4A5S

CRYSTAL STRUCTURE OF HUMAN DPP4 IN COMPLEX WITH A NOVAL HETEROCYCLIC DPP4 INHIBITOR

Structural Biology Knowledgebase: 4A5S SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.164

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4A5S

Classification: HYDROLASE

Total Structure Weight: 176784.69

Macromolecule Entities
Molecule Chains Length Organism Details
DIPEPTIDYL PEPTIDASE 4 SOLUBLE FORM A, B 740 Homo sapiens EC#: 3.4.14.5 IUBMB
Mutation: S437I
Gene Name(s): DPP4 Gene View ADCP2 CD26
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
N7F
Query on N7F

A, B 6-[(3S)-3-AMINOPIPERIDIN-1-YL]-5-BENZYL-4- OXO-3-(QUINOLIN-4-YLMETHYL)-4,5-DIHYDRO-3H- PYRROLO[3,2-D]PYRIMIDINE-7-CARBONITRILE
C29 H27 N7 O
WRJSBPQWADEDBH-QFIPXVFZSA-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)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
N7F IC50: 17 nM (99) BindingDB

IC50: 17 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.164
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 97.18 α = 90.00
b = 121.42 β = 90.00
c = 190.70 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-10-28
  • Released Date: 2012-02-08
  • Deposition author(s): Ostermann, N., Kroemer, M., Zink, F., Gerhartz, B., Sutton, J.M., Clark, D.E., Dunsdon, S.J., Fenton, G., Fillmore, A., Harris, N.V., Higgs, C., Hurley, C.A., Krintel, S.L., Mackenzie, R.E., Duttaroy, A., Gangl, E., Maniara, W., Sedrani, R., Namoto, K., Sirockin, F., Trappe, J., Hassiepen, U., Baeschlin, D.K.

Revision History

No revisions since initial release