Ligand profile

X3J

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

Bound to: VK055_4273 — diaminopimelate decarboxylase

Via homolog PDB 6knk UniProt A0A0H3JPF2 Formula C₈H₁₄N₂O₆
Mol. weight 234.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
X3J
PDB
6knk
UniProt (similar protein)
A0A0H3JPF2
Target protein
VK055_4273

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 234.21 Da
LogP (Crippen) -2.26
H-bond donors 5
H-bond acceptors 5
TPSA 149.95 Ų
Rotatable bonds 7
Aromatic rings 0 / 0
Heavy atoms 16
Fraction sp³ C 0.62
Formula C₈H₁₄N₂O₆

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 150.0
  • −1 ≤ LogP ≤ 5 -2.26
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 234.2
  • LogP ≤ 5 -2.26
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 150.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CNC(=O)C[C@](CC(=O)O)(C(=O)O)O)N
InChI 
InChI=1S/C8H14N2O6/c9-1-2-10-5(11)3-8(16,7(14)15)4-6(12)13/h16H,1-4,9H2,(H,10,11)(H,12,13)(H,14,15)/t8-/m0/s1
InChIKey 
KQWWDTIPDRWKGZ-QMMMGPOBSA-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
PF00278' 'PF02784

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_4273.

PDB 5

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)