Structure

Physi-Chem Properties

Molecular Weight:  256.07
Volume:  264.953
LogP:  3.335
LogD:  2.202
LogS:  -3.392
# Rotatable Bonds:  3
TPSA:  77.76
# H-Bond Aceptor:  4
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.738
Synthetic Accessibility Score:  2.181
Fsp3:  0.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.185
MDCK Permeability:  8.958380021795165e-06
Pgp-inhibitor:  0.001
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.047
20% Bioavailability (F20%):  0.966
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.071
Plasma Protein Binding (PPB):  97.98513793945312%
Volume Distribution (VD):  0.26
Pgp-substrate:  1.416627287864685%

ADMET: Metabolism

CYP1A2-inhibitor:  0.472
CYP1A2-substrate:  0.048
CYP2C19-inhibitor:  0.08
CYP2C19-substrate:  0.046
CYP2C9-inhibitor:  0.469
CYP2C9-substrate:  0.449
CYP2D6-inhibitor:  0.339
CYP2D6-substrate:  0.139
CYP3A4-inhibitor:  0.389
CYP3A4-substrate:  0.065

ADMET: Excretion

Clearance (CL):  3.977
Half-life (T1/2):  0.893

ADMET: Toxicity

hERG Blockers:  0.153
Human Hepatotoxicity (H-HT):  0.627
Drug-inuced Liver Injury (DILI):  0.974
AMES Toxicity:  0.023
Rat Oral Acute Toxicity:  0.051
Maximum Recommended Daily Dose:  0.022
Skin Sensitization:  0.6
Carcinogencity:  0.097
Eye Corrosion:  0.004
Eye Irritation:  0.934
Respiratory Toxicity:  0.839

Download Data

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

  Natural Product: NPC271154

Natural Product ID:  NPC271154
Common Name*:   NYRISADACLJHMJ-VOTSOKGWSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NYRISADACLJHMJ-VOTSOKGWSA-N
Standard InCHI:  InChI=1S/C15H12O4/c16-12-8-11(14(15(18)19)13(17)9-12)7-6-10-4-2-1-3-5-10/h1-9,16-17H,(H,18,19)/b7-6+
SMILES:  c1ccc(cc1)/C=C/c1cc(cc(c1C(=O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   9813767
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000253] Stilbenes

*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
NPO5638 Garcinia livingstonei Species Clusiaceae Eukaryota n.a. fruit n.a. DOI[10.1016/S0040-4020(01)89039-6]
NPO4703 Solanum hispidum Species Solanaceae Eukaryota leaves n.a. n.a. PMID[15217270]
NPO46 Onosma hispida Species Boraginaceae Eukaryota n.a. whole plant n.a. PMID[16079517]
NPO5638 Garcinia livingstonei Species Clusiaceae Eukaryota root bark n.a. n.a. PMID[16562837]
NPO5638 Garcinia livingstonei Species Clusiaceae Eukaryota n.a. fruit n.a. PMID[21028890]
NPO14359 Pentarhizidium orientale Species Onocleaceae Eukaryota Rhizomes n.a. n.a. PMID[28984452]
NPO46 Onosma hispida Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO46 Onosma hispida Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14359 Pentarhizidium orientale Species Onocleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3789 Lyonia formosa Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14359 Pentarhizidium orientale Species Onocleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5638 Garcinia livingstonei Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27945 Cancrinia discoidea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1896 Proteus penneri Species Morganellaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO46 Onosma hispida Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4703 Solanum hispidum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2828 Blaps mucronata Species Tenebrionidae 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 NPC271154 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 NPC271154 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