2XDW

Inhibition of Prolyl Oligopeptidase with a Synthetic Unnatural Dipeptide

• PDB DOI: https://doi.org/10.2210/pdb2XDW/pdb

• Classification: HYDROLASE
• Organism(s): Sus scrofa, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-09 Released: 2010-06-23 
• Deposition Author(s): Racys, D.T., Rea, D., Fulop, V., Wills, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.186 
• R-Value Work: 0.164 
• R-Value Observed: 0.164 

Starting Model: experimental

Literature

Inhibition of Prolyl Oligopeptidase with a Synthetic Unnatural Dipeptide

Racys, D.T., Rea, D., Fulop, V., Wills, M.

(2010) Bioorg Med Chem 18: 4775

• PubMed: 20627594 
• DOI: https://doi.org/10.1016/j.bmc.2010.05.012
• Primary Citation of Related Structures:  
  2XDW


• PubMed Abstract: 
  

  A new inhibitor, containing a linked proline-piperidine structure, for the enzyme prolyl oligopeptidase (POP) has been synthesised and demonstrated to bind covalently with the enzyme at the active site. This provides evidence that covalent inhibitors of POP do not have to be limited to structures containing five-membered N-containing heterocyclic rings.

---

Organizational Affiliation: 

Department of Chemistry, The University of Warwick, Coventry CV47AL, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 82.24 kDa 
• Atom Count: 6,859 
• Modelled Residue Count: 713 
• Deposited Residue Count: 713 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prolyl endopeptidase	A	710	Sus scrofa	Mutation(s): 0  Gene Names: PREP EC: 3.4.21.26
UniProt
Find proteins for P23687 (Sus scrofa) Explore P23687  Go to UniProtKB:  P23687

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SYNTHETIC PEPTIDE PHQ-PRO-YCP	B [auth P]	3	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TAM	C [auth A]	TRIS(HYDROXYETHYL)AMINOMETHANE C7 H17 N O3 GKODZWOPPOTFGA-UHFFFAOYSA-N
GOL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000694	B [auth P]	1-(1-phenylmethoxycarbonylpyrrolidine-2-carbonyl)piperidine-2-carboxylic acid	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.186 
• R-Value Work: 0.164 
• R-Value Observed: 0.164 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.82	α = 90
b = 99.51	β = 90
c = 110.79	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-23 
Deposition Author(s): Racys, D.T., Rea, D., Fulop, V., Wills, M.

Revision History  

• Version 1.0: 2010-06-23
  Type: Initial release
  
• Version 1.1: 2012-02-22
  Changes: Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary
• Version 1.2: 2012-03-28
  Changes: Other
• Version 1.3: 2016-12-28
  Changes: Source and taxonomy, Version format compliance
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 2.0: 2024-08-07
  Changes: Atomic model, Database references, Derived calculations, Source and taxonomy, Structure summary