Structure

Physi-Chem Properties

Molecular Weight:  300.1
Volume:  308.335
LogP:  3.065
LogD:  3.025
LogS:  -3.495
# Rotatable Bonds:  5
TPSA:  75.99
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.655
Synthetic Accessibility Score:  2.141
Fsp3:  0.118
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:  -4.747
MDCK Permeability:  1.6389267329941504e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.02

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.149
Plasma Protein Binding (PPB):  99.5527114868164%
Volume Distribution (VD):  0.442
Pgp-substrate:  1.4236540794372559%

ADMET: Metabolism

CYP1A2-inhibitor:  0.966
CYP1A2-substrate:  0.928
CYP2C19-inhibitor:  0.889
CYP2C19-substrate:  0.14
CYP2C9-inhibitor:  0.78
CYP2C9-substrate:  0.942
CYP2D6-inhibitor:  0.784
CYP2D6-substrate:  0.914
CYP3A4-inhibitor:  0.837
CYP3A4-substrate:  0.301

ADMET: Excretion

Clearance (CL):  11.963
Half-life (T1/2):  0.912

ADMET: Toxicity

hERG Blockers:  0.075
Human Hepatotoxicity (H-HT):  0.107
Drug-inuced Liver Injury (DILI):  0.564
AMES Toxicity:  0.705
Rat Oral Acute Toxicity:  0.887
Maximum Recommended Daily Dose:  0.767
Skin Sensitization:  0.939
Carcinogencity:  0.735
Eye Corrosion:  0.01
Eye Irritation:  0.933
Respiratory Toxicity:  0.834

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

  Natural Product: NPC277947

Natural Product ID:  NPC277947
Common Name*:   JUCNRAJYHMZLOT-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JUCNRAJYHMZLOT-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C17H16O5/c1-21-16-5-3-4-11(17(16)22-2)6-9-14(19)13-8-7-12(18)10-15(13)20/h3-10,18,20H,1-2H3
SMILES:  COc1cccc(C=CC(=O)c2ccc(cc2O)O)c1OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   622927
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0003467] Linear 1,3-diarylpropanoids
        • [CHEMONTID:0001630] Chalcones and dihydrochalcones
          • [CHEMONTID:0003472] 2'-Hydroxychalcones

*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
NPO29027 Khaya grandifoliola Species Meliaceae Eukaryota n.a. seed n.a. PMID[10661881]
NPO15741 Embelia ribes Species Primulaceae Eukaryota n.a. leaf n.a. PMID[17124632]
NPO15741 Embelia ribes Species Primulaceae Eukaryota n.a. fruit n.a. PMID[17124632]
NPO15741 Embelia ribes Species Primulaceae Eukaryota n.a. n.a. n.a. PMID[17125236]
NPO15741 Embelia ribes Species Primulaceae Eukaryota roots n.a. n.a. PMID[17125236]
NPO10682 Cystoseira mediterranea Species Sargassaceae Eukaryota n.a. n.a. n.a. PMID[2045820]
NPO15741 Embelia ribes Species Primulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5457 Dalbergia congestiflora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15741 Embelia ribes Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16096 Astragalus adsurgens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15741 Embelia ribes Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1281 Schleichera trijuga Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10947 Aspilia parvifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10447 Triclisia subcordata Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7887 Schultesia guianensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5457 Dalbergia congestiflora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13641 Napoleonaea vogelii Species Lecythidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13520 Craibiodendron yunnanense Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15553 Barringtonia acutangula Species Lecythidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15206 Mabea fistulifera Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29027 Khaya grandifoliola Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12581 Corydalis densiflora Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16182 Desmodium canadense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10682 Cystoseira mediterranea 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 NPC277947 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 NPC277947 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