Ligand profile

DN3

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

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

Via homolog PDB 4de2 UniProt Q9L5C8 Formula C₁₇H₁₈N₆O
Mol. weight 322.37 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DN3
PDB
4de2
UniProt (similar protein)
Q9L5C8
Target protein
KP13_03128

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 322.37 Da
LogP (Crippen) 2.18
H-bond donors 2
H-bond acceptors 5
TPSA 86.80 Ų
Rotatable bonds 5
Aromatic rings 3 / 3
Heavy atoms 24
Fraction sp³ C 0.18
Formula C₁₇H₁₈N₆O

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 86.8
  • −1 ≤ LogP ≤ 5 2.18
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 322.4
  • LogP ≤ 5 2.18
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 86.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN(C)Cc1cccc(c1)C(=O)Nc2cccc(c2)c3[nH]nnn3
InChI 
InChI=1S/C17H18N6O/c1-23(2)11-12-5-3-7-14(9-12)17(24)18-15-8-4-6-13(10-15)16-19-21-22-20-16/h3-10H,11H2,1-2H3,(H,18,24)(H,19,20,21,22)
InChIKey 
YNFKRUNLXWQDEZ-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)