Structure

Physi-Chem Properties

Molecular Weight:  286.11
Volume:  269.914
LogP:  -0.055
LogD:  -0.181
LogS:  -0.905
# Rotatable Bonds:  3
TPSA:  119.61
# H-Bond Aceptor:  7
# H-Bond Donor:  5
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.477
Synthetic Accessibility Score:  3.463
Fsp3:  0.538
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:  -5.858
MDCK Permeability:  2.7764022888732143e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.906
Human Intestinal Absorption (HIA):  0.426
20% Bioavailability (F20%):  0.05
30% Bioavailability (F30%):  0.946

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.236
Plasma Protein Binding (PPB):  61.3140754699707%
Volume Distribution (VD):  0.678
Pgp-substrate:  38.345760345458984%

ADMET: Metabolism

CYP1A2-inhibitor:  0.141
CYP1A2-substrate:  0.066
CYP2C19-inhibitor:  0.024
CYP2C19-substrate:  0.448
CYP2C9-inhibitor:  0.003
CYP2C9-substrate:  0.677
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.316
CYP3A4-inhibitor:  0.015
CYP3A4-substrate:  0.057

ADMET: Excretion

Clearance (CL):  4.778
Half-life (T1/2):  0.843

ADMET: Toxicity

hERG Blockers:  0.058
Human Hepatotoxicity (H-HT):  0.034
Drug-inuced Liver Injury (DILI):  0.05
AMES Toxicity:  0.495
Rat Oral Acute Toxicity:  0.71
Maximum Recommended Daily Dose:  0.009
Skin Sensitization:  0.86
Carcinogencity:  0.428
Eye Corrosion:  0.045
Eye Irritation:  0.903
Respiratory Toxicity:  0.034

Download Data

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

  Natural Product: NPC17140

Natural Product ID:  NPC17140
Common Name*:   XHEKEYHCIIMZRR-WJTVCTBASA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  XHEKEYHCIIMZRR-WJTVCTBASA-N
Standard InCHI:  InChI=1S/C13H18O7/c1-6-4-7(15)2-3-8(6)19-13-12(18)11(17)10(16)9(5-14)20-13/h2-4,9-18H,5H2,1H3/t9-,10-,11+,12-,13-/m0/s1
SMILES:  Cc1cc(ccc1O[C@@H]1[C@H]([C@@H]([C@H]([C@H](CO)O1)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0004165] Phenolic glycosides

*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
NPO18028 Isodon scoparius Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[19072209]
NPO22059 Eurythoe complanata Species Amphinomidae Eukaryota n.a. n.a. n.a. PMID[20028030]
NPO14409 Dioscorea nipponica Species Dioscoreaceae Eukaryota rhizomes n.a. n.a. PMID[23707257]
NPO18028 Isodon scoparius Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[28654256]
NPO14409 Dioscorea nipponica Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15241 Lamium amplexicaule Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14409 Dioscorea nipponica Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15241 Lamium amplexicaule Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14409 Dioscorea nipponica Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14409 Dioscorea nipponica Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15241 Lamium amplexicaule Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17103 Phellodendron lavallei Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14124 Virola minutiflora Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22059 Eurythoe complanata Species Amphinomidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1163 Mantella expectata Species Mantellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18028 Isodon scoparius Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14409 Dioscorea nipponica Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5670 Chimaphila japonica Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16376 Careya arborea Species Lecythidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17404 Rumex ecklonianus Species Polygonaceae 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 NPC17140 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 NPC17140 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