Ligand profile

CHEMBL3746179

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_0072 — holliday junction DNA helicase RuvB

Via homolog UniProt P55072 Formula C₂₄H₂₃N₉
pchembl 7.82 ~15.1 nM
Mol. weight 437.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3746179
UniProt (similar protein)
P55072
pchembl
7.820 (~15.1 nM)
Target protein
VK055_0072

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 437.51 Da
LogP (Crippen) 3.17
H-bond donors 3
H-bond acceptors 8
TPSA 109.23 Ų
Rotatable bonds 5
Aromatic rings 5 / 6
Heavy atoms 33
Fraction sp³ C 0.21
Formula C₂₄H₂₃N₉

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 109.2
  • −1 ≤ LogP ≤ 5 3.17
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 437.5
  • LogP ≤ 5 3.17
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 109.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc2c(-c3nnn[nH]3)cccc2n1-c1nc2c(c(NCc3ccccc3)n1)CNCC2
InChI 
InChI=1S/C24H23N9/c1-15-12-18-17(23-29-31-32-30-23)8-5-9-21(18)33(15)24-27-20-10-11-25-14-19(20)22(28-24)26-13-16-6-3-2-4-7-16/h2-9,12,25H,10-11,13-14H2,1H3,(H,26,27,28)(H,29,30,31,32)
InChIKey 
QYBPGHMDCTUFOJ-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)