Ligand profile

LRY

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

Bound to: KP13_03217 — putative N-acetylmannosamine-6-phosphate 2-epimerase

Via homolog PDB 4utu UniProt Q8XNZ3 Formula C₈H₁₆NO₉P
Mol. weight 301.19 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
LRY
PDB
4utu
UniProt (similar protein)
Q8XNZ3
Target protein
KP13_03217

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 301.19 Da
LogP (Crippen) -3.12
H-bond donors 6
H-bond acceptors 7
TPSA 173.62 Ų
Rotatable bonds 8
Aromatic rings 0 / 0
Heavy atoms 19
Fraction sp³ C 0.75
Formula C₈H₁₆NO₉P

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 173.6
  • −1 ≤ LogP ≤ 5 -3.12
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 301.2
  • LogP ≤ 5 -3.12
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 173.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)N[C@H](C=O)[C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
InChI 
InChI=1S/C8H16NO9P/c1-4(11)9-5(2-10)7(13)8(14)6(12)3-18-19(15,16)17/h2,5-8,12-14H,3H2,1H3,(H,9,11)(H2,15,16,17)/t5-,6-,7-,8-/m1/s1
InChIKey 
QDSLHWJDSQGPEE-WCTZXXKLSA-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
PF04131

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_03217.

PDB 3

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)