Ligand profile

EKN

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

Bound to: VK055_3227 — argininosuccinate lyase

Via homolog PDB 6g3i UniProt Q11KV9 Formula C₆H₁₂N₂O₄
Mol. weight 176.17 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
EKN
PDB
6g3i
UniProt (similar protein)
Q11KV9
Target protein
VK055_3227

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 176.17 Da
LogP (Crippen) -1.54
H-bond donors 4
H-bond acceptors 4
TPSA 112.65 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 12
Fraction sp³ C 0.67
Formula C₆H₁₂N₂O₄

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 112.7
  • −1 ≤ LogP ≤ 5 -1.54
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 176.2
  • LogP ≤ 5 -1.54
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 112.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CN[C@@H](CC(=O)O)C(=O)O)N
InChI 
InChI=1S/C6H12N2O4/c7-1-2-8-4(6(11)12)3-5(9)10/h4,8H,1-3,7H2,(H,9,10)(H,11,12)/t4-/m0/s1
InChIKey 
PDDUTYPDHMQVSU-BYPYZUCNSA-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
PF00206

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_3227.

PDB 6

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)