Ligand profile

CHEMBL5931306

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_0072 — holliday junction DNA helicase RuvB

Via homolog UniProt P55072 Formula C₂₈H₃₈ClN₅
pchembl 6.92 ~120.2 nM
Mol. weight 480.10 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL5931306
UniProt (similar protein)
P55072
pchembl
6.920 (~120.2 nM)
Target protein
VK055_0072

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 480.10 Da
LogP (Crippen) 5.07
H-bond donors 2
H-bond acceptors 4
TPSA 37.54 Ų
Rotatable bonds 7
Aromatic rings 3 / 5
Heavy atoms 34
Fraction sp³ C 0.50
Formula C₂₈H₃₈ClN₅

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 37.5
  • −1 ≤ LogP ≤ 5 5.07
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 480.1
  • LogP ≤ 5 5.07
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 37.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)N1CCN(CCNC2CCN(c3cccc(-c4cc5cc(Cl)ccc5[nH]4)c3)CC2)CC1
InChI 
InChI=1S/C28H38ClN5/c1-21(2)33-16-14-32(15-17-33)13-10-30-25-8-11-34(12-9-25)26-5-3-4-22(19-26)28-20-23-18-24(29)6-7-27(23)31-28/h3-7,18-21,25,30-31H,8-17H2,1-2H3
InChIKey 
YAYNZYDUVRYTBQ-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
Activity
1138741
Curation
pdb_similarity_tanimoto
Binding sites
PF00004

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)