Ligand profile

ZINC54147573

Virtual-screening candidate from ZINC.

Bound to: KP13_03421 — Glycerol kinase

Via homolog UniProt D3KVM3 Formula C₂₀H₂₀N₂O₄
Tanimoto 0.75
Mol. weight 352.39 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC54147573
UniProt (similar protein)
D3KVM3
Tanimoto
0.750
Target protein
KP13_03421

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 352.39 Da
LogP (Crippen) 2.53
H-bond donors 2
H-bond acceptors 6
TPSA 77.15 Ų
Rotatable bonds 3
Aromatic rings 3 / 4
Heavy atoms 26
Fraction sp³ C 0.25
Formula C₂₀H₂₀N₂O₄

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 77.2
  • −1 ≤ LogP ≤ 5 2.53
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 352.4
  • LogP ≤ 5 2.53
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 77.2
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 
O=c1cc(CN2CCN(c3ccccc3)CC2)c2ccc(O)c(O)c2o1
InChI 
InChI=1S/C20H20N2O4/c23-17-7-6-16-14(12-18(24)26-20(16)19(17)25)13-21-8-10-22(11-9-21)15-4-2-1-3-5-15/h1-7,12,23,25H,8-11,13H2
InChIKey 
CELBURDFNXLJDX-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
6XZ
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)