Ligand profile

26P

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 3tdt UniProt P56220 Formula C₇H₁₁NO₅
Mol. weight 189.17 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
26P
PDB
3tdt
UniProt (similar protein)
P56220
Target protein
VK055_2386

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 189.17 Da
LogP (Crippen) -0.78
H-bond donors 3
H-bond acceptors 4
TPSA 117.69 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 13
Fraction sp³ C 0.57
Formula C₇H₁₁NO₅

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 117.7
  • −1 ≤ LogP ≤ 5 -0.78
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 189.2
  • LogP ≤ 5 -0.78
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 117.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C[C@@H](C(=O)O)N)CC(=O)C(=O)O
InChI 
InChI=1S/C7H11NO5/c8-4(6(10)11)2-1-3-5(9)7(12)13/h4H,1-3,8H2,(H,10,11)(H,12,13)/t4-/m0/s1
InChIKey 
UKCSFKLWNHUBDY-BYPYZUCNSA-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)