3WD9 Hydrolase Hydrolase Inhibitor date Jun 11, 2013
title Crystal Structure Of Phosphodiesterase 4b In Complex With Co
authors M.Takahashi, H.Hanzawa
compound source
Molecule: Camp-Specific 3',5'-Cyclic Phosphodiesterase 4b
Chain: A, B
Fragment: Unp Residues 324-700
Synonym: Dpde4, Pde32
Ec: 3.1.4.17
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dpde4, Pde4b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11d
symmetry Space Group: P 21 21 2
R_factor 0.174 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
81.305 157.376 58.050 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand CA, QPC, ZN enzyme Hydrolase E.C.3.1.4.17 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceSynthesis and biological evaluation of 5-carbamoyl-2-phenylpyrimidine derivatives as novel and potent PDE4 inhibitors., Goto T, Shiina A, Yoshino T, Mizukami K, Hirahara K, Suzuki O, Sogawa Y, Takahashi T, Mikkaichi T, Nakao N, Takahashi M, Hasegawa M, Sasaki S, Bioorg Med Chem. 2013 Nov 15;21(22):7025-37. doi: 10.1016/j.bmc.2013.09.013. Epub, 2013 Sep 19. PMID:24094436
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (125 Kb) [Save to disk]
  • Biological Unit Coordinates (3wd9.pdb1.gz) 61 Kb
  • Biological Unit Coordinates (3wd9.pdb2.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 3WD9
  • CSU: Contacts of Structural Units for 3WD9
  • Structure Factors (816 Kb)
  • Retrieve 3WD9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3WD9 from S2C, [Save to disk]
  • Re-refined 3wd9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3WD9 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 3WD9
  • 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 3WD9, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3wd9] [3wd9_B] [3wd9_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3WD9: [HDc ] by SMART
  • Other resources with information on 3WD9
  • Community annotation for 3WD9 at PDBWiki (http://pdbwiki.org)

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