3VFE Hydrolase date Jan 09, 2012
title Virtual Screening And X-Ray Crystallography For Human Kallik Inhibitors With An Amidinothiophene P1 Group
authors X.Chen, Y.Zhang, T.Xia, R.Wang
compound source
Molecule: Kallikrein-6
Chain: A
Fragment: Hk6 Chain A
Synonym: Neurosin, Protease M, Sp59, Serine Protease 18, Se Protease 9, Zyme;
Ec: 3.4.21.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Klk6, Prss18, Prss9
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
symmetry Space Group: P 21 21 21
R_factor 0.193 R_Free 0.223
crystal
cell
length a length b length c angle alpha angle beta angle gamma
43.938 47.909 107.553 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.88 Å
ligand 0HL enzyme Hydrolase E.C.3.4.21 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceHuman kallikrein 6 inhibitors with a para-amidobenzylanmine P1 group identified through virtual screening., Liang G, Chen X, Aldous S, Pu SF, Mehdi S, Powers E, Xia T, Wang R, Bioorg Med Chem Lett. 2012 Apr 1;22(7):2450-5. Epub 2012 Feb 14. PMID:22386244
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (43 Kb) [Save to disk]
  • Biological Unit Coordinates (3vfe.pdb1.gz) 39 Kb
  • LPC: Ligand-Protein Contacts for 3VFE
  • CSU: Contacts of Structural Units for 3VFE
  • Structure Factors (258 Kb)
  • Retrieve 3VFE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VFE from S2C, [Save to disk]
  • Re-refined 3vfe structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VFE 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 3VFE
  • 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
  • 3D motif for 3VFE, from MSDmotif at EBI
  • Fold representative 3vfe from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vfe_A] [3vfe]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3VFE: [Tryp_SPc ] by SMART
  • Other resources with information on 3VFE
  • Community annotation for 3VFE at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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