Ligand profile

H3P

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

Bound to: VK055_1018 — glutamate dehydrogenase

Via homolog PDB 3ete UniProt P00366 Formula C₁₃H₆Cl₆O₂
Mol. weight 406.91 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
H3P
PDB
3ete
UniProt (similar protein)
P00366
Target protein
VK055_1018

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 406.91 Da
LogP (Crippen) 6.61
H-bond donors 2
H-bond acceptors 2
TPSA 40.46 Ų
Rotatable bonds 2
Aromatic rings 2 / 2
Heavy atoms 21
Fraction sp³ C 0.08
Formula C₁₃H₆Cl₆O₂

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 40.5
  • −1 ≤ LogP ≤ 5 6.61
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 406.9
  • LogP ≤ 5 6.61
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 40.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(c(c(c(c1Cl)Cl)Cc2c(c(cc(c2Cl)Cl)Cl)O)O)Cl
InChI 
InChI=1S/C13H6Cl6O2/c14-6-2-8(16)12(20)4(10(6)18)1-5-11(19)7(15)3-9(17)13(5)21/h2-3,20-21H,1H2
InChIKey 
ACGUYXCXAPNIKK-UHFFFAOYSA-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
PF02812

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_1018.

PDB 5

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

Ligand PDB entry

ChEMBL 2

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)