Structure

Physi-Chem Properties

Molecular Weight:  212.14
Volume:  234.57
LogP:  1.506
LogD:  1.643
LogS:  -2.343
# Rotatable Bonds:  6
TPSA:  46.53
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.561
Synthetic Accessibility Score:  3.092
Fsp3:  0.583
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:  -4.49
MDCK Permeability:  6.888289499329403e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.054
20% Bioavailability (F20%):  0.033
30% Bioavailability (F30%):  0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.981
Plasma Protein Binding (PPB):  71.07835388183594%
Volume Distribution (VD):  0.632
Pgp-substrate:  51.83956527709961%

ADMET: Metabolism

CYP1A2-inhibitor:  0.114
CYP1A2-substrate:  0.083
CYP2C19-inhibitor:  0.1
CYP2C19-substrate:  0.382
CYP2C9-inhibitor:  0.028
CYP2C9-substrate:  0.681
CYP2D6-inhibitor:  0.134
CYP2D6-substrate:  0.282
CYP3A4-inhibitor:  0.045
CYP3A4-substrate:  0.255

ADMET: Excretion

Clearance (CL):  5.754
Half-life (T1/2):  0.88

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.063
Drug-inuced Liver Injury (DILI):  0.057
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.004
Maximum Recommended Daily Dose:  0.336
Skin Sensitization:  0.881
Carcinogencity:  0.094
Eye Corrosion:  0.281
Eye Irritation:  0.968
Respiratory Toxicity:  0.008

Download Data

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

  Natural Product: NPC38213

Natural Product ID:  NPC38213
Common Name*:   GPNYMDBKVQUQRW-FQOLVZPASA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  GPNYMDBKVQUQRW-FQOLVZPASA-N
Standard InCHI:  InChI=1S/C12H20O3/c1-10(7-9-15-11(2)13)6-5-8-12(3,4)14/h5,7-8,14H,6,9H2,1-4H3/b8-5+,10-7+
SMILES:  C/C(=CCOC(=O)C)/C/C=C/C(C)(C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   14191351
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001722] Fatty alcohol esters

*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
NPO1905 Fagraea fragrans Species Gentianaceae Eukaryota bark and leaves Koh Kong Province, Cambodia 2005-DEC PMID[19053508]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4713 Eucalyptus cordata Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO53 Nephelium mutabile Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3212 Bipolaris sorokiniana Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5020 Jasonia montana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2839 Dovyalis abyssinica Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3796 Pseudomonas viridiflava Species Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO1905 Fagraea fragrans Species Gentianaceae 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 NPC38213 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 NPC38213 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