Ligand profile

VPM

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

Bound to: VK055_2493 — 2-isopropylmalate synthase

Via homolog PDB 4ov9 UniProt B0SN40 Formula C₇H₁₂O₅
Mol. weight 176.17 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
VPM
PDB
4ov9
UniProt (similar protein)
B0SN40
Target protein
VK055_2493

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 176.17 Da
LogP (Crippen) -0.07
H-bond donors 3
H-bond acceptors 3
TPSA 94.83 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 12
Fraction sp³ C 0.71
Formula C₇H₁₂O₅

Drug-likeness

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

Permeability proxy Check

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 94.8
  • −1 ≤ LogP ≤ 5 -0.07
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 176.2
  • LogP ≤ 5 -0.07
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 94.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)[C@@](CC(=O)O)(C(=O)O)O
InChI 
InChI=1S/C7H12O5/c1-4(2)7(12,6(10)11)3-5(8)9/h4,12H,3H2,1-2H3,(H,8,9)(H,10,11)/t7-/m0/s1
InChIKey 
BITYXLXUCSKTJS-ZETCQYMHSA-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
PF00682

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_2493.

PDB 6

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)