Structure

Physi-Chem Properties

Molecular Weight:  440.16
Volume:  468.295
LogP:  4.904
LogD:  4.445
LogS:  -5.72
# Rotatable Bonds:  8
TPSA:  61.83
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.471
Synthetic Accessibility Score:  3.359
Fsp3:  0.143
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.898
MDCK Permeability:  2.5512614229228348e-05
Pgp-inhibitor:  0.998
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.952
30% Bioavailability (F30%):  0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.094
Plasma Protein Binding (PPB):  98.93535614013672%
Volume Distribution (VD):  0.426
Pgp-substrate:  1.283555507659912%

ADMET: Metabolism

CYP1A2-inhibitor:  0.834
CYP1A2-substrate:  0.81
CYP2C19-inhibitor:  0.951
CYP2C19-substrate:  0.082
CYP2C9-inhibitor:  0.971
CYP2C9-substrate:  0.061
CYP2D6-inhibitor:  0.509
CYP2D6-substrate:  0.049
CYP3A4-inhibitor:  0.893
CYP3A4-substrate:  0.657

ADMET: Excretion

Clearance (CL):  6.894
Half-life (T1/2):  0.031

ADMET: Toxicity

hERG Blockers:  0.188
Human Hepatotoxicity (H-HT):  0.159
Drug-inuced Liver Injury (DILI):  0.977
AMES Toxicity:  0.015
Rat Oral Acute Toxicity:  0.464
Maximum Recommended Daily Dose:  0.703
Skin Sensitization:  0.934
Carcinogencity:  0.062
Eye Corrosion:  0.003
Eye Irritation:  0.047
Respiratory Toxicity:  0.948

Download Data

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

  Natural Product: NPC9810

Natural Product ID:  NPC9810
Common Name*:   ZDYAFMHRSFOATI-PWNKNYCBSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZDYAFMHRSFOATI-PWNKNYCBSA-N
Standard InCHI:  InChI=1S/C28H24O5/c1-31-26-22(18-19-12-6-3-7-13-19)33-28(30)25(26)23(20-14-8-4-9-15-20)24(27(29)32-2)21-16-10-5-11-17-21/h3-18,23-24H,1-2H3/b22-18+/t23-,24+/m0/s1
SMILES:  COC1=C([C@@H](c2ccccc2)[C@@H](c2ccccc2)C(=O)OC)C(=O)O/C/1=C/c1ccccc1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10939102
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
NPO23208 Pulveroboletus ravenelii Species Boletaceae Eukaryota n.a. n.a. n.a. PMID[12542354]
NPO24047 Hydnellum suaveolens Species Thelephoraceae Eukaryota n.a. fruit body n.a. PMID[16755070]
NPO23543 Hypoxylon fuscum Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18928 Heimia myrtifolia Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23280 Cyclamen graecum Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28079 Holothuria floridana Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23411 Pseudochlorodesmis furcellata Species Bryopsidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24289 Arctodiaptomus salinus Species Diaptomidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18928 Heimia myrtifolia Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21616 Cyclosorus striatus Species Thelypteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23208 Pulveroboletus ravenelii Species Boletaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24003 Argemone alba Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23543 Hypoxylon fuscum Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9592.1 Codonopsis foetens subsp. nervosa Subspecies Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24047 Hydnellum suaveolens Species Thelephoraceae 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 NPC9810 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 NPC9810 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