Ligand profile

JSD

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

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

Via homolog PDB 4xxr UniProt Q9L5C7 Formula C₂₁H₁₇N₂O₄RuS
Mol. weight 494.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JSD
PDB
4xxr
UniProt (similar protein)
Q9L5C7
Target protein
KP13_03128

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 494.51 Da
LogP (Crippen) 0.80
H-bond donors 3
H-bond acceptors 5
TPSA 95.50 Ų
Rotatable bonds 7
Aromatic rings 0 / 11
Heavy atoms 29
Fraction sp³ C 0.43
Formula C₂₁H₁₇N₂O₄RuS

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 95.5
  • −1 ≤ LogP ≤ 5 0.80
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 494.5
  • LogP ≤ 5 0.80
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 95.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1([C@@H](N[C@H](S1)CNC(=O)CCC(=O)C23[C]4[Ru]2567891([C]4[C]5[C]63)[C]2[C]7[C]8[C]9[C]12)C(=O)O)C
InChI 
InChI=1S/C16H17N2O4S.C5.Ru/c1-16(2)14(15(21)22)18-13(23-16)9-17-12(20)8-7-11(19)10-5-3-4-6-10;1-2-4-5-3-1;/h13-14,18H,7-9H2,1-2H3,(H,17,20)(H,21,22);;/t13-,14+;;/m1../s1
InChIKey 
BXJLSZHFWZUFFQ-BQFBZIMZSA-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)