3V9B Hydrolase Hydrolase Inhibitor date Dec 25, 2011
title Crystal Structure Of The Catalytic Domain Of Pde4d2 With (S) [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxyp Yl)-Ethyl]-1h-Pyrazl-3-Yl}Phenyl)Acetamide
authors H.T.Kim, H.J.Chang
compound source
Molecule: Camp-Specific 3',5'-Cyclic Phosphodiesterase 4d
Chain: A, B, C, D
Fragment: Catalytic Domain, Unp Residues 381-740
Synonym: Dpde3, Pde43
Ec: 3.1.4.17
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pde4d
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
symmetry Space Group: P 21 21 21
R_factor 0.206 R_Free 0.236
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.587 110.293 161.607 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand IHM, ZN enzyme Hydrolase E.C.3.1.4.17 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
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] (226 Kb) [Save to disk]
  • Biological Unit Coordinates (3v9b.pdb1.gz) 58 Kb
  • Biological Unit Coordinates (3v9b.pdb2.gz) 57 Kb
  • Biological Unit Coordinates (3v9b.pdb3.gz) 58 Kb
  • Biological Unit Coordinates (3v9b.pdb4.gz) 57 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
  • 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
  • 3D motif for 3V9B, from MSDmotif at EBI
  • 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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