2BUA

Crystal Structure Of Porcine Dipeptidyl Peptidase IV (Cd26) in Complex With a Low Molecular Weight Inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report



Literature

The reversed binding of beta-phenethylamine inhibitors of DPP-IV: X-ray structures and properties of novel fragment and elaborated inhibitors.

Nordhoff, S.Cerezo-Galvez, S.Feurer, A.Hill, O.Matassa, V.G.Metz, G.Rummey, C.Thiemann, M.Edwards, P.J.

(2006) Bioorg Med Chem Lett 16: 1744-1748

  • DOI: 10.1016/j.bmcl.2005.11.103
  • Primary Citation of Related Structures:  
    2BUC, 2BUB, 2BUA

  • PubMed Abstract: 
  • The co-crystal structure of beta-phenethylamine fragment inhibitor 5 bound to DPP-IV revealed that the phenyl ring occupied the proline pocket of the enzyme. This finding provided the basis for a general hypothesis of a reverse binding mode for beta- ...

    The co-crystal structure of beta-phenethylamine fragment inhibitor 5 bound to DPP-IV revealed that the phenyl ring occupied the proline pocket of the enzyme. This finding provided the basis for a general hypothesis of a reverse binding mode for beta-phenethylamine-based DPP-IV inhibitors. Novel inhibitor design concepts that obviate substrate-like structure-activity relationships (SAR) were thereby enabled, and novel, potent inhibitors were discovered.


    Organizational Affiliation

    Medicinal Chemistry, Santhera Pharmaceuticals, Im Neuenheimer Feld 518-519, D-69120 Heidelberg, Germany. sonja.nordhoff@santhera.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIPEPTIDYL PEPTIDASE IVABCD728Sus scrofaMutation(s): 0 
Gene Names: DPP4CD26
EC: 3.4.14.5
Find proteins for P22411 (Sus scrofa)
Explore P22411 
Go to UniProtKB:  P22411
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H, I, J, K, L, M
2 N-Glycosylation
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B, C, D
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
007
Query on 007

Download CCD File 
A, B, C, D
1-METHYLAMINE-1-BENZYL-CYCLOPENTANE
C12 H17 N
SJWOFBVBNFLWLP-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
007IC50:  33000   nM  BindingDB
007IC50:  40000   nM  BindingDB
007IC50:  30000   nM  BindingDB
7IC50 :  30000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.220 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.425α = 112.4
b = 118.131β = 94.98
c = 133.317γ = 90.99
Software Package:
Software NamePurpose
CNXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2018-08-22
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2019-09-04
    Changes: Data collection, Derived calculations
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary