5BVD Transferase Transferase Inhibitor date Jun 05, 2015
title Tetrahydropyrrolo-Diazepenones As Inhibitors Of Erk2 Kinase
authors X.Ma, S.Steven
compound source
Molecule: Mitogen-Activated Protein Kinase 1
Chain: A
Synonym: Mapk 1,Ert1,Extracellular Signal-Regulated Kinase Map Kinase Isoform P42,P42-Mapk,Mitogen-Activated Protein K Mapk 2;
Ec: 2.7.11.24
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mapk1, Erk2, Prkm1, Prkm2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.170 R_Free 0.207
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.271 71.282 120.451 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand 4VF, SO4 enzyme Transferase E.C.2.7.11.24 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • chemical synaptic transmissi...

    • Primary referenceTetrahydropyrrolo-diazepenones as inhibitors of ERK2 kinase., Bagdanoff JT, Jain R, Han W, Zhu S, Madiera AM, Lee PS, Ma X, Poon D, Bioorg Med Chem Lett. 2015 Sep 15;25(18):3788-92. doi:, 10.1016/j.bmcl.2015.07.091. Epub 2015 Jul 30. PMID:26259804
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (126 Kb) [Save to disk]
  • Biological Unit Coordinates (5bvd.pdb1.gz) 121 Kb
  • LPC: Ligand-Protein Contacts for 5BVD
  • CSU: Contacts of Structural Units for 5BVD
  • Structure Factors (1636 Kb)
  • Retrieve 5BVD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5BVD from S2C, [Save to disk]
  • Re-refined 5bvd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5BVD 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 5BVD
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5bvd_A] [5bvd]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5BVD: [S_TKc ] by SMART
    • Other resources with information on 5BVD
  • Community annotation for 5BVD at PDBWiki (http://pdbwiki.org)

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