3WV1 Hydrolase Hydrolase Inhibitor date May 12, 2014
title Crystal Structure Of The Catalytic Domain Of Mmp-13 Complexe (2-((6-Fluoro-2-((3-Methoxybenzyl)Carbamoyl)-4-Oxo-3,4- Dihydroquinazolin-5-Yl)Oxy)Ethyl)Benzoic Acid
authors H.Oki, Y.Tanaka
compound source
Molecule: Collagenase 3
Chain: A, B
Fragment: Catalytic Domain, Residues 104-274
Synonym: Matrix Metalloproteinase-13, Mmp-13
Ec: 3.4.24.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mmp13
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: C 1 2 1
R_factor 0.175 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
134.372 36.058 95.298 90.00 130.90 90.00
method X-Ray Diffractionresolution 1.98 Å
ligand CA, FMT, NA, WHH, ZN enzyme Hydrolase E.C.3.4.24 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceDiscovery of novel, highly potent, and selective quinazoline-2-carboxamide-based matrix metalloproteinase (MMP)-13 inhibitors without a zinc binding group using a structure-based design approach., Nara H, Sato K, Naito T, Mototani H, Oki H, Yamamoto Y, Kuno H, Santou T, Kanzaki N, Terauchi J, Uchikawa O, Kori M, J Med Chem. 2014 Nov 13;57(21):8886-902. doi: 10.1021/jm500981k. Epub 2014 Oct, 15. PMID:25264600
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (122 Kb) [Save to disk]
  • Biological Unit Coordinates (3wv1.pdb1.gz) 60 Kb
  • Biological Unit Coordinates (3wv1.pdb2.gz) 58 Kb
  • Biological Unit Coordinates (3wv1.pdb3.gz) 116 Kb
  • LPC: Ligand-Protein Contacts for 3WV1
  • CSU: Contacts of Structural Units for 3WV1
  • Structure Factors (363 Kb)
  • Retrieve 3WV1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3WV1 from S2C, [Save to disk]
  • Re-refined 3wv1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3WV1 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 3WV1
  • 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 3WV1, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3wv1_B] [3wv1_A] [3wv1]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3WV1: [ZnMc ] by SMART
  • Other resources with information on 3WV1
  • Community annotation for 3WV1 at PDBWiki (http://pdbwiki.org)

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