2BUA

Crystal Structure Of Porcine Dipeptidyl Peptidase IV (Cd26) in Complex With a Low Molecular Weight Inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.220 

wwPDB Validation   3D Report Full Report


This is version 3.1 of the entry. See complete history


Literature

The reversed binding of beta-phenethylamine inhibitors of DPP-IV: X-ray structures and properties of novel fragment and elaborated inhibitors.

Nordhoff, S.Cerezo-Galvez, S.Feurer, A.Hill, O.Matassa, V.G.Metz, G.Rummey, C.Thiemann, M.Edwards, P.J.

(2006) Bioorg Med Chem Lett 16: 1744-1748

  • DOI: https://doi.org/10.1016/j.bmcl.2005.11.103
  • Primary Citation of Related Structures:  
    2BUA, 2BUB, 2BUC

  • PubMed Abstract: 

    The co-crystal structure of beta-phenethylamine fragment inhibitor 5 bound to DPP-IV revealed that the phenyl ring occupied the proline pocket of the enzyme. This finding provided the basis for a general hypothesis of a reverse binding mode for beta-phenethylamine-based DPP-IV inhibitors. Novel inhibitor design concepts that obviate substrate-like structure-activity relationships (SAR) were thereby enabled, and novel, potent inhibitors were discovered.


  • Organizational Affiliation

    Medicinal Chemistry, Santhera Pharmaceuticals, Im Neuenheimer Feld 518-519, D-69120 Heidelberg, Germany. sonja.nordhoff@santhera.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DIPEPTIDYL PEPTIDASE IV
A, B, C, D
728Sus scrofaMutation(s): 0 
EC: 3.4.14.5
UniProt
Find proteins for P22411 (Sus scrofa)
Explore P22411 
Go to UniProtKB:  P22411
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22411
Glycosylation
Glycosylation Sites: 6
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H, I
E, F, G, H, I, J, K, L, M
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
FA [auth C]
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
JA [auth D],
KA [auth D],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
007
Query on 007

Download Ideal Coordinates CCD File 
GA [auth C],
LA [auth D],
R [auth A],
Y [auth B]
1-METHYLAMINE-1-BENZYL-CYCLOPENTANE
C12 H17 N
SJWOFBVBNFLWLP-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth B]
HA [auth C]
IA [auth C]
MA [auth D]
NA [auth D]
AA [auth B],
HA [auth C],
IA [auth C],
MA [auth D],
NA [auth D],
S [auth A],
T [auth A],
Z [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
007 BindingDB:  2BUA IC50: min: 3.00e+4, max: 4.00e+4 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.220 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.425α = 112.4
b = 118.131β = 94.98
c = 133.317γ = 90.99
Software Package:
Software NamePurpose
CNXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2018-08-22
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2019-09-04
    Changes: Data collection, Derived calculations
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2024-11-13
    Changes: Data collection, Database references, Structure summary