Ligand profile

PNN

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

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

Via homolog PDB 5kmw UniProt Q47066 Formula C₁₆H₁₈N₂O₄S
Mol. weight 334.40 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PNN
PDB
5kmw
UniProt (similar protein)
Q47066
Target protein
KP13_03128

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 334.40 Da
LogP (Crippen) 0.86
H-bond donors 2
H-bond acceptors 4
TPSA 86.71 Ų
Rotatable bonds 4
Aromatic rings 1 / 3
Heavy atoms 23
Fraction sp³ C 0.44
Formula C₁₆H₁₈N₂O₄S

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 86.7
  • −1 ≤ LogP ≤ 5 0.86
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 334.4
  • LogP ≤ 5 0.86
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 86.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1([C@@H](N2[C@H](S1)[C@@H](C2=O)NC(=O)Cc3ccccc3)C(=O)O)C
InChI 
InChI=1S/C16H18N2O4S/c1-16(2)12(15(21)22)18-13(20)11(14(18)23-16)17-10(19)8-9-6-4-3-5-7-9/h3-7,11-12,14H,8H2,1-2H3,(H,17,19)(H,21,22)/t11-,12+,14-/m1/s1
InChIKey 
JGSARLDLIJGVTE-MBNYWOFBSA-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
PF00144' 'PF00905' '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)