Ligand profile

TTJ

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

Bound to: VK055_4030 — DNA topoisomerase IV, B subunit

Via homolog PDB 5bod UniProt Q8DQB5 Formula C₁₆H₁₉N₃O₃
Mol. weight 301.35 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TTJ
PDB
5bod
UniProt (similar protein)
Q8DQB5
Target protein
VK055_4030

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 301.35 Da
LogP (Crippen) 2.05
H-bond donors 2
H-bond acceptors 4
TPSA 76.24 Ų
Rotatable bonds 3
Aromatic rings 2 / 3
Heavy atoms 22
Fraction sp³ C 0.38
Formula C₁₆H₁₉N₃O₃

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 76.2
  • −1 ≤ LogP ≤ 5 2.05
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 301.3
  • LogP ≤ 5 2.05
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 76.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc(cc(c1)c2cc([nH]n2)NC(=O)[C@H]3COCCO3)C
InChI 
InChI=1S/C16H19N3O3/c1-10-5-11(2)7-12(6-10)13-8-15(19-18-13)17-16(20)14-9-21-3-4-22-14/h5-8,14H,3-4,9H2,1-2H3,(H2,17,18,19,20)/t14-/m1/s1
InChIKey 
IFBWFTQSSMRHQI-CQSZACIVSA-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)