9O3B | pdb_00009o3b

PKM2 bound to MCTI-566

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

  • Deposited: 2025-04-07 Released: 2025-08-13 
  • 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: 2.42 Å
  • R-Value Free: 
    0.226 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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Literature

A Novel, Long-Acting, Small Molecule PKM2 Activator and Its Potential Broad Application Against Photoreceptor Degeneration.

Pan, W.W.Weh, K.M.Chaudhury, S.Fernando, R.Hager, H.Wen, B.Chinnaswamy, K.Stuckey, J.A.Rech, J.C.Besirli, C.G.Weh, E.Wubben, T.J.

(2025) Transl Vis Sci Technol 14: 26-26

  • DOI: https://doi.org/10.1167/tvst.14.7.26
  • Primary Citation Related Structures: 
    9O3B

  • PubMed Abstract: 

    Activating pyruvate kinase M2 (PKM2) has been shown to be neuroprotective in preclinical models of photoreceptor degeneration. We recently developed novel, small molecule activators for ocular delivery. Here, we sought to characterize the ocular pharmacology, toxicity, and efficacy of MCTI-566, a novel PKM2 activator, to translate this therapeutic strategy to the clinic. X-ray protein crystallography and isothermal titration calorimetry assessed the interaction of MCTI-566 with PKM2. PKM2 activation and tissue pharmacokinetics were examined after intravitreal or systemic administration of MCTI-566. Retinal toxicity was evaluated in rats after intravitreal injection. The effect of MCTI-566 on photoreceptor death was assessed using in vitro and in vivo models of outer retinal stress and on the inflammatory response in the rd10 retina using flow cytometry and quantitative real-time polymerase chain reaction. The PKM2-MCTI-566 co-crystal structure demonstrated a binding pocket distinct from endogenous activators. MCTI-566 increases retinal PK activity 200% following intravitreal or systemic administration. MCTI-566 distributed to the retina after intravitreal or systemic administration, activated the target for ≥90 days and was specific for photoreceptor PKM2. No retinal toxicity was observed after repeated intravitreal administration. MCTI-566 reduced photoreceptor apoptosis in a model of retinal detachment, and delayed photoreceptor degeneration and altered the inflammatory response in the rd10 retina. MCTI-566 is a small molecule drug candidate for photoreceptor neuroprotection. MCTI-566, a long-acting and well-tolerated ocular PKM2 activator, may be a potential therapeutic to combat currently untreatable retinal degenerations.


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

Macromolecule Content 

  • Total Structure Weight: 484.58 kDa 
  • Atom Count: 31,965 
  • Modeled Residue Count: 4,095 
  • Deposited Residue Count: 4,400 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pyruvate kinase PKM
A, B, C, D, E
A, B, C, D, E, F, G, H
550Homo 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
A1B77
(Subject of Investigation/LOI)

Query on A1B77



Download:Ideal Coordinates CCD File
AA [auth F],
IA [auth H],
M [auth B],
R [auth C]
7-[(dimethylamino)methyl]-8-fluoro-5-methyl-3-[(6-methylpyridin-2-yl)methyl]-3,5-dihydro-4H-pyridazino[4,5-b]indol-4-one
C21 H22 F N5 O
PJKMPULWTGCGAQ-UHFFFAOYSA-N
FBP

Query on FBP



Download:Ideal Coordinates CCD File
BA [auth F],
I [auth A],
N [auth B],
X [auth E]
1,6-di-O-phosphono-beta-D-fructofuranose
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
GA [auth G],
LA [auth H],
U [auth C],
W [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
OXL

Query on OXL



Download:Ideal Coordinates CCD File
CA [auth F],
HA [auth H],
J [auth A],
Q [auth C]
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
EA [auth G]
JA [auth H]
K [auth A]
O [auth B]
S [auth C]
EA [auth G],
JA [auth H],
K [auth A],
O [auth B],
S [auth C],
Y [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
DA [auth F]
FA [auth G]
KA [auth H]
L [auth A]
P [auth B]
DA [auth F],
FA [auth G],
KA [auth H],
L [auth A],
P [auth B],
T [auth C],
V [auth D],
Z [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free:  0.226 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.807α = 89.73
b = 93.855β = 89.68
c = 153.66γ = 75.79
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
PDB_EXTRACTdata extraction

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 StatesK08EY031757

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release