6HKQ | pdb_00006hkq

Human GPX4 in complex with covalent Inhibitor ML162 (S enantiomer)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 
    0.184 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.149 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 
    0.151 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of the selenoprotein glutathione peroxidase 4 in its apo form and in complex with the covalently bound inhibitor ML162.

Moosmayer, D.Hilpmann, A.Hoffmann, J.Schnirch, L.Zimmermann, K.Badock, V.Furst, L.Eaton, J.K.Viswanathan, V.S.Schreiber, S.L.Gradl, S.Hillig, R.C.

(2021) Acta Crystallogr D Struct Biol 77: 237-248

  • DOI: https://doi.org/10.1107/S2059798320016125
  • Primary Citation Related Structures: 
    6HKQ, 6HN3

  • PubMed Abstract: 

    Wild-type human glutathione peroxidase 4 (GPX4) was co-expressed with SBP2 (selenocysteine insertion sequence-binding protein 2) in human HEK cells to achieve efficient production of this selenocysteine-containing enzyme on a preparative scale for structural biology. The protein was purified and crystallized, and the crystal structure of the wild-type form of GPX4 was determined at 1.0 Å resolution. The overall fold and the active site are conserved compared with previously determined crystal structures of mutated forms of GPX4. A mass-spectrometry-based approach was developed to monitor the reaction of the active-site selenocysteine Sec46 with covalent inhibitors. This, together with the introduction of a surface mutant (Cys66Ser), enabled the crystal structure determination of GPX4 in complex with the covalent inhibitor ML162 [(S)-enantiomer]. The mass-spectrometry-based approach described here opens the path to further co-complex crystal structures of this potential cancer drug target in complex with covalent inhibitors.


  • Organizational Affiliation
    • Research and Development, Pharmaceuticals, Bayer AG, 13353 Berlin, Germany.

Macromolecule Content 

  • Total Structure Weight: 21.16 kDa 
  • Atom Count: 1,645 
  • Modeled Residue Count: 166 
  • Deposited Residue Count: 176 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phospholipid hydroperoxide glutathione peroxidase176Homo sapiensMutation(s): 1 
Gene Names: GPX4
EC: 1.11.1.12 (PDB Primary Data), 1.11.1.9 (UniProt)
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P36969 (Homo sapiens)
Explore P36969 
Go to UniProtKB:  P36969
PHAROS:  P36969
GTEx:  ENSG00000167468 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36969
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G9N
(Subject of Investigation/LOI)

Query on G9N



Download:Ideal Coordinates CCD File
B [auth A](2~{S})-2-[2-chloranylethanoyl-(3-chloranyl-4-methoxy-phenyl)amino]-~{N}-(2-phenylethyl)-2-thiophen-2-yl-ethanamide
C23 H22 Cl2 N2 O3 S
UNVKYJSNMVDZJE-JOCHJYFZSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS

Query on DMS



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free:  0.184 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.149 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 0.151 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.734α = 90
b = 57.249β = 90
c = 81.311γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data 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: 2020-04-01
    Type: Initial release
  • Version 1.1: 2021-06-16
    Changes: Database references
  • Version 1.2: 2022-12-07
    Changes: Advisory, Database references, Derived calculations, Source and taxonomy
  • Version 1.3: 2025-10-01
    Changes: Data collection, Derived calculations, Structure summary