Ligand profile

6XZ

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

Bound to: KP13_03421 — Glycerol kinase

Via homolog PDB 5gn5 UniProt D3KVM3 Formula C₂₁H₂₂N₂O₅
Mol. weight 382.42 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
6XZ
PDB
5gn5
UniProt (similar protein)
D3KVM3
Target protein
KP13_03421

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 382.42 Da
LogP (Crippen) 2.54
H-bond donors 2
H-bond acceptors 7
TPSA 86.38 Ų
Rotatable bonds 4
Aromatic rings 3 / 4
Heavy atoms 28
Fraction sp³ C 0.29
Formula C₂₁H₂₂N₂O₅

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 86.4
  • −1 ≤ LogP ≤ 5 2.54
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 382.4
  • LogP ≤ 5 2.54
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 86.4
PAINS Alert

Matches PAINS filter: anil_di_alk_C(246). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc(cc1)N2CCN(CC2)CC3=CC(=O)Oc4c3ccc(c4O)O
InChI 
InChI=1S/C21H22N2O5/c1-27-16-4-2-15(3-5-16)23-10-8-22(9-11-23)13-14-12-19(25)28-21-17(14)6-7-18(24)20(21)26/h2-7,12,24,26H,8-11,13H2,1H3
InChIKey 
NSCKGTDRMZINFP-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)