1N1M

Human Dipeptidyl Peptidase IV/CD26 in complex with an inhibitor

Structural Biology Knowledgebase: 1N1M SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.263
  • R-Value Work: 0.208

Literature

Macromolecules
Sequence Display for 1N1M

Classification: HYDROLASE

Total Structure Weight: 176123.34

Macromolecule Entities
Molecule Chains Length Organism Details
Dipeptidyl peptidase IV SOLUBLE FORM A, B 728 Homo sapiens EC#: 3.4.14.5 IUBMB
Fragment: Extracellular domain
Gene Name(s): DPP4 Gene View ADCP2 CD26
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

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

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

A, B MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

B BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
A3M
Query on A3M

A, B 2-AMINO-3-METHYL-1-PYRROLIDIN-1-YL-BUTAN- 1-ONE
C9 H18 N2 O
IHBAVXVTGLANPI-QMMMGPOBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

A, B ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
A3M IC50: 3000 - 5400 nM (100) BindingDB
Ki: 2000 nM (100) BindingDB

Ki: 2000 nM  BindingMOAD
Ki: 2000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.263
  • R-Value Work: 0.208
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 119.23 α = 90.00
b = 123.45 β = 90.00
c = 131.32 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-10-18
  • Released Date: 2002-12-27
  • Deposition author(s): Rasmussen, H.B., Branner, S., Wiberg, F.C., Wagtmann, N.R.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update