8TBT

Structure of human erythrocyte pyruvate kinase in complex with an allosteric activator Compound 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structure-Based Design of AG-946, a Pyruvate Kinase Activator.

Liu, T.Padyana, A.K.Judd, E.T.Jin, L.Hammoudeh, D.Kung, C.Dang, L.

(2024) ChemMedChem 19: e202300559-e202300559

  • DOI: https://doi.org/10.1002/cmdc.202300559
  • Primary Citation of Related Structures:  
    8TBS, 8TBT, 8TBU

  • PubMed Abstract: 

    Pyruvate kinase (PK) is the enzyme that catalyzes the conversion of phosphoenolpyruvate and adenosine diphosphate to pyruvate and adenosine triphosphate in glycolysis and plays a crucial role in regulating cell metabolism. We describe the structure-based design of AG-946, an activator of PK isoforms, including red blood cell-specific forms of PK (PKR). This was designed to have a pseudo-C2-symmetry matching its allosteric binding site on the PK enzyme, which increased its potency toward PKR while reducing activity against off-targets observed from the original scaffold. AG-946 (1) demonstrated activation of human wild-type PK (half-maximal activation concentration [AC 50 ]=0.005 μM) and a panel of mutated PK proteins (K410E [AC 50 =0.0043 μM] and R510Q [AC 50 =0.0069 μM]), (2) displayed a significantly longer half-time of activation (>150-fold) compared with 6-(3-methoxybenzyl)-4-methyl-2-(methylsulfinyl)-4,6-dihydro-5H-thieno[2',3':4,5]pyrrolo[2,3-d]pyridazin-5-one, and (3) stabilized PKR R510Q, an unstable mutant PKR enzyme, and preserved its catalytic activity under increasingly denaturing conditions. As a potent, oral, small-molecule allosteric activator of wild-type and mutant PKR, AG-946 was advanced to human clinical trials.


  • Organizational Affiliation

    Ensem Therapeutics, 880 Winter St, Waltham, MA 02451, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate kinase PKLR
A, B, C, D
544Homo 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
I07 (Subject of Investigation/LOI)
Query on I07

Download Ideal Coordinates CCD File 
I [auth B],
R [auth D]
{6-[(3-methoxyphenyl)methyl]-4-methyl-5-oxo-5,6-dihydro-4H-thieno[2',3':4,5]pyrrolo[2,3-d]pyridazin-2-yl}(methyl)sulfaniumolate
C18 H17 N3 O3 S2
MORBXZMIXGYQDB-AREMUKBSSA-N
FBP
Query on FBP

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
N [auth C],
S [auth D]
1,6-di-O-phosphono-beta-D-fructofuranose
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
PYR
Query on PYR

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
O [auth C],
T [auth D]
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
P [auth C],
U [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
H [auth A],
M [auth B],
Q [auth C],
V [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.354α = 90
b = 174.038β = 94.291
c = 87.336γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Database references