Ligand profile

8H8

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 5z9l UniProt P0AES6 Formula C₇H₄FNO
Mol. weight 137.11 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
8H8
PDB
5z9l
UniProt (similar protein)
P0AES6
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 137.11 Da
LogP (Crippen) 1.40
H-bond donors 1
H-bond acceptors 2
TPSA 44.02 Ų
Rotatable bonds 0
Aromatic rings 1 / 1
Heavy atoms 10
Fraction sp³ C 0.00
Formula C₇H₄FNO

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 44.0
  • −1 ≤ LogP ≤ 5 1.40
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 137.1
  • LogP ≤ 5 1.40
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 44.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(c(cc1O)F)C#N
InChI 
InChI=1S/C7H4FNO/c8-7-3-6(10)2-1-5(7)4-9/h1-3,10H
InChIKey 
REIVHYDACHXPNH-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
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)