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X-ray structure of polypeptide deformylase bound to a acylprolinamide inhibitor

Analyse X-ray structure of polypeptide deformylase bound to a acylprolinamide inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4EOX
Type
protein
Length
192 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Peptide deformylase
EC
3.5.1.88
UniProt
Q8DP79
Ligands
0S5, NI
Pockets
1 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
PPeptide deformylase (EC 3.5.1.88)protein19230% helix, 26% strandQ8DP79

Ligands and binding sites

  • 0S5 · N-benzoyl-1-[(2R)-3-cyclopentyl-2-{[formyl(hydroxy)amino]methyl}propanoyl]-L-prolinamide · ligand · chains P
  • NI · Nickel (II) ion · metal · chains P

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11290.510.81190S5

Compared structures

  • 4EOX · X-ray Structure of Polypeptide Deformylase Bound to a Acylprolinamide inhibitor · the same entry in another collection · chain P against P, TM-score 1.00
  • Q8DP79 · AlphaFold monomer V2.0 prediction for peptide deformylase (Q8DP79) · a predicted model of the same protein · chain P against A, TM-score 0.99

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