NPASS Compound

Structure

NPC57975 OpenBabel06302216202D 26 27 0 0 1 0 0 0 0 0999 V2000 -1.5000 3.3301 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 3.3301 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.4641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 1.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 1.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0000 2.4641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 0.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 -0.1340 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 1.5000 1.5981 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 2.5000 1.5981 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.0000 2.4641 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.0000 2.4641 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.5000 1.5981 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.0000 0.7321 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.5000 -0.1340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5000 -0.1340 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0000 0.7321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5000 1.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5000 3.3301 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5000 3.3301 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 7 1 0 0 0 0 5 6 1 0 0 0 0 7 8 1 0 0 0 0 8 9 2 3 0 0 0 8 15 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 13 2 0 0 0 0 11 14 1 0 0 0 0 16 15 1 1 0 0 0 16 17 1 0 0 0 0 16 23 1 0 0 0 0 17 18 1 0 0 0 0 17 26 1 6 0 0 0 18 19 1 0 0 0 0 18 25 1 1 0 0 0 19 20 1 0 0 0 0 19 24 1 6 0 0 0 20 21 1 1 0 0 0 20 23 1 0 0 0 0 21 22 1 0 0 0 0 M CHG 1 14 -1 M END $$$$

Physi-Chem Properties

Molecular Weight:	409.05
Volume:	350.168
LogP:	-0.436
LogD:	-1.094
LogS:	-0.566
# Rotatable Bonds:	7
TPSA:	166.11
# H-Bond Aceptor:	10
# H-Bond Donor:	5
# Rings:	2
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.168
Synthetic Accessibility Score:	4.112
Fsp3:	0.5
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:	-5.927
MDCK Permeability:	1.8782284314511344e-05
Pgp-inhibitor:	0.007
Pgp-substrate:	0.003
Human Intestinal Absorption (HIA):	0.958
20% Bioavailability (F20%):	0.596
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.078
Plasma Protein Binding (PPB):	91.09844970703125%
Volume Distribution (VD):	0.96
Pgp-substrate:	11.081626892089844%

ADMET: Metabolism

CYP1A2-inhibitor:	0.025
CYP1A2-substrate:	0.032
CYP2C19-inhibitor:	0.022
CYP2C19-substrate:	0.059
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.779
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.12
CYP3A4-inhibitor:	0.004
CYP3A4-substrate:	0.013

ADMET: Excretion

Clearance (CL):	0.897
Half-life (T1/2):	0.759

ADMET: Toxicity

hERG Blockers:	0.019
Human Hepatotoxicity (H-HT):	0.679
Drug-inuced Liver Injury (DILI):	0.972
AMES Toxicity:	0.029
Rat Oral Acute Toxicity:	0.267
Maximum Recommended Daily Dose:	0.01
Skin Sensitization:	0.132
Carcinogencity:	0.042
Eye Corrosion:	0.003
Eye Irritation:	0.015
Respiratory Toxicity:	0.131

Download Data

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

Natural Product: NPC57975

Natural Product ID:	NPC57975
*Common Name:**	QQGLQYQXUKHWPX-LPUQOGTASA-M
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QQGLQYQXUKHWPX-LPUQOGTASA-M
Standard InCHI:	InChI=1S/C14H19NO9S2/c16-7-9-11(17)12(18)13(19)14(23-9)25-10(15-24-26(20,21)22)6-8-4-2-1-3-5-8/h1-5,9,11-14,16-19H,6-7H2,(H,20,21,22)/p-1/t9-,11-,12+,13-,14+/m1/s1
SMILES:	c1ccc(cc1)CC(=NOS(=O)(=O)[O-])S[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	656497
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0001540] Monosaccharides [CHEMONTID:0001498] Hexoses [CHEMONTID:0000373] Glucosinolates [CHEMONTID:0003925] Alkylglucosinolates

*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
NPO19062	Euphorbia coerulescens	Species	Euphorbiaceae	Eukaryota	latices	South African	n.a.	PMID[3236005]
NPO18251	Strychnos angolensis	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6631439]
NPO15116	Astilbe thunbergii	Species	Saxifragaceae	Eukaryota	Rhizomes	n.a.	n.a.	PMID[9722485]
NPO12127	Parmelia saxatilis	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17724	Cinnamomum glanduliferum	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17724	Cinnamomum glanduliferum	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12127	Parmelia saxatilis	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17724	Cinnamomum glanduliferum	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12127	Parmelia saxatilis	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16973	Combretum hereroense	Species	Combretaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12127	Parmelia saxatilis	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1432	Strychnos alvimiana	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2710	Impatiens textorii	Species	Balsaminaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17724	Cinnamomum glanduliferum	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18309	Litsea akoensis	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15116	Astilbe thunbergii	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21814	Triumfetta rhomboidea	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18251	Strychnos angolensis	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19062	Euphorbia coerulescens	Species	Euphorbiaceae	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 NPC57975 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	129
0.1-0.2	1037
0.2-0.3	3917
0.3-0.4	17891
0.4-0.5	16552
0.5-0.6	3051
0.6-0.7	117
0.7-0.8	3
0.8-0.85	0
0.85-0.9	0
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 NPC57975 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	115
0.1-0.2	570
0.2-0.3	1163
0.3-0.4	3899
0.4-0.5	2767
0.5-0.6	608
0.6-0.7	27
0.7-0.8	1
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