	4.164
Half-life (T1/2):	0.854

ADMET: Toxicity

hERG Blockers:	0.009
Human Hepatotoxicity (H-HT):	0.133
Drug-inuced Liver Injury (DILI):	0.921
AMES Toxicity:	0.97
Rat Oral Acute Toxicity:	0.067
Maximum Recommended Daily Dose:	0.972
Skin Sensitization:	0.407
Carcinogencity:	0.982
Eye Corrosion:	0.004
Eye Irritation:	0.572
Respiratory Toxicity:	0.876

Download Data

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

Natural Product: NPC190917

Natural Product ID:	NPC190917
*Common Name:**	RQUKDHNYGQIAOZ-NRFANRHFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RQUKDHNYGQIAOZ-NRFANRHFSA-N
Standard InCHI:	InChI=1S/C15H10N2O3S/c1-21(20)11-6-12(19)17-9-5-3-2-4-8(9)13-10(18)7-16-14(11)15(13)17/h2-7,18H,1H3/t21-/m0/s1
SMILES:	C[S@](=O)c1cc(=O)n2c3ccccc3c3c(cnc1c23)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11300976
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0003805] Indolonaphthyridine alkaloids

*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
NPO22840	Casearia arguta	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21067210]
NPO22840	Casearia arguta	Species	Salicaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21067210]
NPO21885	Furcraea elegans	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22840	Casearia arguta	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21012	Mikania sessilifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20992	Tarenna graveolens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18753	Sideritis serrata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21697	Irpex pachyodon	Species	Irpicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19973	Cupania glabra	Species	Sapindaceae	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 NPC190917 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	732
0.1-0.2	5122
0.2-0.3	12268
0.3-0.4	16951
0.4-0.5	3794
0.5-0.6	2541
0.6-0.7	1201
0.7-0.8	76
0.8-0.85	10
0.85-0.9	2
0.9-0.95	0
0.95-1	0

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 NPC190917 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	370
0.1-0.2	634
0.2-0.3	876
0.3-0.4	2026
0.4-0.5	2531
0.5-0.6	2008
0.6-0.7	682
0.7-0.8	23
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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