2QJR

dipepdyl peptidase IV in complex with inhibitor PZF

Structural Biology Knowledgebase: 2QJR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.191

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2QJR

Classification: HYDROLASE

Total Structure Weight: 177605.36

Macromolecule Entities
Molecule Chains Length Organism Details
Dipeptidyl peptidase 4 A, B 748 Homo sapiens EC#: 3.4.14.5 IUBMB
Fragment: UNP residues 31-766
Gene Name(s): DPP4 Gene View ADCP2 CD26
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PZF
Query on PZF

A, B (3R,4S)-1-[6-(6-METHOXYPYRIDIN-3-YL)PYRIMIDIN- 4-YL]-4-(2,4,5-TRIFLUOROPHENYL)PYRROLIDIN- 3-AMINE
C20 H18 F3 N5 O
IFKWHPAWYJARQJ-DYVFJYSZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NDG
Query on NDG

B 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LGU
Query on LGU

A ALPHA-L-GULURONATE
alpha-L-gulopyranuronic acid (Synonym)
C6 H10 O7
AEMOLEFTQBMNLQ-AZLKCVHYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
PZF IC50: 6.4 - 37 nM (100) BindingDB

IC50: 6.4 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.191
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 65.47 α = 90.00
b = 68.80 β = 90.00
c = 422.61 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-07-09
  • Released Date: 2008-07-29
  • Deposition author(s): Shenping, L.

Revision History

  • 2014-12-17
    Type: Non-polymer description | Details: --
  • 2011-07-13
    Type: Refinement description | Details: Fixed TLS group
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4