6KO9

Crystal structure of the Gefitinib Intermediate 1 bound RamR determined with XtaLAB Synergy


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.224 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Development of a structure determination method using a multidrug-resistance regulator protein as a framework.

Matsumoto, T.Nakashima, R.Yamano, A.Nishino, K.

(2019) Biochem Biophys Res Commun 518: 402-408

  • DOI: https://doi.org/10.1016/j.bbrc.2019.08.070
  • Primary Citation of Related Structures:  
    6KO7, 6KO8, 6KO9

  • PubMed Abstract: 

    The structure determination of organic compounds is desirable for the development of medicines, aroma chemicals, and agricultural chemicals. However, the crystallization of organic compounds is often troublesome, because crystallization requires a relatively large quantity of high purity compounds and crystallization trials often need to be performed repetitively using different conditions. Some proteins are known to be able to bind to various organic compounds. The multidrug-resistance regulator protein RamR is one such protein. We have developed a structure determination method for organic compounds using RamR. RamR bound to organic compounds, including one compound that was not a known ligand for RamR, and the structures of the complexes were successfully determined. Because the RamR crystal is hydrophilic, this method may be useful for compounds that cannot be handled by the crystalline sponge method.


  • Organizational Affiliation

    Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima, Tokyo, 196-8666, Japan. Electronic address: [email protected].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative regulatory protein
A, B, C, D
194Salmonella enterica subsp. enterica serovar Typhimurium str. 14028SMutation(s): 0 
Gene Names: STM14_0676
UniProt
Find proteins for Q8ZR43 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q8ZR43 
Go to UniProtKB:  Q8ZR43
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZR43
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XZ1 (Subject of Investigation/LOI)
Query on XZ1

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
4-[(3-chloranyl-4-fluoranyl-phenyl)amino]-7-methoxy-quinazolin-6-ol
C15 H11 Cl F N3 O2
JLVTVCRXFMLUIF-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D],
M [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.224 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.513α = 74.64
b = 54.792β = 81.94
c = 92.224γ = 89.98
Software Package:
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrysalisProdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description