Ligand profile

CHEMBL4205402

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_1238 — exodeoxyribonuclease III

Via homolog UniProt P27695 Formula C₃₂H₄₂N₆
pchembl 7.24 ~57.5 nM
Mol. weight 510.73 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL4205402
UniProt (similar protein)
P27695
pchembl
7.240 (~57.5 nM)
Target protein
VK055_1238

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 510.73 Da
LogP (Crippen) 3.24
H-bond donors 6
H-bond acceptors 6
TPSA 72.18 Ų
Rotatable bonds 0
Aromatic rings 4 / 5
Heavy atoms 38
Fraction sp³ C 0.38
Formula C₃₂H₄₂N₆

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 72.2
  • −1 ≤ LogP ≤ 5 3.24
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 510.7
  • LogP ≤ 5 3.24
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 72.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc2ccc3cc2cc1CNCCNCCNCc1ccc2ccc(cc2c1)CNCCNCCNC3
InChI 
InChI=1S/C32H42N6/c1-5-29-6-2-26-18-31(29)17-25(1)21-35-13-9-33-10-14-37-23-27-3-7-30-8-4-28(20-32(30)19-27)24-38-16-12-34-11-15-36-22-26/h1-8,17-20,33-38H,9-16,21-24H2
InChIKey 
GOBPKVITNWSXKL-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)