2P8S | pdb_00002p8s

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.227 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2P8S

Ligand Structure Quality Assessment 


This is version 2.2 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: https://doi.org/10.1016/j.bmcl.2007.03.095
  • Primary Citation Related Structures: 
    2P8S

  • 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 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

Macromolecule Content 

  • Total Structure Weight: 174.96 kDa 
  • Atom Count: 13,442 
  • Modeled Residue Count: 1,456 
  • Deposited Residue Count: 1,456 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DIPEPTIDYL PEPTIDASE IV SOLUBLE FORM
A, B
728Homo sapiensMutation(s): 0 
Gene Names: DPP4ADCP2CD26
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
GTEx:  ENSG00000197635 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27487
Glycosylation
Glycosylation Sites: 7Go to GlyGen: P27487-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, E, F, G
C, D, E, F, G, H, I, J, K
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
417

Query on 417



Download:Ideal Coordinates CCD File
P [auth A],
T [auth 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
NAG

Query on NAG



Download:Ideal Coordinates CCD File
L [auth A]
M [auth A]
N [auth A]
Q [auth B]
R [auth B]
L [auth A],
M [auth A],
N [auth A],
Q [auth B],
R [auth B],
S [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
O [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.227 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.139α = 90
b = 126.174β = 90
c = 137.34γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNXphasing
CNXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-16
    Changes: Structure summary