7QDN | pdb_00007qdn

Structure of human liver pyruvate kinase from which the B domain has been deleted


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.217 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 390.37 kDa 
  • Atom Count: 28,811 
  • Modeled Residue Count: 3,415 
  • Deposited Residue Count: 3,576 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pyruvate kinase PKLR
A, B, C, D, E
A, B, C, D, E, F, G, H
447Homo sapiensMutation(s): 0 
Gene Names: PKLRPK1PKL
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
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FBP

Query on FBP



Download:Ideal Coordinates CCD File
BA [auth E]
FA [auth F]
I [auth A]
KA [auth G]
M [auth B]
BA [auth E],
FA [auth F],
I [auth A],
KA [auth G],
M [auth B],
PA [auth H],
R [auth C],
W [auth D]
1,6-di-O-phosphono-beta-D-fructofuranose
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
OXD

Query on OXD



Download:Ideal Coordinates CCD File
CA [auth E]
GA [auth F]
J [auth A]
LA [auth G]
N [auth B]
CA [auth E],
GA [auth F],
J [auth A],
LA [auth G],
N [auth B],
QA [auth H],
S [auth C],
X [auth D]
OXALIC ACID
C2 H2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
EA [auth E]
IA [auth F]
L [auth A]
NA [auth G]
P [auth B]
EA [auth E],
IA [auth F],
L [auth A],
NA [auth G],
P [auth B],
SA [auth H],
U [auth C],
Z [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
DA [auth E]
HA [auth F]
K [auth A]
MA [auth G]
O [auth B]
DA [auth E],
HA [auth F],
K [auth A],
MA [auth G],
O [auth B],
RA [auth H],
T [auth C],
Y [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
AA [auth D]
JA [auth F]
OA [auth G]
Q [auth B]
TA [auth H]
AA [auth D],
JA [auth F],
OA [auth G],
Q [auth B],
TA [auth H],
V [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.217 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.448α = 90
b = 112.687β = 91.36
c = 188.333γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: 2022-03-30
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description