Ligand profile

TR6

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

Bound to: KP13_00955 — DNA gyrase subunit A

Via homolog PDB 4z2e UniProt Q8DPM2 Formula C₂₀H₁₅F₃N₄O₃
Mol. weight 416.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TR6
PDB
4z2e
UniProt (similar protein)
Q8DPM2
Target protein
KP13_00955

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 416.36 Da
LogP (Crippen) 1.89
H-bond donors 2
H-bond acceptors 6
TPSA 101.45 Ų
Rotatable bonds 3
Aromatic rings 3 / 5
Heavy atoms 30
Fraction sp³ C 0.25
Formula C₂₀H₁₅F₃N₄O₃

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 101.5
  • −1 ≤ LogP ≤ 5 1.89
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 416.4
  • LogP ≤ 5 1.89
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 101.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(c(cc1F)F)N2C=C(C(=O)c3c2nc(c(c3)F)N4C[C@@H]5[C@H](C4)C5N)C(=O)O
InChI 
InChI=1S/C20H15F3N4O3/c21-8-1-2-15(13(22)3-8)27-7-12(20(29)30)17(28)9-4-14(23)19(25-18(9)27)26-5-10-11(6-26)16(10)24/h1-4,7,10-11,16H,5-6,24H2,(H,29,30)/t10-,11+,16?
InChIKey 
WVPSKSLAZQPAKQ-SOSAQKQKSA-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 KP13_00955.

PDB 24

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

Ligand PDB entry

ChEMBL 16

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)