Structure

Physi-Chem Properties

Molecular Weight:  250.08
Volume:  247.06
LogP:  1.7
LogD:  1.642
LogS:  -2.162
# Rotatable Bonds:  3
TPSA:  79.9
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.861
Synthetic Accessibility Score:  3.035
Fsp3:  0.308
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:  -4.865
MDCK Permeability:  1.572526707604993e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.859
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.012
30% Bioavailability (F30%):  0.989

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.199
Plasma Protein Binding (PPB):  82.58330535888672%
Volume Distribution (VD):  0.907
Pgp-substrate:  17.6994571685791%

ADMET: Metabolism

CYP1A2-inhibitor:  0.971
CYP1A2-substrate:  0.913
CYP2C19-inhibitor:  0.347
CYP2C19-substrate:  0.413
CYP2C9-inhibitor:  0.481
CYP2C9-substrate:  0.937
CYP2D6-inhibitor:  0.181
CYP2D6-substrate:  0.828
CYP3A4-inhibitor:  0.111
CYP3A4-substrate:  0.192

ADMET: Excretion

Clearance (CL):  10.521
Half-life (T1/2):  0.619

ADMET: Toxicity

hERG Blockers:  0.044
Human Hepatotoxicity (H-HT):  0.369
Drug-inuced Liver Injury (DILI):  0.614
AMES Toxicity:  0.092
Rat Oral Acute Toxicity:  0.048
Maximum Recommended Daily Dose:  0.645
Skin Sensitization:  0.649
Carcinogencity:  0.058
Eye Corrosion:  0.071
Eye Irritation:  0.8
Respiratory Toxicity:  0.104

Download Data

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

  Natural Product: NPC140641

Natural Product ID:  NPC140641
Common Name*:   ORLHWDAVUBPRKN-ZETCQYMHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ORLHWDAVUBPRKN-ZETCQYMHSA-N
Standard InCHI:  InChI=1S/C13H14O5/c1-7(14)3-10-5-8-4-9(17-2)6-11(15)12(8)13(16)18-10/h4-7,14-15H,3H2,1-2H3/t7-/m0/s1
SMILES:  C[C@@H](Cc1cc2cc(cc(c2c(=O)o1)O)OC)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5323561
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0001890] Isocoumarins and derivatives

*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
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. PMID[17944538]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. PMID[22823026]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota leaves and stems Ha Long, Quang Ninh province, Vietnam 2014-Jul PMID[25769817]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. PMID[29792702]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14254 Kandelia candel Species Rhizophoraceae 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
NPT2 Others Unspecified Inhibition = 33.0 % PMID[29792702]

☑ 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 NPC140641 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 NPC140641 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