Ligand profile

M3P

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_4114 — glyoxalase/Bleomycin resistance /Dioxygenase superfamily protein

Via homolog PDB 3hq0 UniProt Q7WYF5 Formula C₇H₈O₄
Mol. weight 156.14 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
M3P
PDB
3hq0
UniProt (similar protein)
Q7WYF5
Target protein
VK055_4114

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 156.14 Da
LogP (Crippen) 0.66
H-bond donors 2
H-bond acceptors 3
TPSA 74.60 Ų
Rotatable bonds 3
Aromatic rings 0 / 0
Heavy atoms 11
Fraction sp³ C 0.14
Formula C₇H₈O₄

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 74.6
  • −1 ≤ LogP ≤ 5 0.66
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 156.1
  • LogP ≤ 5 0.66
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 74.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)\C=C\C=C(/C(=O)O)\O
InChI 
InChI=1S/C7H8O4/c1-5(8)3-2-4-6(9)7(10)11/h2-4,9H,1H3,(H,10,11)/b3-2+,6-4+
InChIKey 
HVZGWILTESYJSP-WJPDYIDTSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00903

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_4114.

PDB 7

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)