Ligand profile

CHEMBL4858461

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_0072 — holliday junction DNA helicase RuvB

Via homolog UniProt P55072 Formula C₂₈H₂₆BN₅O₄
pchembl 7.24 ~57.5 nM
Mol. weight 507.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL4858461
UniProt (similar protein)
P55072
pchembl
7.240 (~57.5 nM)
Target protein
VK055_0072

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 507.36 Da
LogP (Crippen) 3.35
H-bond donors 4
H-bond acceptors 8
TPSA 125.44 Ų
Rotatable bonds 7
Aromatic rings 5 / 6
Heavy atoms 38
Fraction sp³ C 0.18
Formula C₂₈H₂₆BN₅O₄

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 125.4
  • −1 ≤ LogP ≤ 5 3.35
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 507.4
  • LogP ≤ 5 3.35
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 125.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc2c(NC(=O)c3ccco3)cccc2n1-c1nc2c(c(NCc3cccc(B(O)O)c3)n1)CCC2
InChI 
InChI=1S/C28H26BN5O4/c1-17-14-21-23(31-27(35)25-12-5-13-38-25)10-4-11-24(21)34(17)28-32-22-9-3-8-20(22)26(33-28)30-16-18-6-2-7-19(15-18)29(36)37/h2,4-7,10-15,36-37H,3,8-9,16H2,1H3,(H,31,35)(H,30,32,33)
InChIKey 
MPKKRMWUTVZBSM-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)