Ligand profile

LSI

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

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

Via homolog PDB 5ujo UniProt Q9L5C8 Formula C₂₂H₂₂N₂O₅RuS
Mol. weight 527.56 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
LSI
PDB
5ujo
UniProt (similar protein)
Q9L5C8
Target protein
KP13_03128

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 527.56 Da
LogP (Crippen) 2.85
H-bond donors 2
H-bond acceptors 5
TPSA 103.78 Ų
Rotatable bonds 6
Aromatic rings 0 / 12
Heavy atoms 31
Fraction sp³ C 0.73
Formula C₂₂H₂₂N₂O₅RuS

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 103.8
  • −1 ≤ LogP ≤ 5 2.85
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 527.6
  • LogP ≤ 5 2.85
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 103.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=C(N2[C@@H]([C@@H](C2=O)NC(=O)CCC(=O)C34C5[Ru]3678923(C5C6C74)C4C8C9C2C34)SC1)C(=O)O
InChI 
InChI=1S/C17H17N2O5S.C5H5.Ru/c1-9-8-25-16-13(15(22)19(16)14(9)17(23)24)18-12(21)7-6-11(20)10-4-2-3-5-10;1-2-4-5-3-1;/h2-5,13,16H,6-8H2,1H3,(H,18,21)(H,23,24);1-5H;/t13-,16-;;/m1../s1
InChIKey 
VVYXHQVDQWFSGH-DRUSRECESA-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)