Ligand profile

5AD

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

Bound to: KP13_02839 — glycerol dehydratase large subunit

Via homolog PDB 5yrt UniProt Q59470 Formula C₁₀H₁₃N₅O₃
Mol. weight 251.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5AD
PDB
5yrt
UniProt (similar protein)
Q59470
Target protein
KP13_02839

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 251.25 Da
LogP (Crippen) -0.95
H-bond donors 3
H-bond acceptors 8
TPSA 119.31 Ų
Rotatable bonds 1
Aromatic rings 2 / 3
Heavy atoms 18
Fraction sp³ C 0.50
Formula C₁₀H₁₃N₅O₃

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 119.3
  • −1 ≤ LogP ≤ 5 -0.95
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 251.2
  • LogP ≤ 5 -0.95
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 119.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
InChI 
InChI=1S/C10H13N5O3/c1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15/h2-4,6-7,10,16-17H,1H3,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1
InChIKey 
XGYIMTFOTBMPFP-KQYNXXCUSA-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
PF02286

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_02839.

ZINC 50

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

Compound Similarity (Tanimoto)