Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 176.45 kDa 
• Atom Count: 14344 
• Residue Count: 1460 
• Unique protein chains: 1

4N8D

DPP4 complexed with syn-7aa

• DOI: 10.2210/pdb4N8D/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2013-10-17 Released: 2014-02-12 
• Deposition Author(s): Ostermann, N., Zink, F., Kroemer, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.170 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 

Literature

Discovery of C-(1-aryl-cyclohexyl)-methylamines as selective, orally available inhibitors of dipeptidyl peptidase IV.

Namoto, K., Sirockin, F., Ostermann, N., Gessier, F., Flohr, S., Sedrani, R., Gerhartz, B., Trappe, J., Hassiepen, U., Duttaroy, A., Ferreira, S., Sutton, J.M., Clark, D.E., Fenton, G., Beswick, M., Baeschlin, D.K.

(2014) Bioorg Med Chem Lett 24: 731-736

• PubMed: 24439847 
• DOI: 10.1016/j.bmcl.2013.12.118
• Primary Citation of Related Structures:  
  4N8D, 4N8E


• PubMed Abstract: 
  

The successful launches of dipeptidyl peptidase IV (DPP IV) inhibitors as oral anti-diabetics warrant and spur the further quest for additional chemical entities in this promising class of therapeutics. Numerous pharmaceutical companies have pursued their proprietary candidates towards the clinic, resulting in a large body of published chemical structures associated with DPP IV. Herein, we report the discovery of a novel chemotype for DPP IV inhibition based on the C-(1-aryl-cyclohexyl)-methylamine scaffold and its optimization to compounds which selectively inhibit DPP IV at low-nM potency and exhibit an excellent oral pharmacokinetic profile in the rat.

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Organizational Affiliation: 

Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4	A, B	740	Homo sapiens	Mutation(s): 0  Gene Names: DPP4, ADCP2, CD26 EC: 3.4.14.5
Find proteins for P27487 (Homo sapiens) Explore P27487  Go to UniProtKB:  P27487
NIH Common Fund Data Resources
PHAROS:  P27487 GTEx:  ENSG00000197635

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	5		N-Glycosylation

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2KS	A, B	1-(cis-1-phenyl-4-{[(2E)-3-phenylprop-2-en-1-yl]oxy}cyclohexyl)methanamine C22 H27 N O JACSEOHFDRDIAI-VKAAWDBRSA-N
NAG	A, B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
2KS	IC50:  11900   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.170 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.315	α = 90
b = 121.924	β = 90
c = 190.836	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-10-17 
• Released Date: 2014-02-12 
Deposition Author(s): Ostermann, N., Zink, F., Kroemer, M.

Revision History 

• Version 1.0: 2014-02-12
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary