Ligand profile

CHEMBL5937029

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_0072 — holliday junction DNA helicase RuvB

Via homolog UniProt P55072 Formula C₂₉H₄₀FN₅
pchembl 7.60 ~25.1 nM
Mol. weight 477.67 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL5937029
UniProt (similar protein)
P55072
pchembl
7.600 (~25.1 nM)
Target protein
VK055_0072

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 477.67 Da
LogP (Crippen) 4.87
H-bond donors 2
H-bond acceptors 4
TPSA 37.54 Ų
Rotatable bonds 7
Aromatic rings 3 / 5
Heavy atoms 35
Fraction sp³ C 0.52
Formula C₂₉H₄₀FN₅

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 37.5
  • −1 ≤ LogP ≤ 5 4.87
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 477.7
  • LogP ≤ 5 4.87
  • 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 
Cc1ccc(N2CCC(NCCN3CCN(C(C)C)CC3)CC2)cc1-c1cc2cc(F)ccc2[nH]1
InChI 
InChI=1S/C29H40FN5/c1-21(2)34-16-14-33(15-17-34)13-10-31-25-8-11-35(12-9-25)26-6-4-22(3)27(20-26)29-19-23-18-24(30)5-7-28(23)32-29/h4-7,18-21,25,31-32H,8-17H2,1-3H3
InChIKey 
HEDJVQKFOJQGMA-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
1138705
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)