Ligand profile

TDJ

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

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

Via homolog PDB 6vnu UniProt Q9L5C7 Formula C₂₂H₁₃N₂O₆RuS
Mol. weight 534.49 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TDJ
PDB
6vnu
UniProt (similar protein)
Q9L5C7
Target protein
KP13_03128

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 534.49 Da
LogP (Crippen) 0.51
H-bond donors 3
H-bond acceptors 6
TPSA 133.13 Ų
Rotatable bonds 8
Aromatic rings 0 / 11
Heavy atoms 32
Fraction sp³ C 0.27
Formula C₂₂H₁₃N₂O₆RuS

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 133.1
  • −1 ≤ LogP ≤ 5 0.51
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 534.5
  • LogP ≤ 5 0.51
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 133.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C=C1CS[C@@H](N=C1C(=O)O)[C@@H](C(=O)O)NC(=O)CCC(=O)C23[C]4[Ru]2567891([C]4[C]5[C]63)[C]2[C]7[C]8[C]9[C]12
InChI 
InChI=1S/C17H13N2O6S.C5.Ru/c1-9-8-26-15(19-13(9)16(22)23)14(17(24)25)18-12(21)7-6-11(20)10-4-2-3-5-10;1-2-4-5-3-1;/h14-15H,1,6-8H2,(H,18,21)(H,22,23)(H,24,25);;/t14-,15+;;/m0../s1
InChIKey 
XRLHOTFPNKFIOM-FZMMWMHASA-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)