4G1F

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

Structural Biology Knowledgebase: 4G1F SBKB.org


Experimental Data Snapshot

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

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4G1F

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 349444.31

Macromolecule Entities
Molecule Chains Length Organism Details
Dipeptidyl peptidase 4 A, B, C, D 740 Homo sapiens EC#: 3.4.14.5 IUBMB
Fragment: UNP residues 39-766
Gene Name(s): DPP4 Gene View ADCP2 CD26
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0WG
Query on 0WG

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 Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, B, C, D N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
0WG IC50: 17 nM (100) BindingDB

N/A in BindingMoad
IC50: 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
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 121.62 α = 90.00
b = 121.36 β = 114.63
c = 143.26 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-07-10
  • Released Date: 2013-02-27
  • Deposition author(s): Skene, R.J., Gwaltney, S.L.

Revision History

No revisions since initial release