3DDU

Prolyl Oligopeptidase with GSK552

• PDB DOI: https://doi.org/10.2210/pdb3DDU/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-06-06 Released: 2008-08-19 
• Deposition Author(s): Madauss, K.P., Reid, R.A., Haffner, C.D., Miller, A.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.172 
• R-Value Work: 0.147 
• R-Value Observed: 0.149 

Literature

Pyrrolidinyl pyridone and pyrazinone analogues as potent inhibitors of prolyl oligopeptidase (POP)

Haffner, C.D., Diaz, C.J., Miller, A.B., Reid, R.A., Madauss, K.P., Hassell, A., Hanlon, M.H., Porter, D.J., Becherer, J.D., Carter, L.H.

(2008) Bioorg Med Chem Lett 18: 4360-4363

• PubMed: 18606544 
• DOI: https://doi.org/10.1016/j.bmcl.2008.06.067
• Primary Citation of Related Structures:  
  3DDU


• PubMed Abstract: 
  

  We report the synthesis and in vitro activity of a series of novel pyrrolidinyl pyridones and pyrazinones as potent inhibitors of prolyl oligopeptidase (POP). Within this series, compound 39 was co-crystallized within the catalytic site of a human chimeric POP protein which provided a more detailed understanding of how these inhibitors interacted with the key residues within the catalytic pocket.

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Organizational Affiliation: 

Department of Medicinal Chemistry, GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park, NC 27709, USA. [e-mail]

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: 81.46 kDa 
• Atom Count: 6,931 
• Modelled Residue Count: 707 
• Deposited Residue Count: 709 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prolyl endopeptidase	A	709	Homo sapiens	Mutation(s): 5  Gene Names: PREP, PEP EC: 3.4.21.26
UniProt & NIH Common Fund Data Resources
Find proteins for P48147 (Homo sapiens) Explore P48147  Go to UniProtKB:  P48147
PHAROS:  P48147 GTEx:  ENSG00000085377

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
552	G [auth A]	(6S)-1-chloro-3-[(4-fluorobenzyl)oxy]-6-(pyrrolidin-1-ylcarbonyl)pyrrolo[1,2-a]pyrazin-4(6H)-one C19 H17 Cl F N3 O3 HPAFVLDARQIHPU-HNNXBMFYSA-N
GOL	H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
552	Binding MOAD:  3DDU	IC50: 40 (nM) from 1 assay(s)
	PDBBind:  3DDU	IC50: 40 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.172 
• R-Value Work: 0.147 
• R-Value Observed: 0.149 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.221	α = 90
b = 99.883	β = 90
c = 111.853	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-19 
Deposition Author(s): Madauss, K.P., Reid, R.A., Haffner, C.D., Miller, A.B.

Revision History  

• Version 1.0: 2008-08-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-21
  Changes: Data collection