Biological Assembly 1  

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: 168.89 kDa 
• Atom Count: 13,345 
• Modelled Residue Count: 1,452 
• Deposited Residue Count: 1,452 
• Unique protein chains: 1

 2G5T

Crystal structure of human dipeptidyl peptidase IV (DPPIV) complexed with cyanopyrrolidine (C5-pro-pro) inhibitor 21ag

• PDB DOI:  https://doi.org/10.2210/pdb2G5T/pdb

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


• Deposited: 2006-02-23 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: 2.30 Å
• R-Value Free: 0.243 
• R-Value Work: 0.190 

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: https://doi.org/10.1021/jm051283e
• Primary Citation of Related Structures:  
  2G5P, 2G5T, 2G63


• 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	726	Homo sapiens	Mutation(s): 0  Gene Names: DPP4, ADCP2, CD26 EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for P27487 (Homo sapiens) Explore P27487  Go to UniProtKB:  P27487
PHAROS:  P27487

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACF	C [auth A]	3-{[(2R,5S)-5-{[(2S)-2-(AMINOMETHYL)PYRROLIDIN-1-YL]CARBONYL}PYRROLIDIN-2-YL]METHOXY}-4-CHLOROBENZOIC ACID C18 H24 Cl N3 O4 DUMYZIXJYDQLTO-IPYPFGDCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ACF	PDBBind:  2G5T	Ki: 0.82 (nM) from 1 assay(s)
	BindingDB:  2G5T	Ki: 0.82 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.243 
• R-Value Work: 0.190 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.733	α = 90
b = 126.788	β = 99.49
c = 112.292	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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