Ligand profile

5HY

Ligand co-crystallized with this exact protein (Protein Data Bank).

Bound to: KP13_05482 — Hydantoin racemase

Direct evidence PDB 3qvl UniProt A6T9E8 Formula C₅H₆N₂O₄
Mol. weight 158.11 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5HY
PDB
3qvl
UniProt (this protein)
A6T9E8
Target protein
KP13_05482

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 158.11 Da
LogP (Crippen) -1.33
H-bond donors 3
H-bond acceptors 3
TPSA 95.50 Ų
Rotatable bonds 2
Aromatic rings 0 / 1
Heavy atoms 11
Fraction sp³ C 0.40
Formula C₅H₆N₂O₄

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 -1.33
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 158.1
  • LogP ≤ 5 -1.33
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 95.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@@H]1C(=O)NC(=O)N1)C(=O)O
InChI 
InChI=1S/C5H6N2O4/c8-3(9)1-2-4(10)7-5(11)6-2/h2H,1H2,(H,8,9)(H2,6,7,10,11)/t2-/m1/s1
InChIKey 
DQQLZADYSWBCOX-UWTATZPHSA-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
PF01177

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_05482.

PDB 1

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

Ligand PDB entry

ZINC 36

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

Compound Similarity (Tanimoto)