Ligand profile

CHEMBL4864700

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_0072 — holliday junction DNA helicase RuvB

Via homolog UniProt P55072 Formula C₂₈H₂₄BN₅O₃
pchembl 6.94 ~114.8 nM
Mol. weight 489.34 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL4864700
UniProt (similar protein)
P55072
pchembl
6.940 (~114.8 nM)
Target protein
VK055_0072

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 489.34 Da
LogP (Crippen) 3.14
H-bond donors 4
H-bond acceptors 7
TPSA 112.30 Ų
Rotatable bonds 6
Aromatic rings 5 / 5
Heavy atoms 37
Fraction sp³ C 0.11
Formula C₂₈H₂₄BN₅O₃

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 112.3
  • −1 ≤ LogP ≤ 5 3.14
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 489.3
  • LogP ≤ 5 3.14
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 112.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC#CC(=O)Nc1cccc2c1cc(C)n2-c1nc(NCc2cccc(B(O)O)c2)c2ccccc2n1
InChI 
InChI=1S/C28H24BN5O3/c1-3-8-26(35)31-24-13-7-14-25-22(24)15-18(2)34(25)28-32-23-12-5-4-11-21(23)27(33-28)30-17-19-9-6-10-20(16-19)29(36)37/h4-7,9-16,36-37H,17H2,1-2H3,(H,31,35)(H,30,32,33)
InChIKey 
YDZSZHZXSZVVFH-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)