Ligand profile

SYZ

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

Bound to: KP13_31828 — UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase

Via homolog PDB 7b6n UniProt P22188 Formula C₁₃H₁₄N₂O₃S
Mol. weight 278.33 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SYZ
PDB
7b6n
UniProt (similar protein)
P22188
Target protein
KP13_31828

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 278.33 Da
LogP (Crippen) 1.42
H-bond donors 1
H-bond acceptors 4
TPSA 66.48 Ų
Rotatable bonds 4
Aromatic rings 1 / 2
Heavy atoms 19
Fraction sp³ C 0.31
Formula C₁₃H₁₄N₂O₃S

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 66.5
  • −1 ≤ LogP ≤ 5 1.42
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 278.3
  • LogP ≤ 5 1.42
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 66.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cccc(c1)C(=O)NCCN2C(=O)CSC2=O
InChI 
InChI=1S/C13H14N2O3S/c1-9-3-2-4-10(7-9)12(17)14-5-6-15-11(16)8-19-13(15)18/h2-4,7H,5-6,8H2,1H3,(H,14,17)
InChIKey 
LNKJOLQQLIVVPE-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF08245

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_31828.

PDB 17

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 9

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)