5UOY Hydrolase Hydrolase Inhibitor date Feb 01, 2017
title Crystal Structure Of Human Pde1b Catalytic Domain In Complex Inhibitor 16j (6-(4-Methoxybenzyl)-9-((Tetrahydro-2h-Pyran- Methyl)-8,9,10,11-Tetrahydropyrido[4',3':4,5]Thieno[3,2-E][ 4]Triazolo[1,5-C]Pyrimidin-5(6h)-One)
authors E.P.Cedervall, C.K.Allerston, R.Xu, V.Sridhar, R.Barker, K.Aertge
compound source
Molecule: Calciumcalmodulin-Dependent 3',5'-Cyclic Nucleot Phosphodiesterase 1b;
Chain: A
Synonym: Cam-Pde 1b,63 Kda Cam-Pde
Ec: 3.1.4.17
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pde1b, Pde1b1, Pdes1b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 43 21 2
R_factor 0.189 R_Free 0.221
crystal
cell
length a length b length c angle alpha angle beta angle gamma
87.507 87.507 134.714 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.82 Å
ligand 8HM, MG, ZN enzyme Hydrolase E.C.3.1.4.17 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceDiscovery of Selective Phosphodiesterase 1 Inhibitors with Memory Enhancing Properties., Dyck B, Branstetter B, Gharbaoui T, Hudson AR, Breitenbucher JG, Gomez L, Botrous I, Marrone T, Barido R, Allerston CK, Cedervall EP, Xu R, Sridhar V, Barker R, Aertgeerts K, Schmelzer K, Neul D, Lee D, Massari ME, Andersen CB, Sebring K, Zhou X, Petroski R, Limberis J, Augustin M, Chun LE, Edwards TE, Peters M, Tabatabaei A, J Med Chem. 2017 Apr 13. doi: 10.1021/acs.jmedchem.7b00302. PMID:28406621
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (120 Kb) [Save to disk]
  • Biological Unit Coordinates (5uoy.pdb1.gz) 113 Kb
  • LPC: Ligand-Protein Contacts for 5UOY
  • CSU: Contacts of Structural Units for 5UOY
  • Structure Factors (740 Kb)
  • Retrieve 5UOY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5UOY from S2C, [Save to disk]
  • Re-refined 5uoy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5UOY 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 5UOY
  • 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 5uoy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5uoy_A] [5uoy]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5UOY
  • Community annotation for 5UOY at PDBWiki (http://pdbwiki.org)

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