Structure

Physi-Chem Properties

Molecular Weight:  74.0
Volume:  64.246
LogP:  -0.689
LogD:  -1.113
LogS:  0.602
# Rotatable Bonds:  1
TPSA:  54.37
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.329
Synthetic Accessibility Score:  2.37
Fsp3:  0.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.484
MDCK Permeability:  0.0007200493710115552
Pgp-inhibitor:  0.0
Pgp-substrate:  0.006
Human Intestinal Absorption (HIA):  0.061
20% Bioavailability (F20%):  0.029
30% Bioavailability (F30%):  0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.73
Plasma Protein Binding (PPB):  24.32809829711914%
Volume Distribution (VD):  0.276
Pgp-substrate:  68.72254943847656%

ADMET: Metabolism

CYP1A2-inhibitor:  0.016
CYP1A2-substrate:  0.07
CYP2C19-inhibitor:  0.031
CYP2C19-substrate:  0.048
CYP2C9-inhibitor:  0.019
CYP2C9-substrate:  0.441
CYP2D6-inhibitor:  0.027
CYP2D6-substrate:  0.139
CYP3A4-inhibitor:  0.014
CYP3A4-substrate:  0.027

ADMET: Excretion

Clearance (CL):  2.873
Half-life (T1/2):  0.892

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.064
Drug-inuced Liver Injury (DILI):  0.037
AMES Toxicity:  0.218
Rat Oral Acute Toxicity:  0.068
Maximum Recommended Daily Dose:  0.01
Skin Sensitization:  0.598
Carcinogencity:  0.045
Eye Corrosion:  0.994
Eye Irritation:  0.99
Respiratory Toxicity:  0.875

Download Data

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

  Natural Product: NPC307812

Natural Product ID:  NPC307812
Common Name*:   Glyoxylate
IUPAC Name:   oxaldehydic acid
Synonyms:   2-Oxoacetate
Standard InCHIKey:  HHLFWLYXYJOTON-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C2H2O3/c3-1-2(4)5/h1H,(H,4,5)
SMILES:  C(=O)C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1162545
PubChem CID:   760
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0001205] Carboxylic acids

*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

☑ 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
NPT4435 Individual Protein Dihydrodipicolinate synthase Escherichia coli K-12 Ki = 16000.0 nM PMID[568911]
NPT4435 Individual Protein Dihydrodipicolinate synthase Escherichia coli K-12 Kis = 16.0 uM PMID[568913]
NPT4435 Individual Protein Dihydrodipicolinate synthase Escherichia coli K-12 Kii = 28.0 uM PMID[568913]

☑ 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 NPC307812 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
0.76 Intermediate Similarity NPC165122
0.6786 Remote Similarity NPC316272
0.6667 Remote Similarity NPC114586
0.6522 Remote Similarity NPC68873
0.6522 Remote Similarity NPC7922
0.625 Remote Similarity NPC301950
0.6129 Remote Similarity NPC329270
0.6129 Remote Similarity NPC76217
0.6129 Remote Similarity NPC307739
0.6071 Remote Similarity NPC286233
0.5833 Remote Similarity NPC283245
0.5833 Remote Similarity NPC137050
0.5769 Remote Similarity NPC181153
0.5714 Remote Similarity NPC82694
0.5652 Remote Similarity NPC146289
0.5625 Remote Similarity NPC261351
0.56 Remote Similarity NPC237869
0.56 Remote Similarity NPC173862

  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 NPC307812 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
0.7727 Intermediate Similarity NPD7357 Approved
0.7727 Intermediate Similarity NPD7356 Approved
0.6522 Remote Similarity NPD7364 Approved
0.6333 Remote Similarity NPD8206 Approved
0.6333 Remote Similarity NPD54 Approved
0.6333 Remote Similarity NPD8204 Approved
0.6333 Remote Similarity NPD55 Approved
0.6333 Remote Similarity NPD8203 Approved
0.625 Remote Similarity NPD7352 Approved
0.6129 Remote Similarity NPD8205 Approved
0.6129 Remote Similarity NPD8202 Approved
0.6071 Remote Similarity NPD8189 Approved
0.5909 Remote Similarity NPD49 Approved
0.5909 Remote Similarity NPD7363 Approved
0.5909 Remote Similarity NPD7365 Approved
0.5909 Remote Similarity NPD47 Approved
0.5909 Remote Similarity NPD50 Approved
0.5909 Remote Similarity NPD105 Approved
0.5909 Remote Similarity NPD7362 Approved
0.5909 Remote Similarity NPD48 Approved
0.5769 Remote Similarity NPD8201 Phase 2
0.5769 Remote Similarity NPD8190 Phase 2
0.5714 Remote Similarity NPD8207 Approved

  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