Ligand profile

SCO

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 C₂₅H₄₁N₈O₁₉P₃
Mol. weight 850.56 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SCO
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 850.56 Da
LogP (Crippen) -2.61
H-bond donors 11
H-bond acceptors 19
TPSA 412.96 Ų
Rotatable bonds 22
Aromatic rings 2 / 3
Heavy atoms 55
Fraction sp³ C 0.64
Formula C₂₅H₄₁N₈O₁₉P₃

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 413.0
  • −1 ≤ LogP ≤ 5 -2.61
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 850.6
  • LogP ≤ 5 -2.61
  • H-bond donors ≤ 5 11
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 22
  • TPSA ≤ 140 Ų 413.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCNC(=O)CCC(=O)O)O
InChI 
InChI=1S/C25H41N8O19P3/c1-25(2,20(39)23(40)29-6-5-15(35)28-8-7-27-14(34)3-4-16(36)37)10-49-55(46,47)52-54(44,45)48-9-13-19(51-53(41,42)43)18(38)24(50-13)33-12-32-17-21(26)30-11-31-22(17)33/h11-13,18-20,24,38-39H,3-10H2,1-2H3,(H,27,34)(H,28,35)(H,29,40)(H,36,37)(H,44,45)(H,46,47)(H2,26,30,31)(H2,41,42,43)/t13-,18-,19-,20+,24-/m1/s1
InChIKey 
WZEXTLJNSXEEHK-ITIYDSSPSA-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
PF14602

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)