6B1O Hydrolase Hydrolase Inhibitor date Sep 18, 2017
title The Structure Of Dpp4 In Complex With Vildagliptin Analog
authors G.Scapin
compound source
Molecule: Dipeptidyl Peptidase 4
Chain: A, B
Synonym: Adabp,Adenosine Deaminase Complexing Protein 2,Adc Dipeptidyl Peptidase Iv,Dpp Iv,T-Cell Activation Antigen Cd
Ec: 3.4.14.5
Engineered: Yes
Mutation: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dpp4, Adcp2, Cd26
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
symmetry Space Group: P 21 21 21
R_factor 0.172 R_Free 0.202
crystal
cell
length a length b length c angle alpha angle beta angle gamma
119.515 123.342 130.958 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.91 Å
ligand C8S, NAG enzyme Hydrolase E.C.3.4.14.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • virus receptor activity
  • chemorepellent activity


    • Primary referenceA comparative study of the binding properties, dipeptidyl peptidase-4 (DPP-4) inhibitory activity and glucose-lowering efficacy of the DPP-4 inhibitors alogliptin, linagliptin, saxagliptin, sitagliptin and vildagliptin in mice., Berger JP, SinhaRoy R, Pocai A, Kelly TM, Scapin G, Gao YD, Pryor KAD, Wu JK, Eiermann GJ, Xu SS, Zhang X, Tatosian DA, Weber AE, Thornberry NA, Carr RD, Endocrinol Diabetes Metab. 2017 Nov 24;1(1):e00002. doi: 10.1002/edm2.2., eCollection 2018 Jan. PMID:30815539
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (512 Kb) [Save to disk]
  • Biological Unit Coordinates (6b1o.pdb1.gz) 504 Kb
  • LPC: Ligand-Protein Contacts for 6B1O
  • CSU: Contacts of Structural Units for 6B1O
  • Structure Factors (4294 Kb)
  • Retrieve 6B1O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6B1O from S2C, [Save to disk]
    • View 6B1O in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 6B1O
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6b1o_B] [6b1o_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6B1O
  • Community annotation for 6B1O at PDBWiki (http://pdbwiki.org)

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