2P8S

Human dipeptidyl peptidase IV/CD26 in complex with a cyclohexalamine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Rational design of a novel, potent, and orally bioavailable cyclohexylamine DPP-4 inhibitor by application of molecular modeling and X-ray crystallography of sitagliptin

Biftu, T.Scapin, G.Singh, S.Feng, D.Becker, J.W.Eiermann, G.He, H.Lyons, K.Patel, S.Petrov, A.Sinha-Roy, R.Zhang, B.Wu, J.Zhang, X.Doss, G.A.Thornberry, N.A.Weber, A.E.

(2007) Bioorg.Med.Chem.Lett. 17: 3384-3387

  • DOI: 10.1016/j.bmcl.2007.03.095

  • PubMed Abstract: 
  • Molecular modeling was used to design a rigid analog of sitagliptin 1. The X-ray crystal structure of sitagliptin bound to DPP-4 suggested that the central beta-amino butyl amide moiety could be replaced with a cyclohexylamine group. This was confirm ...

    Molecular modeling was used to design a rigid analog of sitagliptin 1. The X-ray crystal structure of sitagliptin bound to DPP-4 suggested that the central beta-amino butyl amide moiety could be replaced with a cyclohexylamine group. This was confirmed by structural analysis and the resulting analog 2a was synthesized and found to be a potent DPP-4 inhibitor (IC(50)=21 nM) with excellent in vivo activity and pharmacokinetic profile.


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA. Tesfaye_Biftu@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIPEPTIDYL PEPTIDASE IV SOLUBLE FORM
A, B
728Homo sapiensMutation(s): 0 
Gene Names: DPP4 (ADCP2, CD26)
EC: 3.4.14.5
Find proteins for P27487 (Homo sapiens)
Go to Gene View: DPP4
Go to UniProtKB:  P27487
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
417
Query on 417

Download SDF File 
Download CCD File 
A, B
(1S,2R,5S)-5-[3-(TRIFLUOROMETHYL)-5,6-DIHYDRO[1,2,4]TRIAZOLO[4,3-A]PYRAZIN-7(8H)-YL]-2-(2,4,5-TRIFLUOROPHENYL)CYCLOHEXANAMINE
C18 H19 F6 N5
CNKRZILQBKJWDS-WMFXKJRFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
417IC50: 21 nM (99) BINDINGDB
417IC50: 21 nM BINDINGMOAD
417IC50: 21 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 118.139α = 90.00
b = 126.174β = 90.00
c = 137.340γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
ADSCdata collection
CNXrefinement
CNSrefinement
SCALEPACKdata scaling
CNXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-03-23 
  • Released Date: 2007-05-22 
  • Deposition Author(s): Scapin, G., Biftu, T.

Revision History 

  • Version 1.0: 2007-05-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance