Ligand profile

MFX

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 5cdq UniProt P66937 Formula C₂₁H₂₄FN₃O₄
Mol. weight 401.44 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MFX
PDB
5cdq
UniProt (similar protein)
P66937
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 401.44 Da
LogP (Crippen) 2.37
H-bond donors 2
H-bond acceptors 6
TPSA 83.80 Ų
Rotatable bonds 4
Aromatic rings 2 / 5
Heavy atoms 29
Fraction sp³ C 0.52
Formula C₂₁H₂₄FN₃O₄

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 2.37
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 401.4
  • LogP ≤ 5 2.37
  • 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 
COc1c2c(cc(c1N3C[C@@H]4CCCN[C@@H]4C3)F)C(=O)C(=CN2C5CC5)C(=O)O
InChI 
InChI=1S/C21H24FN3O4/c1-29-20-17-13(19(26)14(21(27)28)9-25(17)12-4-5-12)7-15(22)18(20)24-8-11-3-2-6-23-16(11)10-24/h7,9,11-12,16,23H,2-6,8,10H2,1H3,(H,27,28)/t11-,16+/m0/s1
InChIKey 
FABPRXSRWADJSP-MEDUHNTESA-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_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)