Ligand profile

CHEMBL1256924

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_4925 — apurinic endonuclease family protein

Via homolog UniProt P0A6C1 Formula C₂₉H₃₈N₄O₆
pchembl 6.00 ~1.0 µM
Mol. weight 538.65 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL1256924
UniProt (similar protein)
P0A6C1
pchembl
6.000 (~1.0 µM)
Target protein
VK055_4925

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 538.65 Da
LogP (Crippen) 3.54
H-bond donors 2
H-bond acceptors 7
TPSA 123.51 Ų
Rotatable bonds 9
Aromatic rings 2 / 4
Heavy atoms 39
Fraction sp³ C 0.45
Formula C₂₉H₃₈N₄O₆

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 123.5
  • −1 ≤ LogP ≤ 5 3.54
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 538.6
  • LogP ≤ 5 3.54
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 123.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccccc1N1CCN(CCN(C(=O)C2CCCCC2)c2ccccn2)CC1.O=C(O)/C=C\C(=O)O
InChI 
InChI=1S/C25H34N4O2.C4H4O4/c1-31-23-12-6-5-11-22(23)28-18-15-27(16-19-28)17-20-29(24-13-7-8-14-26-24)25(30)21-9-3-2-4-10-21;5-3(6)1-2-4(7)8/h5-8,11-14,21H,2-4,9-10,15-20H2,1H3;1-2H,(H,5,6)(H,7,8)/b;2-1-
InChIKey 
XIGAHNVCEFUYOV-BTJKTKAUSA-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)