Ligand profile

6Y0

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

Bound to: KP13_03421 — Glycerol kinase

Via homolog PDB 5gn6 UniProt D3KVM3 Formula C₁₃H₁₄O₄
Mol. weight 234.25 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
6Y0
PDB
5gn6
UniProt (similar protein)
D3KVM3
Target protein
KP13_03421

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 234.25 Da
LogP (Crippen) 2.55
H-bond donors 2
H-bond acceptors 4
TPSA 70.67 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 17
Fraction sp³ C 0.31
Formula C₁₃H₁₄O₄

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 70.7
  • −1 ≤ LogP ≤ 5 2.55
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 234.3
  • LogP ≤ 5 2.55
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 70.7
PAINS Alert

Matches PAINS filter: catechol_A(92). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCC1=CC(=O)Oc2c1ccc(c2O)O
InChI 
InChI=1S/C13H14O4/c1-2-3-4-8-7-11(15)17-13-9(8)5-6-10(14)12(13)16/h5-7,14,16H,2-4H2,1H3
InChIKey 
GDGBIWNBPUQGGZ-UHFFFAOYSA-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
PF00370' 'PF02782

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_03421.

PDB 12

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)