Ligand profile

CHEMBL5780988

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_0072 — holliday junction DNA helicase RuvB

Via homolog UniProt P55072 Formula C₂₈H₃₉N₅O
pchembl 7.00 ~100.0 nM
Mol. weight 461.65 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL5780988
UniProt (similar protein)
P55072
pchembl
7.000 (~100.0 nM)
Target protein
VK055_0072

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 461.65 Da
LogP (Crippen) 4.12
H-bond donors 3
H-bond acceptors 5
TPSA 57.77 Ų
Rotatable bonds 7
Aromatic rings 3 / 5
Heavy atoms 34
Fraction sp³ C 0.50
Formula C₂₈H₃₉N₅O

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 57.8
  • −1 ≤ LogP ≤ 5 4.12
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 461.7
  • LogP ≤ 5 4.12
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 57.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)N1CCN(CCNC2CCN(c3cccc(-c4cc5cc(O)ccc5[nH]4)c3)CC2)CC1
InChI 
InChI=1S/C28H39N5O/c1-21(2)32-16-14-31(15-17-32)13-10-29-24-8-11-33(12-9-24)25-5-3-4-22(18-25)28-20-23-19-26(34)6-7-27(23)30-28/h3-7,18-21,24,29-30,34H,8-17H2,1-2H3
InChIKey 
SKDFZRUGWNQTPN-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
1138729
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)