4G1F

Crystal Structure of human Dipeptidyl Peptidase IV in complex with a pyridopyrimidinedione analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure-based design of pyridopyrimidinediones as dipeptidyl peptidase IV inhibitors.

Lam, B.Zhang, Z.Stafford, J.A.Skene, R.J.Shi, L.Gwaltney, S.L.

(2012) Bioorg.Med.Chem.Lett. 22: 6628-6631

  • DOI: 10.1016/j.bmcl.2012.08.110

  • PubMed Abstract: 
  • Dipeptidyl peptidase IV (DPP-4) inhibitors have been shown to enhance GLP-1 levels and thereby improve hyperglycemia in type II diabetes. From a small fragment hit, using structure-based design, we have discovered a new class of non-covalent, potent ...

    Dipeptidyl peptidase IV (DPP-4) inhibitors have been shown to enhance GLP-1 levels and thereby improve hyperglycemia in type II diabetes. From a small fragment hit, using structure-based design, we have discovered a new class of non-covalent, potent and selective DPP-4 inhibitors.


    Organizational Affiliation

    Takeda California, 10410 Science Center Drive, San Diego, CA 92121, USA. blam@takedasd.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptidyl peptidase 4
A, B, C, D
740Homo 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
0WG
Query on 0WG

Download SDF File 
Download CCD File 
A, B, C, D
7-amino-6-(aminomethyl)-5-(2-bromophenyl)-1,3-dimethylpyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione
C16 H16 Br N5 O2
JGBNONXELAWFNR-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0WGIC50: 17 nM (100) BINDINGDB
0WGIC50: 17 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 121.622α = 90.00
b = 121.362β = 114.63
c = 143.257γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release