8G2E | pdb_00008g2e

PKM2 bound to compound 2

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-02-03 Released: 2023-05-17 
  • Deposition Author(s): Stuckey, J.A.
  • Funding Organization(s): National Institutes of Health/National Eye Institute (NIH/NEI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 
    0.190 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8G2E

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Development of Novel Small-Molecule Activators of Pyruvate Kinase Muscle Isozyme 2, PKM2, to Reduce Photoreceptor Apoptosis.

Wubben, T.J.Chaudhury, S.Watch, B.T.Stuckey, J.A.Weh, E.Fernando, R.Goswami, M.Pawar, M.Rech, J.C.Besirli, C.G.

(2023) Pharmaceuticals (Basel) 16

  • DOI: https://doi.org/10.3390/ph16050705
  • Primary Citation Related Structures: 
    8G2E

  • PubMed Abstract: 

    Treatment options are lacking to prevent photoreceptor death and subsequent vision loss. Previously, we demonstrated that reprogramming metabolism via the pharmacologic activation of PKM2 is a novel photoreceptor neuroprotective strategy. However, the features of the tool compound used in those studies, ML-265, preclude its advancement as an intraocular, clinical candidate. This study sought to develop the next generation of small-molecule PKM2 activators, aimed specifically for delivery into the eye. Compounds were developed that replaced the thienopyrrolopyridazinone core of ML-265 and modified the aniline and methyl sulfoxide functional groups. Compound 2 demonstrated that structural changes to the ML-265 scaffold are tolerated from a potency and efficacy standpoint, allow for a similar binding mode to the target, and circumvent apoptosis in models of outer retinal stress. To overcome the low solubility and problematic functional groups of ML-265, compound 2 's efficacious and versatile core structure for the incorporation of diverse functional groups was then utilized to develop novel PKM2 activators with improved solubility, lack of structural alerts, and retained potency. No other molecules are in the pharmaceutical pipeline for the metabolic reprogramming of photoreceptors. Thus, this study is the first to cultivate the next generation of novel, structurally diverse, small-molecule PKM2 activators for delivery into the eye.


  • Organizational Affiliation
    • Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, MI 48105, USA.

Macromolecule Content 

  • Total Structure Weight: 61.7 kDa 
  • Atom Count: 4,585 
  • Modeled Residue Count: 519 
  • Deposited Residue Count: 550 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pyruvate kinase PKM550Homo sapiensMutation(s): 0 
Gene Names: PKMOIP3PK2PK3PKM2
EC: 2.7.1.40 (PDB Primary Data), 2.7.11.1 (UniProt), 2.7.10.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P14618 (Homo sapiens)
Explore P14618 
Go to UniProtKB:  P14618
PHAROS:  P14618
GTEx:  ENSG00000067225 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14618
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YII
(Subject of Investigation/LOI)

Query on YII



Download:Ideal Coordinates CCD File
B [auth A]3-[(3-aminophenyl)methyl]-5-methyl-7-[methyl(oxidanyl)-$l^{3}-sulfanyl]pyridazino[4,5-b]indol-4-one
C19 H18 N4 O2 S
NJHOCORPIDXRKR-AREMUKBSSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
OXL

Query on OXL



Download:Ideal Coordinates CCD File
E [auth A]OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
EDO

Query on EDO



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

Query on MG



Download:Ideal Coordinates CCD File
Q [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
R [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free:  0.190 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.81α = 90
b = 115.965β = 90
c = 131.841γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesR01EY029675
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesNEI P30 EY007003

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-17
    Type: Initial release
  • Version 1.1: 2023-06-07
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection