Ligand profile

2B7

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

Bound to: VK055_4030 — DNA topoisomerase IV, B subunit

Via homolog PDB 4mot UniProt Q8DQB5 Formula C₂₀H₂₃N₅O₂S
Mol. weight 397.50 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2B7
PDB
4mot
UniProt (similar protein)
Q8DQB5
Target protein
VK055_4030

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 397.50 Da
LogP (Crippen) 3.87
H-bond donors 2
H-bond acceptors 6
TPSA 88.91 Ų
Rotatable bonds 7
Aromatic rings 3 / 3
Heavy atoms 28
Fraction sp³ C 0.30
Formula C₂₀H₂₃N₅O₂S

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 88.9
  • −1 ≤ LogP ≤ 5 3.87
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 397.5
  • LogP ≤ 5 3.87
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 88.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)CCN1c2c(nc(s2)NC(=O)NCC=C)C=C(C1=O)c3cccnc3
InChI 
InChI=1S/C20H23N5O2S/c1-4-8-22-19(27)24-20-23-16-11-15(14-6-5-9-21-12-14)17(26)25(18(16)28-20)10-7-13(2)3/h4-6,9,11-13H,1,7-8,10H2,2-3H3,(H2,22,23,24,27)
InChIKey 
HDSYKPYXRVXIRI-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
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)