5B25 Hydrolase Hydrolase Inhibitor date Jan 07, 2016
title Crystal Structure Of Human Pde1b With Inhibitor 3
authors K.Ida, W.Lane, G.Snell, S.Sogabe
compound source
Molecule: Calciumcalmodulin-Dependent 3',5'-Cyclic Nucleot Phosphodiesterase 1b;
Chain: A, B, C, D
Fragment: Unp Residues 146-506
Synonym: Cam-Pde 1b
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pde1b, Pde1b1, Pdes1b
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pe-Sumopro Amp
symmetry Space Group: P 43 21 2
R_factor 0.172 R_Free 0.203
length a length b length c angle alpha angle beta angle gamma
102.875 102.875 294.848 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand 4QJ, GOL, MG, SO4, ZN enzyme Hydrolase E.C. BRENDA
A, D, C, B

Primary referenceDiscovery of Potent and Selective Inhibitors of Phosphodiesterase 1 for the Treatment of Cognitive Impairment Associated with Neurodegenerative and Neuropsychiatric Diseases., Li P, Zheng H, Zhao J, Zhang L, Yao W, Zhu H, Beard JD, Ida K, Lane W, Snell G, Sogabe S, Heyser CJ, Snyder GL, Hendrick JP, Vanover KE, Davis RE, Wennogle LP, J Med Chem. 2016 Feb 2. PMID:26789933
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (472 Kb) [Save to disk]
  • Biological Unit Coordinates (5b25.pdb1.gz) 119 Kb
  • Biological Unit Coordinates (5b25.pdb2.gz) 119 Kb
  • Biological Unit Coordinates (5b25.pdb3.gz) 120 Kb
  • Biological Unit Coordinates (5b25.pdb4.gz) 120 Kb
  • LPC: Ligand-Protein Contacts for 5B25
  • CSU: Contacts of Structural Units for 5B25
  • Structure Factors (2164 Kb)
  • Retrieve 5B25 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5B25 from S2C, [Save to disk]
  • Re-refined 5b25 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5B25 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 5B25
  • 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
  • Fold representative 5b25 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5b25] [5b25_D] [5b25_B] [5b25_A] [5b25_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5B25: [HDc ] by SMART
  • Other resources with information on 5B25
  • Community annotation for 5B25 at PDBWiki (http://pdbwiki.org)

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