2QTB

Human dipeptidyl peptidase iv/cd26 in complex with a 4-aryl cyclohexylalanine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

4-Arylcyclohexylalanine analogs as potent, selective, and orally active inhibitors of dipeptidyl peptidase IV.

Kaelin, D.E.Smenton, A.L.Eiermann, G.J.He, H.Leiting, B.Lyons, K.A.Patel, R.A.Patel, S.B.Petrov, A.Scapin, G.Wu, J.K.Thornberry, N.A.Weber, A.E.Duffy, J.L.

(2007) Bioorg.Med.Chem.Lett. 17: 5806-5811

  • DOI: 10.1016/j.bmcl.2007.08.049
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A novel series of 4-arylcyclohexylalanine DPP-4 inhibitors was synthesized and tested for inhibitory activity as well as selectivity over the related proline-specific enzymes DPP-8 and DPP-9. Optimization of this series led to 28 (DPP-4 IC(50)=4.8 nM ...

    A novel series of 4-arylcyclohexylalanine DPP-4 inhibitors was synthesized and tested for inhibitory activity as well as selectivity over the related proline-specific enzymes DPP-8 and DPP-9. Optimization of this series led to 28 (DPP-4 IC(50)=4.8 nM), which showed an excellent pharmacokinetic profile across several preclinical species. Evaluation of 28 in an oral glucose tolerance test demonstrated that this compound effectively reduced glucose excursion in lean mice.


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, Rahway, NJ 07065, USA. david_kaelin@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptidyl peptidase 4
A, B
766Homo sapiensMutation(s): 1 
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 4 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
474
Query on 474

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Download CCD File 
A, B
(2S,3S)-3-AMINO-4-(3,3-DIFLUOROPYRROLIDIN-1-YL)-N,N-DIMETHYL-4-OXO-2-(TRANS-4-[1,2,4]TRIAZOLO[1,5-A]PYRIDIN-6-YLCYCLOHEXYL)BUTANAMIDE
6-(4-{(1S,2S)-2-AMMONIO-3-(3,3-DIFLUOROPYRROLIDIN-1-YL)-1-[(DIMETHYLAMINO)CARBONYL] -3-OXOPROPYL}CYCLOHEXYL)[1,2,4]TRIAZOLO[1,5-A]PYRIDIN-1-IUM
C22 H30 F2 N6 O2
JNAZOMVWUGPITI-LNMJFAINSA-N
 Ligand Interaction
NDG
Query on NDG

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Download CCD File 
L, M, O, P
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, L, M, O, P, Q, R, S, T
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
474IC50: 4.8 - 130 nM (99) BINDINGDB
474IC50: 4.8 nM BINDINGMOAD
474IC50: 4.8 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 117.863α = 90.00
b = 125.629β = 90.00
c = 136.806γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
CNXphasing
DENZOdata reduction
PDB_EXTRACTdata extraction
CNXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-08-01 
  • Released Date: 2007-11-06 
  • Deposition Author(s): Scapin, G.

Revision History 

  • Version 1.0: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description