5BPA Hydrolase Hydrolase Inhibitor date May 27, 2015
title X-Ray Co-Structure Of Mmp-13 With 4-[({5-[2-(Ethoxycarbonyl) 5-Yl]-1-Methyl-1h-Pyrazol-3-Yl}Formamido)Methyl]Benzoate
authors N.A.Farrow, S.M.Margarit
compound source
Molecule: Collagenase 3
Chain: A, B
Fragment: Unp Residues 104-274
Synonym: Matrix Metalloproteinase-13,Mmp-13
Ec: 3.4.24.-
Engineered: Yes
Fragment: 104-274
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mmp13
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: C 1 2 1
R_factor 0.237 R_Free 0.280
crystal
cell
length a length b length c angle alpha angle beta angle gamma
135.281 36.141 96.097 90.00 131.48 90.00
method X-Ray Diffractionresolution 1.79 Å
ligand 4UF, CA, ZN enzyme Hydrolase E.C.3.4.24 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceFragment-based discovery of indole inhibitors of matrix metalloproteinase-13., Taylor SJ, Abeywardane A, Liang S, Muegge I, Padyana AK, Xiong Z, Hill-Drzewi M, Farmer B, Li X, Collins B, Li JX, Heim-Riether A, Proudfoot J, Zhang Q, Goldberg D, Zuvela-Jelaska L, Zaher H, Li J, Farrow NA, J Med Chem. 2011 Dec 8;54(23):8174-87. doi: 10.1021/jm201129m. Epub 2011 Nov 9. PMID:22017539
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (68 Kb) [Save to disk]
  • Biological Unit Coordinates (5bpa.pdb1.gz) 62 Kb
  • LPC: Ligand-Protein Contacts for 5BPA
  • CSU: Contacts of Structural Units for 5BPA
  • Structure Factors (285 Kb)
  • Retrieve 5BPA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5BPA from S2C, [Save to disk]
  • Re-refined 5bpa structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5BPA 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 5BPA
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 5BPA, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5bpa_B] [5bpa_A] [5bpa]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5BPA: [ZnMc ] by SMART
  • Other resources with information on 5BPA
  • Community annotation for 5BPA at PDBWiki (http://pdbwiki.org)

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