4FFW

Crystal Structure of Dipeptidyl Peptidase IV (DPP4, DPP-IV, CD26) in Complex with Fab + sitagliptin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.287 
  • R-Value Observed: 0.288 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

An Inhibitory Antibody Against DPP IV Improves Glucose Tolerance in vivo - Validation of Large Molecule Approach for DPP IV Inhibition

Tang, J.Majeti, J.Sudom, A.Xiong, Y.Lu, M.Liu, Q.Higbee, J.Zhang, Y.Wang, Y.Wang, W.Cao, P.Xia, Z.Johnstone, S.Yang, X.Yu, T.Sharkov, N.Walker, N.Tu, H.Shen, W.Wang, Z.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4
A, B
730Rattus norvegicusMutation(s): 0 
Gene Names: Dpp4Cd26
EC: 3.4.14.5
UniProt
Find proteins for P14740 (Rattus norvegicus)
Explore P14740 
Go to UniProtKB:  P14740
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14740
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab light chainC,
F [auth L]
210Mus musculusMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab heavy chainD,
E [auth H]
217Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
715
Query on 715

Download Ideal Coordinates CCD File 
G [auth A],
H [auth B]
(2R)-4-OXO-4-[3-(TRIFLUOROMETHYL)-5,6-DIHYDRO[1,2,4]TRIAZOLO[4,3-A]PYRAZIN-7(8H)-YL]-1-(2,4,5-TRIFLUOROPHENYL)BUTAN-2-A MINE
C16 H15 F6 N5 O
MFFMDFFZMYYVKS-SECBINFHSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
715 BindingDB:  4FFW Kd: min: 1.3, max: 14 (nM) from 3 assay(s)
IC50: min: 3.5, max: 120 (nM) from 29 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.287 
  • R-Value Observed: 0.288 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.77α = 90
b = 200.86β = 93.64
c = 97.93γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-12
    Type: Initial release
  • Version 1.1: 2018-06-06
    Changes: Data collection
  • Version 1.2: 2021-05-19
    Changes: Derived calculations, Source and taxonomy, Structure summary