2I3Z | pdb_00002i3z

rat DPP-IV with xanthine mimetic inhibitor #7

• PDB DOI: https://doi.org/10.2210/pdb2I3Z/pdb

• Classification: HYDROLASE
• Organism(s): Rattus norvegicus
• Mutation(s): No 


• Deposited: 2006-08-21 Released: 2006-12-12 
• Deposition Author(s): Kurukulasuriya, R., Rohde, J.J., Szczepankiewicz, B.G., Basha, F., Lai, C., Winn, M., Stewart, K.D., Longenecker, K.L., Lubben, T.W., Ballaron, S.J., Sham, H.L., VonGeldern, T.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.290 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.247 (DCC) 

Literature

Xanthine mimetics as potent dipeptidyl peptidase IV inhibitors.

Kurukulasuriya, R., Rohde, J.J., Szczepankiewicz, B.G., Basha, F., Lai, C., Jae, H.S., Winn, M., Stewart, K.D., Longenecker, K.L., Lubben, T.W., Ballaron, S.J., Sham, H.L., von Geldern, T.W.

(2006) Bioorg Med Chem Lett 16: 6226-6230

• PubMed: 17010607 
• DOI: https://doi.org/10.1016/j.bmcl.2006.09.024
• Primary Citation Related Structures: 
  2I3Z


• PubMed Abstract: 
  

  A series of xanthine mimetics containing 5,5 and 5,6 heterocycle fused imidazoles were synthesized as dipeptidyl peptidase IV inhibitors. Compound 7 is potent (h-DPPIV K(i)=2nM) and exhibits excellent selectivity and no species specificity against rat and human enzymes. The X-ray structure confirms that the binding mode of 7 to rat DPPIV is similar to the parent xanthines.

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Organizational Affiliation: 
• Metabolic Disease Research, Global Pharmaceutical Research and Development, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL 60064-6098, USA. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 169.04 kDa 
• Atom Count: 11,867 
• Modeled Residue Count: 1,460 
• Deposited Residue Count: 1,460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV)	A, B	730	Rattus norvegicus	Mutation(s): 0  EC: 3.4.14.5
UniProt
Find proteins for P14740 (Rattus norvegicus) Explore P14740  Go to UniProtKB:  P14740

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LIR	C [auth A]	2-[(3S)-3-AMINOPIPERIDIN-1-YL]-1-(2-CYANOBENZYL)-5-METHYL-4,6-DIOXO-3,4,5,6-TETRAHYDROPYRROLO[3,4-D]IMIDAZOL-1-IUM C19 H21 N6 O2 WVRGIUWTFUXDGX-AWEZNQCLSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.290 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.247 (DCC) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 207.293	α = 90
b = 207.293	β = 90
c = 207.293	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-12 
Deposition Author(s): Kurukulasuriya, R., Rohde, J.J., Szczepankiewicz, B.G., Basha, F., Lai, C., Winn, M., Stewart, K.D., Longenecker, K.L., Lubben, T.W., Ballaron, S.J., Sham, H.L., VonGeldern, T.W.

Revision History  

• Version 1.0: 2006-12-12
  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
• Version 1.4: 2018-01-24
  Changes: Structure summary
• Version 1.5: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary