Ligand profile

CHEMBL5946783

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_0072 — holliday junction DNA helicase RuvB

Via homolog UniProt P55072 Formula C₂₈H₃₉N₅
pchembl 6.85 ~141.3 nM
Mol. weight 445.66 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL5946783
UniProt (similar protein)
P55072
pchembl
6.850 (~141.3 nM)
Target protein
VK055_0072

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 445.66 Da
LogP (Crippen) 4.42
H-bond donors 2
H-bond acceptors 4
TPSA 37.54 Ų
Rotatable bonds 6
Aromatic rings 3 / 5
Heavy atoms 33
Fraction sp³ C 0.50
Formula C₂₈H₃₉N₅

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 4.42
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 445.7
  • LogP ≤ 5 4.42
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 37.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1CN(CCNC2CCN(c3cccc(-c4cc5ccccc5[nH]4)c3)CC2)C[C@H](C)N1C
InChI 
InChI=1S/C28H39N5/c1-21-19-32(20-22(2)31(21)3)16-13-29-25-11-14-33(15-12-25)26-9-6-8-23(17-26)28-18-24-7-4-5-10-27(24)30-28/h4-10,17-18,21-22,25,29-30H,11-16,19-20H2,1-3H3/t21-,22+
InChIKey 
PBAUKVCKKCMRSU-SZPZYZBQSA-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
1138661
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)