Structure

Physi-Chem Properties

Molecular Weight:  334.21
Volume:  350.138
LogP:  3.588
LogD:  3.158
LogS:  -3.519
# Rotatable Bonds:  2
TPSA:  74.6
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  4
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.794
Synthetic Accessibility Score:  5.512
Fsp3:  0.9
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:  -5.9
MDCK Permeability:  8.902783520170487e-06
Pgp-inhibitor:  0.009
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.976

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.205
Plasma Protein Binding (PPB):  92.18524932861328%
Volume Distribution (VD):  0.489
Pgp-substrate:  8.421013832092285%

ADMET: Metabolism

CYP1A2-inhibitor:  0.008
CYP1A2-substrate:  0.599
CYP2C19-inhibitor:  0.01
CYP2C19-substrate:  0.503
CYP2C9-inhibitor:  0.025
CYP2C9-substrate:  0.156
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.097
CYP3A4-inhibitor:  0.081
CYP3A4-substrate:  0.024

ADMET: Excretion

Clearance (CL):  0.655
Half-life (T1/2):  0.703

ADMET: Toxicity

hERG Blockers:  0.018
Human Hepatotoxicity (H-HT):  0.561
Drug-inuced Liver Injury (DILI):  0.045
AMES Toxicity:  0.004
Rat Oral Acute Toxicity:  0.03
Maximum Recommended Daily Dose:  0.475
Skin Sensitization:  0.767
Carcinogencity:  0.385
Eye Corrosion:  0.058
Eye Irritation:  0.25
Respiratory Toxicity:  0.938

Download Data

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

  Natural Product: NPC65799

Natural Product ID:  NPC65799
Common Name*:   VYDMSJMCDXSXHU-BQBZGAKWSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VYDMSJMCDXSXHU-BQBZGAKWSA-N
Standard InCHI:  InChI=1S/C10H13NO4/c1-6-2-3-7(10(14)15-6)11-8(12)4-5-9(11)13/h6-7H,2-5H2,1H3/t6-,7-/m0/s1
SMILES:  C[C@H]1CC[C@@H](C(=O)O1)N1C(=O)CCC1=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11275849
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0000394] Alpha amino acid 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
NPO20125 Cleistanthus schlechteri Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22024 Agathosma serpyllacea Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22965 Saussurea elegans Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23191 Plectranthus striatus Species Lamiaceae 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 NPC65799 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 NPC65799 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