Ligand profile

ZINC58172409

Virtual-screening candidate from ZINC.

Bound to: VK055_0072 — holliday junction DNA helicase RuvB

Via homolog UniProt P55072 Formula C₂₄H₃₁FN₄O
Tanimoto 0.74
Mol. weight 410.54 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC58172409
UniProt (similar protein)
P55072
Tanimoto
0.744
Target protein
VK055_0072

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 410.54 Da
LogP (Crippen) 3.97
H-bond donors 1
H-bond acceptors 4
TPSA 38.82 Ų
Rotatable bonds 5
Aromatic rings 2 / 4
Heavy atoms 30
Fraction sp³ C 0.46
Formula C₂₄H₃₁FN₄O

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 38.8
  • −1 ≤ LogP ≤ 5 3.97
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 410.5
  • LogP ≤ 5 3.97
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 38.8
PAINS Alert

Matches PAINS filter: anil_di_alk_A(478). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(CN1CCN(c2ccc(F)cc2)CC1)Nc1ccc(N2CCCCCC2)cc1
InChI 
InChI=1S/C24H31FN4O/c25-20-5-9-22(10-6-20)29-17-15-27(16-18-29)19-24(30)26-21-7-11-23(12-8-21)28-13-3-1-2-4-14-28/h5-12H,1-4,13-19H2,(H,26,30)
InChIKey 
MSNXRCCBXNQODS-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
EJQ
Homolog
P55072

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 100

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)