Ligand profile

D4X

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

Bound to: VK055_4164 — lysine--tRNA ligase

Via homolog PDB 6kbf UniProt W7JP72 Formula C₁₇H₂₃NO₃
Mol. weight 289.38 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
D4X
PDB
6kbf
UniProt (similar protein)
W7JP72
Target protein
VK055_4164

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 289.38 Da
LogP (Crippen) 2.97
H-bond donors 3
H-bond acceptors 3
TPSA 69.56 Ų
Rotatable bonds 2
Aromatic rings 1 / 3
Heavy atoms 21
Fraction sp³ C 0.59
Formula C₁₇H₂₃NO₃

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 69.6
  • −1 ≤ LogP ≤ 5 2.97
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 289.4
  • LogP ≤ 5 2.97
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 69.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]1CCC[C@@H](C1)C[C@H]2Cc3cc(cc(c3C(=O)N2)O)O
InChI 
InChI=1S/C17H23NO3/c1-10-3-2-4-11(5-10)6-13-7-12-8-14(19)9-15(20)16(12)17(21)18-13/h8-11,13,19-20H,2-7H2,1H3,(H,18,21)/t10-,11-,13-/m0/s1
InChIKey 
YKYWGEWGZHSEGR-GVXVVHGQSA-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)