Ligand profile

E4O

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

Bound to: VK055_0276 — threonine--tRNA ligase

Via homolog PDB 6l2q UniProt V7II86 Formula C₁₆H₁₈Cl₂N₄O₃
Mol. weight 385.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
E4O
PDB
6l2q
UniProt (similar protein)
V7II86
Target protein
VK055_0276

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 385.25 Da
LogP (Crippen) 1.08
H-bond donors 3
H-bond acceptors 6
TPSA 110.24 Ų
Rotatable bonds 6
Aromatic rings 2 / 2
Heavy atoms 25
Fraction sp³ C 0.31
Formula C₁₆H₁₈Cl₂N₄O₃

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 110.2
  • −1 ≤ LogP ≤ 5 1.08
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 385.3
  • LogP ≤ 5 1.08
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 110.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]([C@@H](C(=O)NC/C=C/CN1C=Nc2cc(c(cc2C1=O)Cl)Cl)N)O
InChI 
InChI=1S/C16H18Cl2N4O3/c1-9(23)14(19)15(24)20-4-2-3-5-22-8-21-13-7-12(18)11(17)6-10(13)16(22)25/h2-3,6-9,14,23H,4-5,19H2,1H3,(H,20,24)/b3-2+/t9-,14+/m1/s1
InChIKey 
YXMAQAPNMNRQQB-XKKUMHBKSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF00587

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_0276.

PDB 11

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

Ligand PDB entry

ChEMBL 28

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)