Ligand profile

NSN

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

Bound to: VK055_2429 — aspartate 1-decarboxylase

Via homolog PDB 1uhe UniProt P56065 Formula C₇H₁₁N₃O₄
Mol. weight 201.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NSN
PDB
1uhe
UniProt (similar protein)
P56065
Target protein
VK055_2429

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 201.18 Da
LogP (Crippen) -4.99
H-bond donors 3
H-bond acceptors 4
TPSA 140.28 Ų
Rotatable bonds 5
Aromatic rings 0 / 0
Heavy atoms 14
Fraction sp³ C 0.43
Formula C₇H₁₁N₃O₄

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 140.3
  • −1 ≤ LogP ≤ 5 -4.99
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 201.2
  • LogP ≤ 5 -4.99
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 140.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=[NH+][C@@H](CC(=O)[O-])C(=O)N)C(=O)N
InChI 
InChI=1S/C7H11N3O4/c1-3(6(8)13)10-4(7(9)14)2-5(11)12/h4H,2H2,1H3,(H2,8,13)(H2,9,14)(H,11,12)/t4-/m0/s1
InChIKey 
YZKQNDLOQTXCHV-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
PF02261

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_2429.

PDB 9

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)