Structure

Physi-Chem Properties

Molecular Weight:  186.05
Volume:  174.41
LogP:  0.254
LogD:  0.124
LogS:  -1.743
# Rotatable Bonds:  3
TPSA:  72.83
# H-Bond Aceptor:  5
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.46
Synthetic Accessibility Score:  3.897
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.748
MDCK Permeability:  0.0001073501116479747
Pgp-inhibitor:  0.001
Pgp-substrate:  0.01
Human Intestinal Absorption (HIA):  0.061
20% Bioavailability (F20%):  0.049
30% Bioavailability (F30%):  0.222

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.961
Plasma Protein Binding (PPB):  23.794498443603516%
Volume Distribution (VD):  0.822
Pgp-substrate:  73.46257019042969%

ADMET: Metabolism

CYP1A2-inhibitor:  0.015
CYP1A2-substrate:  0.844
CYP2C19-inhibitor:  0.037
CYP2C19-substrate:  0.773
CYP2C9-inhibitor:  0.014
CYP2C9-substrate:  0.067
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.153
CYP3A4-inhibitor:  0.023
CYP3A4-substrate:  0.854

ADMET: Excretion

Clearance (CL):  4.074
Half-life (T1/2):  0.797

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.378
Drug-inuced Liver Injury (DILI):  0.746
AMES Toxicity:  0.318
Rat Oral Acute Toxicity:  0.046
Maximum Recommended Daily Dose:  0.065
Skin Sensitization:  0.688
Carcinogencity:  0.025
Eye Corrosion:  0.961
Eye Irritation:  0.969
Respiratory Toxicity:  0.419

Download Data

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

  Natural Product: NPC13510

Natural Product ID:  NPC13510
Common Name*:   YGCFLXLGPRNGTJ-MRVPVSSYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  YGCFLXLGPRNGTJ-MRVPVSSYSA-N
Standard InCHI:  InChI=1S/C8H10O5/c1-12-5-3-6(9)8(11,4-5)7(10)13-2/h3,11H,4H2,1-2H3/t8-/m1/s1
SMILES:  COC1=CC(=O)[C@](C1)(C(=O)OC)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   335090
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0002088] Acyloins

*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
NPO3499 Macaranga conifera Species Euphorbiaceae Eukaryota n.a. leaf n.a. DOI[10.1016/S0031-9422(02)00378-3]
NPO3499 Macaranga conifera Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[21275386]
NPO3499 Macaranga conifera Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3499 Macaranga conifera Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11051 Nicotiana cavicola Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3499 Macaranga conifera Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2271 Cassia reticulata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28869 Neonectria obtusispora Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8684 Nymphaea ampla Species Nymphaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19426 Diospyros ferrea Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO370 Rhizophora apiculata Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6631 Elaeagnus glabra Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO155 Artemisia lanata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5288 Stomatanthes corumbensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4483 Ganonema farinosum Species Liagoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9378 Halocynthia aurantium Species Pyuridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1779 Sargassum kjellmanianum Species Sargassaceae 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 NPC13510 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 NPC13510 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