7FS4

Structure of liver pyruvate kinase in complex with allosteric modulator 16


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Tuning liver pyruvate kinase activity up or down with a new class of allosteric modulators.

Nain-Perez, A.Nilsson, O.Lulla, A.Haversen, L.Brear, P.Liljenberg, S.Hyvonen, M.Boren, J.Grotli, M.

(2023) Eur J Med Chem 250: 115177-115177

  • DOI: https://doi.org/10.1016/j.ejmech.2023.115177
  • Primary Citation of Related Structures:  
    7FRV, 7FRW, 7FRX, 7FRY, 7FRZ, 7FS0, 7FS1, 7FS2, 7FS3, 7FS4, 7FS5, 7FS6, 7FS7, 7FS8, 7FS9, 7FSA, 7FSB, 7FSC, 7FSD

  • PubMed Abstract: 

    The liver isoform of pyruvate kinase (PKL) has gained interest due to its potential capacity to regulate fatty acid synthesis involved in the progression of non-alcoholic fatty liver disease (NAFLD). Here we describe a novel series of PKL modulators that can either activate or inhibit the enzyme allosterically, from a cryptic site at the interface of two protomers in the tetrameric enzyme. Starting from urolithin D, we designed and synthesised 42 new compounds. The effect of these compounds on PKL enzymatic activity was assessed after incubation with cell lysates obtained from a liver cell line. Pronounced activation of PKL activity, up to 3.8-fold, was observed for several compounds at 10 μM, while other compounds were prominent PKL inhibitors reducing its activity to 81% at best. A structure-activity relationship identified linear-shaped sulfone-sulfonamides as activators and non-linear compounds as inhibitors. Crystal structures revealed the conformations of these modulators, which were used as a reference for designing new modulators.


  • 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
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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O9R (Subject of Investigation/LOI)
Query on O9R

Download Ideal Coordinates CCD File 
IA [auth F],
NA [auth G],
Q [auth C],
Z [auth D]
4,4',5-trihydroxy-N-{[4-(3-hydroxybenzene-1-sulfonyl)phenyl]methyl}[1,1'-biphenyl]-2-sulfonamide
C25 H21 N O8 S2
GAYXUPABCIZYGF-UHFFFAOYSA-N
FBP
Query on FBP

Download Ideal Coordinates CCD File 
AA [auth E]
EA [auth F]
I [auth A]
JA [auth G]
M [auth B]
AA [auth E],
EA [auth F],
I [auth A],
JA [auth G],
M [auth B],
OA [auth H],
R [auth C],
V [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 
BA [auth E]
FA [auth F]
J [auth A]
KA [auth G]
N [auth B]
BA [auth E],
FA [auth F],
J [auth A],
KA [auth G],
N [auth B],
PA [auth H],
S [auth C],
W [auth D]
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
K
Query on K

Download Ideal Coordinates CCD File 
DA [auth E]
HA [auth F]
L [auth A]
MA [auth G]
P [auth B]
DA [auth E],
HA [auth F],
L [auth A],
MA [auth G],
P [auth B],
RA [auth H],
U [auth C],
Y [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
CA [auth E]
GA [auth F]
K [auth A]
LA [auth G]
O [auth B]
CA [auth E],
GA [auth F],
K [auth A],
LA [auth G],
O [auth B],
QA [auth H],
T [auth C],
X [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.146α = 90
b = 113.021β = 91.93
c = 188.617γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
BUSTERrefinement
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: 2023-04-12
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection