Ligand profile

CHEMBL4530376

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_0072 — holliday junction DNA helicase RuvB

Via homolog UniProt P55072 Formula C₂₅H₂₅N₅O₂
pchembl 6.89 ~128.8 nM
Mol. weight 427.51 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL4530376
UniProt (similar protein)
P55072
pchembl
6.890 (~128.8 nM)
Target protein
VK055_0072

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 427.51 Da
LogP (Crippen) 4.37
H-bond donors 2
H-bond acceptors 6
TPSA 81.07 Ų
Rotatable bonds 5
Aromatic rings 4 / 5
Heavy atoms 32
Fraction sp³ C 0.24
Formula C₂₅H₂₅N₅O₂

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 81.1
  • −1 ≤ LogP ≤ 5 4.37
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 427.5
  • LogP ≤ 5 4.37
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 81.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)Nc1cccc2c1cc(C)n2-c1nc2c(c(NCc3ccccc3)n1)COCC2
InChI 
InChI=1S/C25H25N5O2/c1-16-13-19-21(27-17(2)31)9-6-10-23(19)30(16)25-28-22-11-12-32-15-20(22)24(29-25)26-14-18-7-4-3-5-8-18/h3-10,13H,11-12,14-15H2,1-2H3,(H,27,31)(H,26,28,29)
InChIKey 
PZNIQGLCFGPNCA-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
Curation
pdb_similarity_tanimoto
Binding sites
PF00004' 'PF17862

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_0072.

PDB 9

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)