Ligand profile

5VR

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

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

Via homolog PDB 5fa7 UniProt Q9EXV5 Formula C₉H₁₆N₄O₇S
Mol. weight 324.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5VR
PDB
5fa7
UniProt (similar protein)
Q9EXV5
Target protein
KP13_03128

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 324.31 Da
LogP (Crippen) -2.53
H-bond donors 4
H-bond acceptors 7
TPSA 154.14 Ų
Rotatable bonds 5
Aromatic rings 0 / 1
Heavy atoms 21
Fraction sp³ C 0.67
Formula C₉H₁₆N₄O₇S

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 154.1
  • −1 ≤ LogP ≤ 5 -2.53
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 324.3
  • LogP ≤ 5 -2.53
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 154.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)NNC(=O)[C@@H]1CC[C@H](CN1C=O)NOS(=O)(=O)O
InChI 
InChI=1S/C9H16N4O7S/c1-6(15)10-11-9(16)8-3-2-7(4-13(8)5-14)12-20-21(17,18)19/h5,7-8,12H,2-4H2,1H3,(H,10,15)(H,11,16)(H,17,18,19)/t7-,8+/m1/s1
InChIKey 
XVXACCGCTLPGSZ-SFYZADRCSA-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)