Ligand profile

920

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 4ksg UniProt Q839Z1 Formula C₂₃H₂₅FN₈O
Mol. weight 448.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
920
PDB
4ksg
UniProt (similar protein)
Q839Z1
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 448.51 Da
LogP (Crippen) 3.36
H-bond donors 3
H-bond acceptors 8
TPSA 117.87 Ų
Rotatable bonds 4
Aromatic rings 4 / 6
Heavy atoms 33
Fraction sp³ C 0.39
Formula C₂₃H₂₅FN₈O

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 117.9
  • −1 ≤ LogP ≤ 5 3.36
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 448.5
  • LogP ≤ 5 3.36
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 117.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ncc(cn1)Oc2nc3c(c4cc(cc(c4[nH]3)NC)F)c(n2)N5C[C@@H]6[C@@H](C[C@@]6(C5)C)N
InChI 
InChI=1S/C23H25FN8O/c1-11-27-7-13(8-28-11)33-22-30-20-18(14-4-12(24)5-17(26-3)19(14)29-20)21(31-22)32-9-15-16(25)6-23(15,2)10-32/h4-5,7-8,15-16,26H,6,9-10,25H2,1-3H3,(H,29,30,31)/t15-,16-,23-/m1/s1
InChIKey 
UYSFLJHCRMWPCF-CKNGIIGNSA-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 KP13_00051.

PDB 87

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

Ligand PDB entry

ChEMBL 100

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)