Ligand profile

PNK

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

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

Via homolog PDB 3hvf UniProt Q9L5C8 Formula C₁₆H₂₀N₂O₅S
Mol. weight 352.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PNK
PDB
3hvf
UniProt (similar protein)
Q9L5C8
Target protein
KP13_03128

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 352.41 Da
LogP (Crippen) 0.69
H-bond donors 4
H-bond acceptors 5
TPSA 115.73 Ų
Rotatable bonds 6
Aromatic rings 1 / 2
Heavy atoms 24
Fraction sp³ C 0.44
Formula C₁₆H₂₀N₂O₅S

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

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 115.7
  • −1 ≤ LogP ≤ 5 0.69
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 352.4
  • LogP ≤ 5 0.69
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 115.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1([C@@H](N[C@H](S1)[C@@H](C(=O)O)NC(=O)Cc2ccccc2)C(=O)O)C
InChI 
InChI=1S/C16H20N2O5S/c1-16(2)12(15(22)23)18-13(24-16)11(14(20)21)17-10(19)8-9-6-4-3-5-7-9/h3-7,11-13,18H,8H2,1-2H3,(H,17,19)(H,20,21)(H,22,23)/t11-,12-,13+/m0/s1
InChIKey 
HCYWNSXLUZRKJX-RWMBFGLXSA-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
PF00144' '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)