6PLB

Adducts formed after 1 month in the reaction of dichlorido(1,3-dimethylbenzimida zol-2-ylidene)(eta5-pentamethylcyclopentadienyl)iridium(III) with HEWL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Probing the Paradigm of Promiscuity for N-Heterocyclic Carbene Complexes and their Protein Adduct Formation.

Sullivan, M.P.Cziferszky, M.Tolbatov, I.Truong, D.Mercadante, D.Re, N.Gust, R.Goldstone, D.C.Hartinger, C.

(2021) Angew Chem Int Ed Engl 

  • DOI: https://doi.org/10.1002/anie.202106906
  • Primary Citation of Related Structures:  
    6PL9, 6PLA, 6PLB

  • PubMed Abstract: 

    Metal complexes can be considered a "paradigm of promiscuity" when it comes to their interactions with proteins. They often form adducts with a variety of donor atoms in an unselective manner. We have characterized the adducts formed between a series of isostructural N-heterocyclic carbene (NHC) complexes with Ru, Os, Rh, and Ir centers and the model protein hen egg white lysozyme by X-ray crystallography and mass spectrometry. Distinctive behavior for the metal compounds was observed with the more labile Ru and Rh complexes targeting mainly a surface l-histidine moiety through cleavage of p-cymene or NHC co-ligands, respectively. In contrast, the more inert Os and Ir derivatives were detected abundantly in an electronegative binding pocket after undergoing ligand exchange of a chlorido ligand for an amino acid side chain. Computational studies supported the binding profiles and hinted at the role of the protein microenvironment for metal complexes eliciting selectivity for specific binding sites on the protein.


  • Organizational Affiliation

    School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OT1 (Subject of Investigation/LOI)
Query on OT1

Download Ideal Coordinates CCD File 
B [auth A]2-(1-chloranyl-2,3,4,5,6-pentamethyl-1$l^{7}-iridapentacyclo[2.2.0.0^{1,3}.0^{1,5}.0^{2,6}]hexan-1-yl)-1,3-dimethyl-benzimidazole
C19 H25 Cl Ir N2
FEMPBTXZISTUOL-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.338α = 90
b = 78.338β = 90
c = 37.833γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2021-07-14
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description