Ligand profile

LN1

Ligand co-crystallized with this exact protein (Protein Data Bank).

Bound to: KP13_32248 — Beta-lactamase SHV-12

Direct evidence PDB 3d4f UniProt P0AD64 Formula C₂₂H₂₂N₂O₉S
Mol. weight 490.49 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
LN1
PDB
3d4f
UniProt (this protein)
P0AD64
Target protein
KP13_32248

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 490.49 Da
LogP (Crippen) 1.79
H-bond donors 5
H-bond acceptors 9
TPSA 174.87 Ų
Rotatable bonds 10
Aromatic rings 3 / 3
Heavy atoms 34
Fraction sp³ C 0.23
Formula C₂₂H₂₂N₂O₉S

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 174.9
  • −1 ≤ LogP ≤ 5 1.79
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 490.5
  • LogP ≤ 5 1.79
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 174.9
PAINS Alert

Matches PAINS filter: catechol_A(92). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@](COC(=O)Cc1ccc(c(c1)O)O)([C@H](C(=O)O)Nc2c(cc3n2cccc3)C=O)[S@@](=O)O
InChI 
InChI=1S/C22H22N2O9S/c1-22(34(31)32,12-33-18(28)9-13-5-6-16(26)17(27)8-13)19(21(29)30)23-20-14(11-25)10-15-4-2-3-7-24(15)20/h2-8,10-11,19,23,26-27H,9,12H2,1H3,(H,29,30)(H,31,32)/t19-,22-/m0/s1
InChIKey 
DEOZLEGRVHDNKC-UGKGYDQZSA-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' '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_32248.

PDB 43

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)