3V9B Crystal structure of the catalytic domain of PDE4D2 with (S)-N-(3-{1-[1-(3-Cyclopropylmethoxy-4-difluoromethoxyphenyl)-2-(1-oxypyridin-4-yl)-ethyl]-1H-pyrazl-3-yl}phenyl)acetamide date
authors Kim, H.T., Chang, H.J.
compound source
R_Free 0.236
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.10
ligand IHM, ZN enzyme
A, D, C, B

Primary referenceStereoselective synthesis of novel pyrazole derivatives using tert-butansulfonamide as a chiral auxiliary., Park CM, Jeon DJ, Org Biomol Chem. 2012 Apr 7;10(13):2613-20. doi: 10.1039/c2ob06495b. Epub 2012, Feb 27. PMID:22371117
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (231 Kb) [Save to disk]
  • Biological Unit Coordinates (3v9b.pdb1.gz) 60 Kb
  • Biological Unit Coordinates (3v9b.pdb2.gz) 59 Kb
  • Biological Unit Coordinates (3v9b.pdb3.gz) 59 Kb
  • Biological Unit Coordinates (3v9b.pdb4.gz) 59 Kb
  • LPC: Ligand-Protein Contacts for 3V9B
  • CSU: Contacts of Structural Units for 3V9B
  • Structure Factors (1352 Kb)
  • Retrieve 3V9B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3V9B from S2C, [Save to disk]
  • Re-refined 3v9b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3V9B 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 3V9B
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3V9B, from MSDmotif at EBI
  • Fold representative 3v9b from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3v9b_A] [3v9b_C] [3v9b_B] [3v9b_D] [3v9b]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3V9B: [HDc ] by SMART
  • Other resources with information on 3V9B
  • Community annotation for 3V9B at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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