2ONC

Crystal structure of human DPP-4

Structural Biology Knowledgebase: 2ONC SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.195

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2ONC

Classification: HYDROLASE

Total Structure Weight: 346992.81

Macromolecule Entities
Molecule Chains Length Organism Details
Dipeptidyl peptidase 4 A, B, C, D 731 Homo sapiens EC#: 3.4.14.5 IUBMB
Gene Name(s): DPP4 Gene View ADCP2 CD26

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

A, B, C, D N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
JSmol
SY1
Query on SY1

A, B, C, D 2-({2-[(3R)-3-AMINOPIPERIDIN-1-YL]-4-OXOQUINAZOLIN- 3(4H)-YL}METHYL)BENZONITRILE
C21 H21 N5 O
OYNURZXTLNNKAP-QGZVFWFLSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
SY1 IC50: 13 nM (99) BindingDB

N/A in BindingMoad
IC50: 13 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.195
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 122.36 α = 90.00
b = 123.70 β = 114.89
c = 145.36 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-01-23
  • Released Date: 2008-03-04
  • Deposition author(s): Feng, J., Zhang, Z., Wallace, M.B., Stafford, J.A., Kaldor, S.W., Kassel, D.B., Navre, M., Shi, L., Skene, R.J., Asakawa, T., Takeuchi, K., Xu, R., Webb, D.R., Gwaltney, S.L.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Refinement description | Details: Fixed TLS group
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4