Ligand profile

1EU

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

Bound to: VK055_4030 — DNA topoisomerase IV, B subunit

Via homolog PDB 3fv5 UniProt P20083 Formula C₁₇H₁₇N₅O₂
Mol. weight 323.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1EU
PDB
3fv5
UniProt (similar protein)
P20083
Target protein
VK055_4030

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 323.36 Da
LogP (Crippen) 2.97
H-bond donors 3
H-bond acceptors 4
TPSA 99.77 Ų
Rotatable bonds 4
Aromatic rings 3 / 3
Heavy atoms 24
Fraction sp³ C 0.18
Formula C₁₇H₁₇N₅O₂

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 99.8
  • −1 ≤ LogP ≤ 5 2.97
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 323.4
  • LogP ≤ 5 2.97
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 99.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCNC(=O)Nc1[nH]c2cc(cc(c2n1)C(=O)C)c3cccnc3
InChI 
InChI=1S/C17H17N5O2/c1-3-19-17(24)22-16-20-14-8-12(11-5-4-6-18-9-11)7-13(10(2)23)15(14)21-16/h4-9H,3H2,1-2H3,(H3,19,20,21,22,24)
InChIKey 
KDHATIBQZJAMKQ-UHFFFAOYSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF02518

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)