Ligand profile

CHEMBL1256839

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_4925 — apurinic endonuclease family protein

Via homolog UniProt P0A6C1 Formula C₂₁H₃₀ClNO₄
pchembl 6.90 ~125.9 nM
Mol. weight 395.93 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL1256839
UniProt (similar protein)
P0A6C1
pchembl
6.900 (~125.9 nM)
Target protein
VK055_4925

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 395.93 Da
LogP (Crippen) 3.86
H-bond donors 0
H-bond acceptors 5
TPSA 40.16 Ų
Rotatable bonds 10
Aromatic rings 2 / 2
Heavy atoms 27
Fraction sp³ C 0.43
Formula C₂₁H₃₀ClNO₄

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 40.2
  • −1 ≤ LogP ≤ 5 3.86
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 395.9
  • LogP ≤ 5 3.86
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 40.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc(CCN(C)CCc2ccc(OC)c(OC)c2)cc1OC.Cl
InChI 
InChI=1S/C21H29NO4.ClH/c1-22(12-10-16-6-8-18(23-2)20(14-16)25-4)13-11-17-7-9-19(24-3)21(15-17)26-5;/h6-9,14-15H,10-13H2,1-5H3;1H
InChIKey 
GYBONEHHSUABAO-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
ChEMBL
Activity
Inconclusive
Binding sites
PF01261

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_4925.

PDB 1

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

Ligand PDB entry

ChEMBL 63

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)