Ligand profile

ZINC5547487

Virtual-screening candidate from ZINC.

Bound to: KP13_03421 — Glycerol kinase

Via homolog UniProt D3KVM3 Formula C₁₂H₁₂O₄
Tanimoto 0.84
Mol. weight 220.22 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5547487
UniProt (similar protein)
D3KVM3
Tanimoto
0.838
Target protein
KP13_03421

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 220.22 Da
LogP (Crippen) 2.16
H-bond donors 2
H-bond acceptors 4
TPSA 70.67 Ų
Rotatable bonds 2
Aromatic rings 2 / 2
Heavy atoms 16
Fraction sp³ C 0.25
Formula C₁₂H₁₂O₄

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 2.16
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 220.2
  • LogP ≤ 5 2.16
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • 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 
CCCc1cc(=O)oc2c(O)c(O)ccc12
InChI 
InChI=1S/C12H12O4/c1-2-3-7-6-10(14)16-12-8(7)4-5-9(13)11(12)15/h4-6,13,15H,2-3H2,1H3
InChIKey 
PHPUSFBIYOLWBJ-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
6Y0
Homolog
D3KVM3

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 13

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)