2QJR | pdb_00002qjr

dipepdyl peptidase IV in complex with inhibitor PZF

• PDB DOI: https://doi.org/10.2210/pdb2QJR/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2007-07-09 Released: 2008-07-29 
• Deposition Author(s): Shenping, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.253 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

(3R,4S)-4-(2,4,5-Trifluorophenyl)-pyrrolidin-3-ylamine inhibitors of dipeptidyl peptidase IV: synthesis, in vitro, in vivo, and X-ray crystallographic characterization.

Wright, S.W., Ammirati, M.J., Andrews, K.M., Brodeur, A.M., Danley, D.E., Doran, S.D., Lillquist, J.S., Liu, S., McClure, L.D., McPherson, R.K., Olson, T.V., Orena, S.J., Parker, J.C., Rocke, B.N., Soeller, W.C., Soglia, C.B., Treadway, J.L., Vanvolkenburg, M.A., Zhao, Z., Cox, E.D.

(2007) Bioorg Med Chem Lett 17: 5638-5642

• PubMed: 17822893 
• DOI: https://doi.org/10.1016/j.bmcl.2007.07.081
• Primary Citation Related Structures: 
  2QJR


• PubMed Abstract: 
  

  A series of pyrrolidine based inhibitors of dipeptidyl peptidase IV were developed from a high throughput screening hit for the treatment of type 2 diabetes. Potency, selectivity, and pharmacokinetic properties were optimized resulting in the identification of a pre-clinical candidate for further profiling.

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Organizational Affiliation: 
• Pfizer Global Research and Development, Cardiovascular and Metabolic Diseases, MS 8220-3141, Eastern Point Road, Groton, CT 06340, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 177.62 kDa 
• Atom Count: 12,532 
• Modeled Residue Count: 1,456 
• Deposited Residue Count: 1,496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4 membrane form	A, B	748	Homo sapiens	Mutation(s): 0  Gene Names: DPP4, ADCP2, CD26 EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for P27487 (Homo sapiens) Explore P27487  Go to UniProtKB:  P27487
PHAROS:  P27487 GTEx:  ENSG00000197635
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: P27487-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, E, F, G, H	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-alpha-L-gulopyranuronic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	4		N-Glycosylation

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PZF	J [auth A], M [auth B]	(3R,4S)-1-[6-(6-METHOXYPYRIDIN-3-YL)PYRIMIDIN-4-YL]-4-(2,4,5-TRIFLUOROPHENYL)PYRROLIDIN-3-AMINE C20 H18 F3 N5 O IFKWHPAWYJARQJ-DYVFJYSZSA-N
NAG	I [auth A], L [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
LGU	K [auth A]	alpha-L-gulopyranuronic acid C6 H10 O7 AEMOLEFTQBMNLQ-AZLKCVHYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.253 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.47	α = 90
b = 68.796	β = 90
c = 422.611	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-29 
Deposition Author(s): Shenping, L.

Revision History  

• Version 1.0: 2008-07-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Derived calculations, Refinement description, Version format compliance
• Version 1.2: 2014-12-17
  Changes: Non-polymer description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 3.0: 2022-04-20
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 3.1: 2024-11-06
  Changes: Data collection, Refinement description, Structure summary