7QZU

Structure of liver pyruvate kinase in complex with anthraquinone derivative 47


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Anthraquinone derivatives as ADP-competitive inhibitors of liver pyruvate kinase.

Nain-Perez, A.Foller Fuchtbauer, A.Haversen, L.Lulla, A.Gao, C.Matic, J.Monjas, L.Rodriguez, A.Brear, P.Kim, W.Hyvonen, M.Boren, J.Mardinoglu, A.Uhlen, M.Grotli, M.

(2022) Eur J Med Chem 234: 114270-114270

  • DOI: https://doi.org/10.1016/j.ejmech.2022.114270
  • Primary Citation of Related Structures:  
    5SC8, 5SC9, 5SCA, 5SCB, 5SCC, 5SCD, 5SCE, 5SCF, 5SCG, 5SCH, 5SCI, 5SCJ, 5SCK, 5SCL, 5SDT, 7QDN, 7QZU

  • PubMed Abstract: 

    Liver pyruvate kinase (PKL) is a major regulator of metabolic flux and ATP production during liver cell glycolysis and is considered a potential drug target for the treatment of non-alcoholic fatty liver disease (NAFLD). In this study, we report the first ADP-competitive PKL inhibitors and identify several starting points for the further optimization of these inhibitors. Modeling and structural biology guided the optimization of a PKL-specific anthraquinone-based compound. A structure-activity relationship study of 47 novel synthetic derivatives revealed PKL inhibitors with half-maximal inhibitory concentration (IC 50 ) values in the 200 nM range. Despite the difficulty involved in studying a binding site as exposed as the ADP site, these derivatives feature expanded structural diversity and chemical spaces that may be used to improve their inhibitory activities against PKL. The obtained results expand the knowledge of the structural requirements for interactions with the ADP-binding site of PKL.


  • Organizational Affiliation

    Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PKL
A, B, C, D, E
A, B, C, D, E, F, G, H
447Homo sapiensMutation(s): 0 
EC: 2.7.1.40
UniProt & NIH Common Fund Data Resources
Find proteins for P30613 (Homo sapiens)
Explore P30613 
Go to UniProtKB:  P30613
PHAROS:  P30613
GTEx:  ENSG00000143627 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30613
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I4L (Subject of Investigation/LOI)
Query on I4L

Download Ideal Coordinates CCD File 
FA [auth E]
KA [auth F]
M [auth A]
PA [auth G]
R [auth B]
FA [auth E],
KA [auth F],
M [auth A],
PA [auth G],
R [auth B],
W [auth C]
(2~{S})-2-[2-[4-[3,4-bis(oxidanyl)-9,10-bis(oxidanylidene)anthracen-2-yl]sulfonylpiperazin-1-yl]-2-oxidanylidene-ethyl]-2-oxidanyl-butanedioic acid
C24 H22 N2 O12 S
PYHLNZSMOIJZLQ-DEOSSOPVSA-N
FBP
Query on FBP

Download Ideal Coordinates CCD File 
BA [auth E]
GA [auth F]
I [auth A]
LA [auth G]
N [auth B]
BA [auth E],
GA [auth F],
I [auth A],
LA [auth G],
N [auth B],
QA [auth H],
S [auth C],
X [auth D]
1,6-di-O-phosphono-beta-D-fructofuranose
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
OXL
Query on OXL

Download Ideal Coordinates CCD File 
CA [auth E]
HA [auth F]
J [auth A]
MA [auth G]
O [auth B]
CA [auth E],
HA [auth F],
J [auth A],
MA [auth G],
O [auth B],
RA [auth H],
T [auth C],
Y [auth D]
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
K
Query on K

Download Ideal Coordinates CCD File 
AA [auth D]
EA [auth E]
JA [auth F]
L [auth A]
OA [auth G]
AA [auth D],
EA [auth E],
JA [auth F],
L [auth A],
OA [auth G],
Q [auth B],
TA [auth H],
V [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
DA [auth E]
IA [auth F]
K [auth A]
NA [auth G]
P [auth B]
DA [auth E],
IA [auth F],
K [auth A],
NA [auth G],
P [auth B],
SA [auth H],
U [auth C],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
I4L BindingDB:  7QZU IC50: 200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.629α = 90
b = 112.593β = 91.58
c = 188.797γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
STARANISOdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description