Ligand profile

2GK

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

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

Via homolog PDB 4len UniProt Q9L5C8 Formula C₁₁H₉BO₄S
Mol. weight 248.07 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2GK
PDB
4len
UniProt (similar protein)
Q9L5C8
Target protein
KP13_03128

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 248.07 Da
LogP (Crippen) 0.68
H-bond donors 3
H-bond acceptors 4
TPSA 77.76 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 17
Fraction sp³ C 0.00
Formula C₁₁H₉BO₄S

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 77.8
  • −1 ≤ LogP ≤ 5 0.68
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 248.1
  • LogP ≤ 5 0.68
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 77.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
B(c1c(c2ccccc2s1)/C=C/C(=O)O)(O)O
InChI 
InChI=1S/C11H9BO4S/c13-10(14)6-5-8-7-3-1-2-4-9(7)17-11(8)12(15)16/h1-6,15-16H,(H,13,14)/b6-5+
InChIKey 
IYRVQPJBSDCZBO-AATRIKPKSA-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)