Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 346.32 kDa 
• Atom Count: 25244 
• Residue Count: 2912 
• Unique protein chains: 1

2BUA

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

• DOI: 10.2210/pdb2BUA/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2005-06-09 Released: 2006-01-23 
• Deposition Author(s): Nordhoff, S., Cerezo-Galvez, S., Feurer, A., Hill, O., Matassa, V.G., Metz, G., Rummey, C., Thiemann, M., Edwards, P.J.

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Experimental Data Snapshot

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

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

• PubMed: 16376544 
• DOI: 10.1016/j.bmcl.2005.11.103
• Primary Citation of Related Structures:  
  2BUC, 2BUB, 2BUA


• 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.

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Organizational Affiliation: 

Medicinal Chemistry, Santhera Pharmaceuticals, Im Neuenheimer Feld 518-519, D-69120 Heidelberg, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIPEPTIDYL PEPTIDASE IV	A, B, C, D	728	Sus scrofa	Mutation(s): 0  Gene Names: DPP4, CD26 EC: 3.4.14.5
Find proteins for P22411 (Sus scrofa) Explore P22411  Go to UniProtKB:  P22411

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H, I, J, K, L, M	2		N-Glycosylation

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B, C, D	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
007	A, B, C, D	1-METHYLAMINE-1-BENZYL-CYCLOPENTANE C12 H17 N SJWOFBVBNFLWLP-UHFFFAOYSA-N
SO4	A, B, C, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
007	IC50:  33000   nM  BindingDB
007	IC50:  40000   nM  BindingDB
007	IC50:  30000   nM  BindingDB
7	IC50 :  30000   nM  PDBBind

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 = 62.425	α = 112.4
b = 118.131	β = 94.98
c = 133.317	γ = 90.99

Software Package:

Software Name	Purpose
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-06-09 
• Released Date: 2006-01-23 
Deposition Author(s): Nordhoff, S., Cerezo-Galvez, S., Feurer, A., Hill, O., Matassa, V.G., Metz, G., Rummey, C., Thiemann, M., Edwards, P.J.

Revision History 

• 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