Ligand profile

CHEMBL3747647

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_0072 — holliday junction DNA helicase RuvB

Via homolog UniProt P55072 Formula C₂₄H₂₄N₆O
pchembl 7.40 ~39.8 nM
Mol. weight 412.50 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3747647
UniProt (similar protein)
P55072
pchembl
7.400 (~39.8 nM)
Target protein
VK055_0072

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 412.50 Da
LogP (Crippen) 3.09
H-bond donors 3
H-bond acceptors 6
TPSA 97.86 Ų
Rotatable bonds 5
Aromatic rings 4 / 5
Heavy atoms 31
Fraction sp³ C 0.21
Formula C₂₄H₂₄N₆O

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 97.9
  • −1 ≤ LogP ≤ 5 3.09
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 412.5
  • LogP ≤ 5 3.09
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 97.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc2c(C(N)=O)cccc2n1-c1nc2c(c(NCc3ccccc3)n1)CNCC2
InChI 
InChI=1S/C24H24N6O/c1-15-12-18-17(22(25)31)8-5-9-21(18)30(15)24-28-20-10-11-26-14-19(20)23(29-24)27-13-16-6-3-2-4-7-16/h2-9,12,26H,10-11,13-14H2,1H3,(H2,25,31)(H,27,28,29)
InChIKey 
JYYSDZNVELJCGG-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)