Ligand profile

IM2

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

Bound to: VK055_0891 — beta-lactamase SHV-24

Via homolog PDB 1bt5 UniProt P62593 Formula C₁₂H₁₉N₃O₄S
Mol. weight 301.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
IM2
PDB
1bt5
UniProt (similar protein)
P62593
Target protein
VK055_0891

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 301.37 Da
LogP (Crippen) -0.23
H-bond donors 5
H-bond acceptors 6
TPSA 122.51 Ų
Rotatable bonds 9
Aromatic rings 0 / 1
Heavy atoms 20
Fraction sp³ C 0.58
Formula C₁₂H₁₉N₃O₄S

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 122.5
  • −1 ≤ LogP ≤ 5 -0.23
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 301.4
  • LogP ≤ 5 -0.23
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 122.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[H]/N=C/NCCSC1=C(N[C@H](C1)[C@H](C=O)[C@@H](C)O)C(=O)O
InChI 
InChI=1S/C12H19N3O4S/c1-7(17)8(5-16)9-4-10(11(15-9)12(18)19)20-3-2-14-6-13/h5-9,15,17H,2-4H2,1H3,(H2,13,14)(H,18,19)/t7-,8-,9-/m1/s1
InChIKey 
UACUABDJLSUFFC-IWSPIJDZSA-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 VK055_0891.

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)