Ligand profile

GFN

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

Bound to: KP13_00955 — DNA gyrase subunit A

Via homolog PDB 5btd UniProt P9WG47 Formula C₁₉H₂₂FN₃O₄
Mol. weight 375.40 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GFN
PDB
5btd
UniProt (similar protein)
P9WG47
Target protein
KP13_00955

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 375.40 Da
LogP (Crippen) 1.98
H-bond donors 2
H-bond acceptors 6
TPSA 83.80 Ų
Rotatable bonds 4
Aromatic rings 2 / 4
Heavy atoms 27
Fraction sp³ C 0.47
Formula C₁₉H₂₂FN₃O₄

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 83.8
  • −1 ≤ LogP ≤ 5 1.98
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 375.4
  • LogP ≤ 5 1.98
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 83.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]1CN(CCN1)c2c(cc3c(c2OC)N(C=C(C3=O)C(=O)O)C4CC4)F
InChI 
InChI=1S/C19H22FN3O4/c1-10-8-22(6-5-21-10)16-14(20)7-12-15(18(16)27-2)23(11-3-4-11)9-13(17(12)24)19(25)26/h7,9-11,21H,3-6,8H2,1-2H3,(H,25,26)/t10-/m0/s1
InChIKey 
XUBOMFCQGDBHNK-JTQLQIEISA-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)