Ligand profile

XYH

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

Bound to: VK055_4383 — glucarate dehydratase

Via homolog PDB 1ec9 UniProt P0AES2 Formula C₅H₈NO₇⁻
Mol. weight 194.12 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
XYH
PDB
1ec9
UniProt (similar protein)
P0AES2
Target protein
VK055_4383

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 194.12 Da
LogP (Crippen) -4.68
H-bond donors 5
H-bond acceptors 7
TPSA 150.15 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 13
Fraction sp³ C 0.60
Formula C₅H₈NO₇⁻

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 150.1
  • −1 ≤ LogP ≤ 5 -4.68
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 194.1
  • LogP ≤ 5 -4.68
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 150.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[C@H]([C@@H](C(=O)NO)O)([C@H](C(=O)[O-])O)O
InChI 
InChI=1S/C5H9NO7/c7-1(3(9)5(11)12)2(8)4(10)6-13/h1-3,7-9,13H,(H,6,10)(H,11,12)/p-1/t1-,2-,3+/m0/s1
InChIKey 
DMGBHBFPSRKPBV-XZIMBLGRSA-M

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
PF13378

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_4383.

PDB 6

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)