Ligand profile

EZ3

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

Bound to: VK055_4164 — lysine--tRNA ligase

Via homolog PDB 6m0t UniProt Q8IDJ8 Formula C₁₆H₂₀O₆
Mol. weight 308.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
EZ3
PDB
6m0t
UniProt (similar protein)
Q8IDJ8
Target protein
VK055_4164

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 308.33 Da
LogP (Crippen) 1.50
H-bond donors 3
H-bond acceptors 6
TPSA 96.22 Ų
Rotatable bonds 2
Aromatic rings 1 / 3
Heavy atoms 22
Fraction sp³ C 0.56
Formula C₁₆H₂₀O₆

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 96.2
  • −1 ≤ LogP ≤ 5 1.50
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 308.3
  • LogP ≤ 5 1.50
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 96.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]1CCC[C@@H](O1)[C@H]([C@H]2Cc3cc(cc(c3C(=O)O2)O)O)O
InChI 
InChI=1S/C16H20O6/c1-8-3-2-4-12(21-8)15(19)13-6-9-5-10(17)7-11(18)14(9)16(20)22-13/h5,7-8,12-13,15,17-19H,2-4,6H2,1H3/t8-,12+,13+,15+/m0/s1
InChIKey 
YVPGTQQTPNCAJJ-VFJFRJDUSA-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
PF00152

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_4164.

PDB 17

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

Ligand PDB entry

ChEMBL 2

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)