2I78 | pdb_00002i78

Crystal structure of human dipeptidyl peptidase IV (DPP IV) complexed with ABT-341, a cyclohexene-constrained phenethylamine inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.275 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.220 (DCC) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted KIQClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history. 


Literature

Discovery of Cyclohexene-constrained Phenethylamine ABT-341, a Highly Potent, Selective, Orally Bioavailable, Safe and Potential Next-generation Dipeptidyl Peptidase IV Inhibitor for the Treatment of Type 2 Diabetes

Pei, Z., Li, X., vonGeldern, T.W., Madar, D.J., L Longenecker, K., Yong, H., Lubben, T.H., Stewart, K.D., Zinker, B.A., Backes, B.J., Judd, A.S., Mulhern, M., Ballaron, S.J., Stashko, M.A., Mika, A.K., Beno, D.W.A., Reinhart, G.A., Fryer, R.M., Preusser, L.C., Kempf-Grote, A.J., Sham, H.L., Trevillyan, J.M.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase IV
A, B, C, D
726Homo sapiensMutation(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
GTEx:  ENSG00000197635 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27487
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KIQ
Query on KIQ
Download Ideal Coordinates CCD File 
E [auth B](1S,6R)-3-{[3-(TRIFLUOROMETHYL)-5,6-DIHYDRO[1,2,4]TRIAZOLO[4,3-A]PYRAZIN-7(8H)-YL]CARBONYL}-6-(2,4,5-TRIFLUOROPHENYL)CYCLOHEX-3-EN-1-AMINE
C19 H17 F6 N5 O
NVVSPGQEXMJZIR-BMIGLBTASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.275 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.933α = 90
b = 126.419β = 100.26
c = 127.531γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted KIQClick on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary