Ligand profile

9YK

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

Bound to: KP13_05461 — Periplasmic murein peptide-binding protein

Via homolog PDB 5on1 UniProt P33590 Formula C₂₁H₂₆N₂O₆S
Mol. weight 434.51 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
9YK
PDB
5on1
UniProt (similar protein)
P33590
Target protein
KP13_05461

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 434.51 Da
LogP (Crippen) 2.29
H-bond donors 4
H-bond acceptors 7
TPSA 121.54 Ų
Rotatable bonds 12
Aromatic rings 2 / 2
Heavy atoms 30
Fraction sp³ C 0.33
Formula C₂₁H₂₆N₂O₆S

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 121.5
  • −1 ≤ LogP ≤ 5 2.29
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 434.5
  • LogP ≤ 5 2.29
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 121.5
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 
CSc1ccccc1CN(CCN(Cc2cccc(c2O)O)CC(=O)O)CC(=O)O
InChI 
InChI=1S/C21H26N2O6S/c1-30-18-8-3-2-5-15(18)11-22(13-19(25)26)9-10-23(14-20(27)28)12-16-6-4-7-17(24)21(16)29/h2-8,24,29H,9-14H2,1H3,(H,25,26)(H,27,28)
InChIKey 
CCWNBVUPGJNFLR-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)