Ligand profile

PDQ

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_4030 — DNA topoisomerase IV, B subunit

Via homolog PDB 3ltn UniProt Q59961 Formula C₁₈H₂₄FN₅O₂
Mol. weight 361.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PDQ
PDB
3ltn
UniProt (similar protein)
Q59961
Target protein
VK055_4030

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 361.42 Da
LogP (Crippen) 0.83
H-bond donors 2
H-bond acceptors 7
TPSA 99.28 Ų
Rotatable bonds 3
Aromatic rings 2 / 4
Heavy atoms 26
Fraction sp³ C 0.56
Formula C₁₈H₂₄FN₅O₂

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 99.3
  • −1 ≤ LogP ≤ 5 0.83
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 361.4
  • LogP ≤ 5 0.83
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 99.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c2c(cc(c1N3CC[C@H](C3)[C@H](C)N)F)C(=O)N(C(=O)N2C4CC4)N
InChI 
InChI=1S/C18H24FN5O2/c1-9-15-13(17(25)24(21)18(26)23(15)12-3-4-12)7-14(19)16(9)22-6-5-11(8-22)10(2)20/h7,10-12H,3-6,8,20-21H2,1-2H3/t10-,11+/m0/s1
InChIKey 
SMONLCFJGCJROJ-WDEREUQCSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00521' 'PF01751

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_4030.

PDB 19

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 18

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)