Structure

Physi-Chem Properties

Molecular Weight:  256.07
Volume:  259.033
LogP:  3.784
LogD:  3.178
LogS:  -3.687
# Rotatable Bonds:  2
TPSA:  62.83
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.736
Synthetic Accessibility Score:  2.2
Fsp3:  0.067
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.853
MDCK Permeability:  1.3107600352668669e-05
Pgp-inhibitor:  0.008
Pgp-substrate:  0.968
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.984
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.029
Plasma Protein Binding (PPB):  98.05573272705078%
Volume Distribution (VD):  0.837
Pgp-substrate:  2.373056411743164%

ADMET: Metabolism

CYP1A2-inhibitor:  0.993
CYP1A2-substrate:  0.842
CYP2C19-inhibitor:  0.882
CYP2C19-substrate:  0.062
CYP2C9-inhibitor:  0.468
CYP2C9-substrate:  0.958
CYP2D6-inhibitor:  0.923
CYP2D6-substrate:  0.933
CYP3A4-inhibitor:  0.96
CYP3A4-substrate:  0.141

ADMET: Excretion

Clearance (CL):  9.86
Half-life (T1/2):  0.747

ADMET: Toxicity

hERG Blockers:  0.088
Human Hepatotoxicity (H-HT):  0.113
Drug-inuced Liver Injury (DILI):  0.7
AMES Toxicity:  0.106
Rat Oral Acute Toxicity:  0.066
Maximum Recommended Daily Dose:  0.929
Skin Sensitization:  0.928
Carcinogencity:  0.07
Eye Corrosion:  0.016
Eye Irritation:  0.944
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: NPC28

Natural Product ID:  NPC28
Common Name*:   GKLYIPFNWWXSGN-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  GKLYIPFNWWXSGN-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C15H12O4/c1-18-13-5-10(4-12(17)7-13)14-6-9-2-3-11(16)8-15(9)19-14/h2-8,16-17H,1H3
SMILES:  COc1cc(cc(c1)O)c1cc2ccc(cc2o1)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:0003405] 2-arylbenzofuran flavonoids

*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
NPO28803 Artocarpus chama Species Moraceae Eukaryota n.a. root n.a. PMID[15165133]
NPO27320 Morus notabilis Species Moraceae Eukaryota n.a. n.a. n.a. PMID[21737271]
NPO27320 Morus notabilis Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27071 Spirastrella coccinea Species Spirastrellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27089 Nectandra glabrescens Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28584 Euphorbia indica Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28803 Artocarpus chama Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27368 Sinularia mayi Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27589 Artemisia lehmanniana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27280 Stachys spectabilis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27147 Habenaria repens Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29149 Zexmenia phyllocephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27478 Geodia japonica Species Geodiidae 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 NPC28 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 NPC28 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