3F8S

Crystal structure of dipeptidyl peptidase IV in complex with inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report



Literature

(3,3-Difluoro-pyrrolidin-1-yl)-[(2S,4S)-(4-(4-pyrimidin-2-yl-piperazin-1-yl)-pyrrolidin-2-yl]-methanone: a potent, selective, orally active dipeptidyl peptidase IV inhibitor.

Ammirati, M.J., Andrews, K.M., Boyer, D.D., Brodeur, A.M., Danley, D.E., Doran, S.D., Hulin, B., Liu, S., McPherson, R.K., Orena, S.J., Parker, J.C., Polivkova, J., Qiu, X., Soglia, C.B., Treadway, J.L., VanVolkenburg, M.A., Wilder, D.C., Piotrowski, D.W.

(2009) Bioorg Med Chem Lett 19: 1991-1995

  • DOI: 10.1016/j.bmcl.2009.02.041
  • Primary Citation of Related Structures:  
    3F8S

  • PubMed Abstract: 

    • A series of 4-substituted proline amides was synthesized and evaluated as inhibitors of dipeptidyl pepdidase IV for the treatment of type 2 diabetes. (3,3-Difluoro-pyrrolidin-1-yl)-[(2S,4S)-(4-(4-pyrimidin-2-yl-piperazin-1-yl)-pyrrolidin-2-yl]-methanone ...

    A series of 4-substituted proline amides was synthesized and evaluated as inhibitors of dipeptidyl pepdidase IV for the treatment of type 2 diabetes. (3,3-Difluoro-pyrrolidin-1-yl)-[(2S,4S)-(4-(4-pyrimidin-2-yl-piperazin-1-yl)-pyrrolidin-2-yl]-methanone (5) emerged as a potent (IC(50) = 13 nM) and selective compound, with high oral bioavailability in preclinical species and low plasma protein binding. Compound 5, PF-00734200, was selected for development as a potential new treatment for type 2 diabetes.

    Organizational Affiliation: 

    Pfizer Global Research & Development, Groton/New London Laboratories, Pfizer Inc, Groton, CT 06340, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4 A, B748Homo sapiensMutation(s): 0 
Gene Names: DPP4, ADCP2, CD26
EC: 3.4.14.5
Find proteins for P27487 (Homo sapiens)
Explore P27487 
Go to UniProtKB:  P27487
NIH Common Fund Data Resources
PHAROS:  P27487
GTEx:  ENSG00000197635
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, E, F
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PF2
Query on PF2
Download Ideal Coordinates CCD File 
A, B
2-(4-{(3S,5S)-5-[(3,3-difluoropyrrolidin-1-yl)carbonyl]pyrrolidin-3-yl}piperazin-1-yl)pyrimidine
C17 H24 F2 N6 O
QWEWGXUTRTXFRF-KBPBESRZSA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PF2IC50 :  13   nM  PDBBind
PF2IC50:  13   nM  BindingDB
PF2IC50:  11   nM  BindingDB
PF2IC50:  13   nM  BindingDB
PF2IC50:  12.899999618530273   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.429α = 90
b = 67.141β = 90
c = 421.529γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary