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) 
  • R-Value Work: 
    0.216 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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.

Macromolecule Content 

  • Total Structure Weight: 337.45 kDa 
  • Atom Count: 24,449 
  • Modeled Residue Count: 2,904 
  • Deposited Residue Count: 2,904 
  • Unique protein chains: 1

Macromolecules

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|  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) 
  • R-Value Work:  0.216 (Depositor) 
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

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Ligand Structure Quality Assessment 


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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