Ligand profile

NPI

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

Bound to: VK055_2386 — 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Via homolog PDB 1kgq UniProt P56220 Formula C₇H₁₃NO₄
Mol. weight 175.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NPI
PDB
1kgq
UniProt (similar protein)
P56220
Target protein
VK055_2386

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 175.18 Da
LogP (Crippen) 0.04
H-bond donors 3
H-bond acceptors 3
TPSA 100.62 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 12
Fraction sp³ C 0.71
Formula C₇H₁₃NO₄

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 100.6
  • −1 ≤ LogP ≤ 5 0.04
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 175.2
  • LogP ≤ 5 0.04
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 100.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CCC(=O)O)C[C@@H](C(=O)O)N
InChI 
InChI=1S/C7H13NO4/c8-5(7(11)12)3-1-2-4-6(9)10/h5H,1-4,8H2,(H,9,10)(H,11,12)/t5-/m0/s1
InChIKey 
JUQLUIFNNFIIKC-YFKPBYRVSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF14805

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_2386.

PDB 4

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)