Ligand profile

D4U

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

Bound to: VK055_4164 — lysine--tRNA ligase

Via homolog PDB 6kab UniProt W7JP72 Formula C₁₆H₂₀O₄
Mol. weight 276.33 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
D4U
PDB
6kab
UniProt (similar protein)
W7JP72
Target protein
VK055_4164

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 276.33 Da
LogP (Crippen) 3.15
H-bond donors 2
H-bond acceptors 4
TPSA 66.76 Ų
Rotatable bonds 2
Aromatic rings 1 / 3
Heavy atoms 20
Fraction sp³ C 0.56
Formula C₁₆H₂₀O₄

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 66.8
  • −1 ≤ LogP ≤ 5 3.15
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 276.3
  • LogP ≤ 5 3.15
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 66.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(cc(c2c1C[C@@H](OC2=O)CC3CCCCC3)O)O
InChI 
InChI=1S/C16H20O4/c17-12-7-11-8-13(6-10-4-2-1-3-5-10)20-16(19)15(11)14(18)9-12/h7,9-10,13,17-18H,1-6,8H2/t13-/m0/s1
InChIKey 
DGZHGFFAXFRYBW-ZDUSSCGKSA-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)