Ligand profile

53Q

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

Bound to: VK055_2378 — di-trans,poly-cis-decaprenylcistransferase

Via homolog PDB 7jlj UniProt O31751 Formula C₂₆H₂₈ClNO
Mol. weight 405.97 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
53Q
PDB
7jlj
UniProt (similar protein)
O31751
Target protein
VK055_2378

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 405.97 Da
LogP (Crippen) 6.56
H-bond donors 0
H-bond acceptors 2
TPSA 12.47 Ų
Rotatable bonds 9
Aromatic rings 3 / 3
Heavy atoms 29
Fraction sp³ C 0.23
Formula C₂₆H₂₈ClNO

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 12.5
  • −1 ≤ LogP ≤ 5 6.56
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 406.0
  • LogP ≤ 5 6.56
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 12.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCN(CC)CCOc1ccc(cc1)/C(=C(\c2ccccc2)/Cl)/c3ccccc3
InChI 
InChI=1S/C26H28ClNO/c1-3-28(4-2)19-20-29-24-17-15-22(16-18-24)25(21-11-7-5-8-12-21)26(27)23-13-9-6-10-14-23/h5-18H,3-4,19-20H2,1-2H3/b26-25+
InChIKey 
GKIRPKYJQBWNGO-OCEACIFDSA-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
PF01255

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_2378.

PDB 3

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

Ligand PDB entry

ChEMBL 17

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)