Ligand profile

GKR

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

Bound to: VK055_4383 — glucarate dehydratase

Via homolog PDB 3pfr UniProt A6VQF6 Formula C₆H₈O₈²⁻
Mol. weight 208.12 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GKR
PDB
3pfr
UniProt (similar protein)
A6VQF6
Target protein
VK055_4383

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 208.12 Da
LogP (Crippen) -6.07
H-bond donors 4
H-bond acceptors 8
TPSA 161.18 Ų
Rotatable bonds 5
Aromatic rings 0 / 0
Heavy atoms 14
Fraction sp³ C 0.67
Formula C₆H₈O₈²⁻

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 161.2
  • −1 ≤ LogP ≤ 5 -6.07
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 208.1
  • LogP ≤ 5 -6.07
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 161.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[C@H]([C@@H]([C@@H](C(=O)[O-])O)O)([C@H](C(=O)[O-])O)O
InChI 
InChI=1S/C6H10O8/c7-1(3(9)5(11)12)2(8)4(10)6(13)14/h1-4,7-10H,(H,11,12)(H,13,14)/p-2/t1-,2-,3-,4+/m0/s1
InChIKey 
DSLZVSRJTYRBFB-LLEIAEIESA-L

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
PF02746' '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)