5KYK Hydrolase Hydrolase Inhibitor date Jul 21, 2016
title Covalent Gtp-Competitive Inhibitors Of Kras G12c: Guanosine Bisphosphonate Analogs
authors Y.Xiong, J.Lu, J.Hunter, L.Li, D.Scott, A.Manandhar, S.Gondi, K.D.W N.S.Gray
compound source
Molecule: Gtpase Kras
Chain: A, B, C
Fragment: Unp Residues 1-168
Synonym: K-Ras 2,Ki-Ras,C-K-Ras,C-Ki-Ras
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kras, Kras2, Rask2
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
symmetry Space Group: C 1 2 1
R_factor 0.267 R_Free 0.314
crystal
cell
length a length b length c angle alpha angle beta angle gamma
114.830 66.155 98.006 90.00 112.98 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand 6ZD enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceCovalent Guanosine Mimetic Inhibitors of G12C KRAS., Xiong Y, Lu J, Hunter J, Li L, Scott D, Choi HG, Lim SM, Manandhar A, Gondi S, Sim T, Westover KD, Gray NS, ACS Med Chem Lett. 2016 Nov 30;8(1):61-66. doi: 10.1021/acsmedchemlett.6b00373., eCollection 2017 Jan 12. PMID:28105276
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (174 Kb) [Save to disk]
  • Biological Unit Coordinates (5kyk.pdb1.gz) 57 Kb
  • Biological Unit Coordinates (5kyk.pdb2.gz) 58 Kb
  • Biological Unit Coordinates (5kyk.pdb3.gz) 58 Kb
  • LPC: Ligand-Protein Contacts for 5KYK
  • CSU: Contacts of Structural Units for 5KYK
  • Structure Factors (119 Kb)
  • Retrieve 5KYK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5KYK from S2C, [Save to disk]
  • Re-refined 5kyk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5KYK 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 5KYK
  • 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: [5kyk] [5kyk_A] [5kyk_B] [5kyk_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5KYK
  • Community annotation for 5KYK at PDBWiki (http://pdbwiki.org)

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