Ligand profile

CHEMBL3746912

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_0072 — holliday junction DNA helicase RuvB

Via homolog UniProt P55072 Formula C₂₃H₂₀N₆O
pchembl 6.96 ~109.6 nM
Mol. weight 396.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3746912
UniProt (similar protein)
P55072
pchembl
6.960 (~109.6 nM)
Target protein
VK055_0072

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 396.45 Da
LogP (Crippen) 4.17
H-bond donors 2
H-bond acceptors 7
TPSA 90.88 Ų
Rotatable bonds 5
Aromatic rings 5 / 5
Heavy atoms 30
Fraction sp³ C 0.09
Formula C₂₃H₂₀N₆O

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 90.9
  • −1 ≤ LogP ≤ 5 4.17
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 396.5
  • LogP ≤ 5 4.17
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 90.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1cccc2c(NCc3ccccc3)nc(-n3c(N)nc4ccccc43)nc12
InChI 
InChI=1S/C23H20N6O/c1-30-19-13-7-10-16-20(19)27-23(28-21(16)25-14-15-8-3-2-4-9-15)29-18-12-6-5-11-17(18)26-22(29)24/h2-13H,14H2,1H3,(H2,24,26)(H,25,27,28)
InChIKey 
NHAMBLRUUJAFOY-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)