Ligand profile

DN6

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

Bound to: KP13_03128 — Beta-lactamase CTX-M-2

Via homolog PDB 4ddy UniProt Q9L5C8 Formula C₁₅H₁₀F₃N₅O
Mol. weight 333.27 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DN6
PDB
4ddy
UniProt (similar protein)
Q9L5C8
Target protein
KP13_03128

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 333.27 Da
LogP (Crippen) 3.14
H-bond donors 2
H-bond acceptors 4
TPSA 83.56 Ų
Rotatable bonds 3
Aromatic rings 3 / 3
Heavy atoms 24
Fraction sp³ C 0.07
Formula C₁₅H₁₀F₃N₅O

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 83.6
  • −1 ≤ LogP ≤ 5 3.14
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 333.3
  • LogP ≤ 5 3.14
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 83.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(cc(c1)NC(=O)c2cccc(c2)C(F)(F)F)c3[nH]nnn3
InChI 
InChI=1S/C15H10F3N5O/c16-15(17,18)11-5-1-4-10(7-11)14(24)19-12-6-2-3-9(8-12)13-20-22-23-21-13/h1-8H,(H,19,24)(H,20,21,22,23)
InChIKey 
DVYVZPGHRBVPAG-UHFFFAOYSA-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
PF13354

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_03128.

PDB 51

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

Ligand PDB entry

ChEMBL 6

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)