2BUB

Crystal Structure Of Human Dipeptidyl Peptidase IV (CD26) in Complex with a Reversed Amide Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIPEPTIDYL PEPTIDASE 4
A, B
728Homo sapiensMutation(s): 0 
Gene Names: DPP4 (ADCP2, CD26)
EC: 3.4.14.5
Find proteins for P27487 (Homo sapiens)
Go to Gene View: DPP4
Go to UniProtKB:  P27487
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
FPB
Query on FPB

Download SDF File 
Download CCD File 
A, B
N-({(2S)-1-[(3R)-3-AMINO-4-(2-FLUOROPHENYL)BUTANOYL]PYRROLIDIN-2-YL}METHYL)BENZAMIDE
C22 H26 F N3 O2
ANQHSFFUNMTTRS-MOPGFXCFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FPBIC50: 90 - 410 nM (100) BINDINGDB
FPBIC50: 90 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.258 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.486α = 90.00
b = 66.773β = 90.00
c = 425.407γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 2.0: 2018-08-22
    Type: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary