Ligand profile

CHEMBL5893353

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_0072 — holliday junction DNA helicase RuvB

Via homolog UniProt P55072 Formula C₃₀H₄₀N₆
pchembl 7.07 ~85.1 nM
Mol. weight 484.69 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL5893353
UniProt (similar protein)
P55072
pchembl
7.070 (~85.1 nM)
Target protein
VK055_0072

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 484.69 Da
LogP (Crippen) 4.60
H-bond donors 2
H-bond acceptors 5
TPSA 61.33 Ų
Rotatable bonds 7
Aromatic rings 3 / 5
Heavy atoms 36
Fraction sp³ C 0.50
Formula C₃₀H₄₀N₆

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 61.3
  • −1 ≤ LogP ≤ 5 4.60
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 484.7
  • LogP ≤ 5 4.60
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 61.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ccc(N2CCC(NCCN3CCN(C(C)C)CC3)CC2)cc1-c1cc2cc(C#N)ccc2[nH]1
InChI 
InChI=1S/C30H40N6/c1-22(2)35-16-14-34(15-17-35)13-10-32-26-8-11-36(12-9-26)27-6-4-23(3)28(20-27)30-19-25-18-24(21-31)5-7-29(25)33-30/h4-7,18-20,22,26,32-33H,8-17H2,1-3H3
InChIKey 
SHWDUHXDNIGOOM-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
1138723
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)