NPASS Compound

Structure

NPC226710 OpenBabel06302215242D 27 30 0 0 0 0 0 0 0 0999 V2000 -1.0108 -2.3353 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9340 -2.1925 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6621 -1.6072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5336 -1.9467 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2657 -1.3568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1365 -1.6934 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1216 -0.4338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2454 -0.1006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5180 -0.6841 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6529 -0.3493 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5096 0.5687 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2298 1.1619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0857 2.0850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2149 2.4215 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8249 2.6651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6892 2.3353 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8334 1.4123 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1021 0.8173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7001 1.0668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4300 1.6489 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8434 0.1489 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4191 2.9174 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 -0.9277 -0.9277 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9277 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.8553 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9277 -0.9277 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 2 1 0 0 0 0 2 3 1 0 0 0 0 3 9 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 7 21 1 0 0 0 0 7 8 2 0 0 0 0 8 18 1 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 10 23 1 0 0 0 0 11 12 1 0 0 0 0 12 18 2 0 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 16 2 0 0 0 0 16 17 1 0 0 0 0 16 22 1 0 0 0 0 17 18 1 0 0 0 0 17 19 2 0 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 2 0 0 0 0 24 27 1 0 0 0 0 M CHG 1 22 -1 M END $$$$

Physi-Chem Properties

Molecular Weight:	395.98
Volume:	327.88
LogP:	-0.106
LogD:	0.346
LogS:	-3.333
# Rotatable Bonds:	3
TPSA:	173.71
# H-Bond Aceptor:	11
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.334
Synthetic Accessibility Score:	3.686
Fsp3:	0.067
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.544
MDCK Permeability:	2.3424323444487527e-05
Pgp-inhibitor:	0.006
Pgp-substrate:	0.004
Human Intestinal Absorption (HIA):	0.881
20% Bioavailability (F20%):	0.593
30% Bioavailability (F30%):	0.958

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.005
Plasma Protein Binding (PPB):	82.1319808959961%
Volume Distribution (VD):	0.603
Pgp-substrate:	19.21192741394043%

ADMET: Metabolism

CYP1A2-inhibitor:	0.542
CYP1A2-substrate:	0.915
CYP2C19-inhibitor:	0.018
CYP2C19-substrate:	0.054
CYP2C9-inhibitor:	0.097
CYP2C9-substrate:	0.414
CYP2D6-inhibitor:	0.014
CYP2D6-substrate:	0.127
CYP3A4-inhibitor:	0.034
CYP3A4-substrate:	0.014

ADMET: Excretion

Clearance (CL):	1.977
Half-life (T1/2):	0.463

ADMET: Toxicity

hERG Blockers:	0.0
Human Hepatotoxicity (H-HT):	0.752
Drug-inuced Liver Injury (DILI):	0.986
AMES Toxicity:	0.044
Rat Oral Acute Toxicity:	0.132
Maximum Recommended Daily Dose:	0.894
Skin Sensitization:	0.788
Carcinogencity:	0.711
Eye Corrosion:	0.012
Eye Irritation:	0.409
Respiratory Toxicity:	0.299

Download Data

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

Natural Product: NPC226710

Natural Product ID:	NPC226710
*Common Name:**	JNGMKNATQGRSDF-UHFFFAOYSA-M
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JNGMKNATQGRSDF-UHFFFAOYSA-M
Standard InCHI:	InChI=1S/C15H8O11S/c1-23-7-3-6(18)12-11-9(7)15(26-27(20,21)22)25-13-5(17)2-4(16)8(10(11)13)14(19)24-12/h2-3,16,19H,1H3,(H,20,21,22)/p-1
SMILES:	COc1cc(=O)c2c3c1c(oc1c(=O)cc(c(c31)c(O)o2)[O-])OS(=O)(=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000145] Coumarins 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
NPO11616	Vibrio parahaemolyticus	Species	Vibrionaceae	Bacteria	n.a.	North Sea	n.a.	PMID[14640534]
NPO11616	Vibrio parahaemolyticus	Species	Vibrionaceae	Bacteria	n.a.	n.a.	n.a.	PMID[7853008]
NPO11616	Vibrio parahaemolyticus	Species	Vibrionaceae	Bacteria	n.a.	n.a.	n.a.	DOI[DOI: 10.1111/j.1574-6968.1992.tb05311.x]
NPO15413	Glycyrrhiza pallidiflora	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15151	Syringa vulgaris	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15413	Glycyrrhiza pallidiflora	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15413	Glycyrrhiza pallidiflora	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3488	Glossocalyx brevipes	Species	Siparunaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15413	Glycyrrhiza pallidiflora	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15762	Eucalyptus sieberiana	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15151	Syringa vulgaris	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15972	Quercus gilva	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14896	Reaumuria mucronata	Species	Tamaricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11241	Arisarum vulgare	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16439	Alphitonia macrocarpa	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13257	Euphorbia officinarum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15027	Helianthus divaricatus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11616	Vibrio parahaemolyticus	Species	Vibrionaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO9827	Indigofera linnaei	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16526	Papularia sphaerosperma	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO13005	Aplophyllum telephioides	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO5473	Streptomyces orinoci	Species	Streptomycetaceae	Bacteria	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 NPC226710 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	491
0.1-0.2	2232
0.2-0.3	5210
0.3-0.4	11268
0.4-0.5	6877
0.5-0.6	5340
0.6-0.7	5120
0.7-0.8	5918
0.8-0.85	228
0.85-0.9	13
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 NPC226710 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	445
0.1-0.2	1060
0.2-0.3	2024
0.3-0.4	2709
0.4-0.5	1835
0.5-0.6	757
0.6-0.7	198
0.7-0.8	116
0.8-0.85	6
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