5KID | pdb_00005kid

Tightening the Recognition of Tetravalent Zr and Th Complexes by the Siderophore-Binding Mammalian Protein Siderocalin for Theranostic Applications


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.263 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.232 (Depositor) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Engineered Recognition of Tetravalent Zirconium and Thorium by Chelator-Protein Systems: Toward Flexible Radiotherapy and Imaging Platforms.

Captain, I.Deblonde, G.J.Rupert, P.B.An, D.D.Illy, M.C.Rostan, E.Ralston, C.Y.Strong, R.K.Abergel, R.J.

(2016) Inorg Chem 55: 11930-11936

  • DOI: https://doi.org/10.1021/acs.inorgchem.6b02041
  • Primary Citation Related Structures: 
    5KHP, 5KID

  • PubMed Abstract: 

    Targeted α therapy holds tremendous potential as a cancer treatment: it offers the possibility of delivering a highly cytotoxic dose to targeted cells while minimizing damage to surrounding healthy tissue. The metallic α-generating radioisotopes 225 Ac and 227 Th are promising radionuclides for therapeutic use, provided adequate chelation and targeting. Here we demonstrate a new chelating platform composed of a multidentate high-affinity oxygen-donating ligand 3,4,3-LI(CAM) bound to the mammalian protein siderocalin. Respective stability constants log β 110 = 29.65 ± 0.65, 57.26 ± 0.20, and 47.71 ± 0.08, determined for the Eu III (a lanthanide surrogate for Ac III ), Zr IV , and Th IV complexes of 3,4,3-LI(CAM) through spectrophotometric titrations, reveal this ligand to be one of the most powerful chelators for both trivalent and tetravalent metal ions at physiological pH. The resulting metal-ligand complexes are also recognized with extremely high affinity by the siderophore-binding protein siderocalin, with dissociation constants below 40 nM and tight electrostatic interactions, as evidenced by X-ray structures of the protein:ligand:metal adducts with Zr IV and Th IV . Finally, differences in biodistribution profiles between free and siderocalin-bound 238 Pu IV -3,4,3-LI(CAM) complexes confirm in vivo stability of the protein construct. The siderocalin:3,4,3-LI(CAM) assembly can therefore serve as a "lock" to consolidate binding to the therapeutic 225 Ac and 227 Th isotopes or to the positron emission tomography emitter 89 Zr, independent of metal valence state.


  • Organizational Affiliation
    • Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States.

Macromolecule Content 

  • Total Structure Weight: 65.58 kDa 
  • Atom Count: 4,269 
  • Modeled Residue Count: 516 
  • Deposited Residue Count: 540 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neutrophil gelatinase-associated lipocalin
A, B, C
180Homo sapiensMutation(s): 0 
Gene Names: LCN2HNLNGAL
UniProt & NIH Common Fund Data Resources
Find proteins for P80188 (Homo sapiens)
Explore P80188 
Go to UniProtKB:  P80188
PHAROS:  P80188
GTEx:  ENSG00000148346 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80188
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7K9

Query on 7K9



Download:Ideal Coordinates CCD File
E [auth A],
L [auth B],
N [auth C]
N,N'-(butane-1,4-diyl)bis(N-{3-[(2,3-dihydroxybenzene-1-carbonyl)amino]propyl}-2,3-dihydroxybenzamide)
C38 H42 N4 O12
WNIXXCINEMCWIS-UHFFFAOYSA-N
TH

Query on TH



Download:Ideal Coordinates CCD File
D [auth A],
K [auth B],
M [auth C]
THORIUM ION
Th
YMURPAJPLBCAQW-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
O [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
H [auth A],
P [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.263 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.232 (Depositor) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.547α = 90
b = 115.547β = 90
c = 118.028γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary