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)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 337.41 kDa 
• Atom Count: 28111 
• Residue Count: 2904 
• Unique protein chains: 1

2G63

Crystal structure of human dipeptidyl peptidase IV (DPPIV) complexed with cyanopyrrolidine (C5-pro-pro) inhibitor 24b

• DOI: 10.2210/pdb2G63/pdb

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


• Deposited: 2006-02-24 Released: 2006-07-04 
• Deposition Author(s): Longenecker, K.L., Fry, E.H., Lake, M.R., Solomon, L.R., Pei, Z., Li, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.251 
• R-Value Work: 0.215 

Literature

Discovery, structure-activity relationship, and pharmacological evaluation of (5-substituted-pyrrolidinyl-2-carbonyl)-2-cyanopyrrolidines as potent dipeptidyl peptidase IV inhibitors.

Pei, Z., Li, X., Longenecker, K., Von Geldern, T.W., Wiedeman, P.E., Lubben, T.H., Zinker, B.A., Stewart, K., Ballaron, S.J., Stashko, M.A., Mika, A.K., Beno, D.W., Long, M., Wells, H., Kempf-Grote, A.J., Madar, D.J., McDermott, T.S., Bhagavatula, L., Fickes, M.G., Pireh, D., Solomon, L.R., Lake, M.R., Edalji, R., Fry, E.H., Sham, H.L., Trevillyan, J.M.

(2006) J Med Chem 49: 3520-3535

• PubMed: 16759095 
• DOI: 10.1021/jm051283e
• Primary Citation of Related Structures:  
  2G5T, 2G63, 2G5P


• PubMed Abstract: 
  

A series of (5-substituted pyrrolidinyl-2-carbonyl)-2-cyanopyrrolidine (C5-Pro-Pro) analogues was discovered as dipeptidyl peptidase IV (DPPIV) inhibitors as a potential treatment of diabetes and obesity. X-ray crystallography data show that these inhibitors bind to the catalytic site of DPPIV with the cyano group forming a covalent bond with the serine residue of DPPIV. The C5-substituents make various interactions with the enzyme and affect potency, chemical stability, selectivity, and PK properties of the inhibitors. Optimized analogues are extremely potent with subnanomolar K(i)'s, are chemically stable, show very little potency decrease in the presence of plasma, and exhibit more than 1,000-fold selectivity against related peptidases. The best compounds also possess good PK and are efficacious in lowering blood glucose in an oral glucose tolerance test in ZDF rats.

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Organizational Affiliation: 

Department of Exploratory Pharmacokinetics and Pharmaceutics, Metabolic Disease Research, Global Pharmaceutical Research and Development, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, Illinois 60064-3500, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4	A, B, C, D	726	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AAF	B	METHYL 4-{[({[(2R,5S)-5-{[(2S)-2-(AMINOMETHYL)PYRROLIDIN-1-YL]CARBONYL}PYRROLIDIN-2-YL]METHYL}AMINO)CARBONYL]AMINO}BENZOATE C20 H29 N5 O4 USDCNOQKDUFKRD-IKGGRYGDSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
AAF	Ki:  6.699999809265137   nM  BindingDB
AAF	Ki :  6.699999809265137   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.251 
• R-Value Work: 0.215 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.128	α = 90
b = 126.502	β = 96.66
c = 127.374	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-02-24 
• Released Date: 2006-07-04 
Deposition Author(s): Longenecker, K.L., Fry, E.H., Lake, M.R., Solomon, L.R., Pei, Z., Li, X.

Revision History 

• Version 1.0: 2006-07-04
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description