Ligand profile

2RH

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

Bound to: VK055_2674 — 2-hydroxyglutaryl-CoA dehydratase, D-component family protein

Via homolog PDB 3o3o UniProt Q5U923 Formula C₆H₁₂O₃
Mol. weight 132.16 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2RH
PDB
3o3o
UniProt (similar protein)
Q5U923
Target protein
VK055_2674

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 132.16 Da
LogP (Crippen) 0.48
H-bond donors 2
H-bond acceptors 2
TPSA 57.53 Ų
Rotatable bonds 3
Aromatic rings 0 / 0
Heavy atoms 9
Fraction sp³ C 0.83
Formula C₆H₁₂O₃

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 57.5
  • −1 ≤ LogP ≤ 5 0.48
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 132.2
  • LogP ≤ 5 0.48
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 57.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)C[C@H](C(=O)O)O
InChI 
InChI=1S/C6H12O3/c1-4(2)3-5(7)6(8)9/h4-5,7H,3H2,1-2H3,(H,8,9)/t5-/m1/s1
InChIKey 
LVRFTAZAXQPQHI-RXMQYKEDSA-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
PF06050

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_2674.

PDB 3

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

Ligand PDB entry

ZINC 4

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

Compound Similarity (Tanimoto)