Ligand profile

9YH

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

Bound to: KP13_05461 — Periplasmic murein peptide-binding protein

Via homolog PDB 5on0 UniProt P33590 Formula C₂₂H₂₈N₂O₆S
Mol. weight 448.54 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
9YH
PDB
5on0
UniProt (similar protein)
P33590
Target protein
KP13_05461

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 448.54 Da
LogP (Crippen) 2.60
H-bond donors 3
H-bond acceptors 7
TPSA 110.54 Ų
Rotatable bonds 13
Aromatic rings 2 / 2
Heavy atoms 31
Fraction sp³ C 0.36
Formula C₂₂H₂₈N₂O₆S

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 110.5
  • −1 ≤ LogP ≤ 5 2.60
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 448.5
  • LogP ≤ 5 2.60
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 110.5
PAINS Alert

Matches PAINS filter: mannich_A(296). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1cccc(c1O)CN(CCN(Cc2ccccc2SC)CC(=O)O)CC(=O)O
InChI 
InChI=1S/C22H28N2O6S/c1-30-18-8-5-7-17(22(18)29)13-24(15-21(27)28)11-10-23(14-20(25)26)12-16-6-3-4-9-19(16)31-2/h3-9,29H,10-15H2,1-2H3,(H,25,26)(H,27,28)
InChIKey 
WFZIZUYYKZMMKQ-UHFFFAOYSA-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
PF00496

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_05461.

PDB 20

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

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)