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: 176.17 kDa 
• Atom Count: 13126 
• Residue Count: 1458 
• Unique protein chains: 1

3VJL

Crystal structure of human depiptidyl peptidase IV (DPP-4) in complex with a prolylthiazolidine inhibitor #2

• DOI: 10.2210/pdb3VJL/pdb

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


• Deposited: 2011-10-24 Released: 2012-10-24 
• Deposition Author(s): Akahoshi, F., Kishida, H., Miyaguchi, I., Yoshida, T., Ishii, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.230 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

Discovery and preclinical profile of teneligliptin (3-[(2S,4S)-4-[4-(3-methyl-1-phenyl-1H-pyrazol-5-yl)piperazin-1-yl]pyrrolidin-2-ylcarbonyl]thiazolidine): A highly potent, selective, long-lasting and orally active dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes

Yoshida, T., Akahoshi, F., Sakashita, H., Kitajima, H., Nakamura, M., Sonda, S., Takeuchi, M., Tanaka, Y., Ueda, N., Sekiguchi, S., Ishige, T., Shima, K., Nabeno, M., Abe, Y., Anabuki, J., Soejima, A., Yoshida, K., Takashina, Y., Ishii, S., Kiuchi, S., Fukuda, S., Tsutsumiuchi, R., Kosaka, K., Murozono, T., Nakamaru, Y., Utsumi, H., Masutomi, N., Kishida, H., Miyaguchi, I., Hayashi, Y.

(2012) Bioorg Med Chem 20: 5705-5719

• PubMed: 22959556 
• DOI: 10.1016/j.bmc.2012.08.012
• Primary Citation of Related Structures:  
  3VJK, 3VJL


• PubMed Abstract: 
  

Dipeptidyl peptidase IV (DPP-4) inhibition is suitable mechanism for once daily oral dosing regimen because of its low risk of hypoglycemia. We explored linked bicyclic heteroarylpiperazines substituted at the γ-position of the proline structure in the course of the investigation of l-prolylthiazolidines. The efforts led to the discovery of a highly potent, selective, long-lasting and orally active DPP-4 inhibitor, 3-[(2S,4S)-4-[4-(3-methyl-1-phenyl-1H-pyrazol-5-yl)piperazin-1-yl]pyrrolidin-2-ylcarbonyl]thiazolidine (8 g), which has a unique structure characterized by five consecutive rings. An X-ray co-crystal structure of 8 g in DPP-4 demonstrated that the key interaction between the phenyl ring on the pyrazole and the S(2) extensive subsite of DPP-4 not only boosted potency, but also increased selectivity. Compound 8 g, at 0.03 mg/kg or higher doses, significantly inhibited the increase of plasma glucose levels after an oral glucose load in Zucker fatty rats. Compound 8 g (teneligliptin) has been approved for the treatment of type 2 diabetes in Japan.

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Organizational Affiliation: 

Research Division, Mitsubishi Tanabe Pharma Corporation, 2-2-50, Kawagishi, Toda-shi, Saitama 335-8505, Japan.

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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F, G	2		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
W94	A, B	[(2S,4S)-4-{4-[1-phenyl-3-(trifluoromethyl)-1H-pyrazol-5-yl]piperidin-1-yl}pyrrolidin-2-yl](1,3-thiazolidin-3-yl)methanone C23 H28 F3 N5 O S CYNIHEXFNGMKLP-OALUTQOASA-N
NAG	A, B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
W94	IC50:  5.599999904632568   nM  BindingDB
W94	IC50:  5.599999904632568   nM  Binding MOAD
W94	IC50:  2.5   nM  BindingDB
W94	IC50 :  5.599999904632568   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.230 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.81	α = 90
b = 125.83	β = 90
c = 137.129	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-10-24 
• Released Date: 2012-10-24 
Deposition Author(s): Akahoshi, F., Kishida, H., Miyaguchi, I., Yoshida, T., Ishii, S.

Revision History 

• Version 1.0: 2012-10-24
  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