Ligand profile

CHEMBL4210534

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_1238 — exodeoxyribonuclease III

Via homolog UniProt P27695 Formula C₃₂H₄₀N₄O₂
pchembl 7.26 ~55.0 nM
Mol. weight 512.70 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL4210534
UniProt (similar protein)
P27695
pchembl
7.260 (~55.0 nM)
Target protein
VK055_1238

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 512.70 Da
LogP (Crippen) 4.10
H-bond donors 4
H-bond acceptors 6
TPSA 66.58 Ų
Rotatable bonds 0
Aromatic rings 4 / 5
Heavy atoms 38
Fraction sp³ C 0.38
Formula C₃₂H₄₀N₄O₂

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 66.6
  • −1 ≤ LogP ≤ 5 4.10
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 512.7
  • LogP ≤ 5 4.10
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 66.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc2ccc3cc2cc1CNCCOCCNCc1ccc2ccc(cc2c1)CNCCOCCNC3
InChI 
InChI=1S/C32H40N4O2/c1-5-29-6-2-26-18-31(29)17-25(1)21-33-9-13-37-14-10-35-23-27-3-7-30-8-4-28(20-32(30)19-27)24-36-12-16-38-15-11-34-22-26/h1-8,17-20,33-36H,9-16,21-24H2
InChIKey 
GAVOKMJEFXZQJQ-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
Binding sites
PF03372

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_1238.

PDB 1

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

Ligand PDB entry

ChEMBL 99

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)