GL1X · GenesisL1 explorer

MolNFT v1 · #187594 · protein

Vanin-1 complexed with compound 11

7SLX · Pantetheinase: “Vanin-1 complexed with compound 11”. X-ray diffraction, 4 ligands (9SS, NAG, BMA), 3 pockets (best druggability 0.67). MolNFT v1 #187594 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
7SLX
Type
protein
Length
461 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Pantetheinase
EC
3.5.1.92
UniProt
O95497
Ligands
9SS, NAG, BMA, NA
Pockets
3 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 36% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
APantetheinase (EC 3.5.1.92)protein46118% helix, 36% strandO95497

Ligands and binding sites

  • 9SS · (3R)-1-(2-{[1-(pyrimidin-5-yl) cyclopropyl]amino}pyrimidine-5-carbonyl)piperidine-3-carbonitrile · ligand · chains A
  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
  • BMA · beta-D-mannopyranose · sugar · 5 copies · chains A
  • NA · Sodium ion · metal · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12490.670.84419SS
21800.510.7824empty
3510.340.7815empty

Modifications

Observed in the structure: 5 disulfide, 4 glycan, 1 modified (disulfide, N-glycosylation, oxidation).

Compared structures

  • 7SLX · Vanin-1 complexed with Compound 11 · the same entry in another collection · chain A against A, TM-score 1.00
  • O95497 · AlphaFold monomer V2.0 prediction for pantetheinase (O95497) · a predicted model of the same protein · chain A against A, TM-score 1.00

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