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- PDB-8g2e: PKM2 bound to compound 2 -

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Basic information

Entry
Database: PDB / ID: 8g2e
TitlePKM2 bound to compound 2
ComponentsPyruvate kinase PKM
KeywordsTRANSFERASE / activator / small molecule
Function / homology
Function and homology information


programmed cell death / pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / histone H3T11 kinase activity / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum ...programmed cell death / pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / histone H3T11 kinase activity / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / glycolytic process / non-specific protein-tyrosine kinase / cilium / cellular response to insulin stimulus / extracellular vesicle / MHC class II protein complex binding / protein tyrosine kinase activity / collagen-containing extracellular matrix / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / transcription coactivator activity / non-specific serine/threonine protein kinase / cadherin binding / phosphorylation / mRNA binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / extracellular exosome / extracellular region / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily ...Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
OXALATE ION / Chem-YII / Pyruvate kinase PKM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.838 Å
AuthorsStuckey, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01EY029675 United States
National Institutes of Health/National Eye Institute (NIH/NEI)NEI P30 EY007003 United States
CitationJournal: Pharmaceuticals / Year: 2023
Title: Development of Novel Small-Molecule Activators of Pyruvate Kinase Muscle Isozyme 2, PKM2, to Reduce Photoreceptor Apoptosis.
Authors: 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.
History
DepositionFeb 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,69918
Polymers60,0501
Non-polymers1,64917
Water9,602533
1
A: Pyruvate kinase PKM
hetero molecules

A: Pyruvate kinase PKM
hetero molecules

A: Pyruvate kinase PKM
hetero molecules

A: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,79572
Polymers240,2004
Non-polymers6,59468
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area29590 Å2
ΔGint-603 kcal/mol
Surface area70310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.810, 115.965, 131.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-601-

YII

21A-601-

YII

31A-601-

YII

41A-963-

HOH

51A-969-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pyruvate kinase PKM / Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate ...Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate kinase 2/3 / Pyruvate kinase muscle isozyme / Thyroid hormone-binding protein 1 / THBP1 / Tumor M2-PK / p58


Mass: 60050.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKM, OIP3, PK2, PK3, PKM2 / Production host: Escherichia coli (E. coli) / References: UniProt: P14618, pyruvate kinase

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Non-polymers , 7 types, 550 molecules

#2: Chemical ChemComp-YII / 3-[(3-aminophenyl)methyl]-5-methyl-7-[methyl(oxidanyl)-$l^{3}-sulfanyl]pyridazino[4,5-b]indol-4-one


Mass: 366.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18N4O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM ammonium sulfate and 20% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12723 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12723 Å / Relative weight: 1
ReflectionResolution: 1.838→50 Å / Num. obs: 53268 / % possible obs: 94.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.038 / Χ2: 0.834 / Net I/σ(I): 29.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.84-1.873.80.13826370.745195.3
1.87-1.913.90.12426710.793195.4
1.91-1.943.90.11426770.833195.8
1.94-1.983.90.09726760.844195.7
1.98-2.033.80.08726700.827195.3
2.03-2.073.80.07926400.851195.2
2.07-2.123.80.06926410.864194.3
2.12-2.183.70.06126220.909193.8
2.18-2.253.70.05425950.872193.3
2.25-2.323.60.0526520.915193.7
2.32-2.43.60.04626030.935193.9
2.4-2.53.30.04126970.873194.8
2.5-2.613.50.03926840.873195.8
2.61-2.7540.03927010.912196.1
2.75-2.924.10.03527010.869196
2.92-3.154.10.03227400.871195.9
3.15-3.464.20.0326640.855194.2
3.46-3.964.10.02726960.814194.1
3.96-4.993.70.02726440.773191.6
4.99-504.50.0326570.827188.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.838→35.66 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.12 / SU Rfree Blow DPI: 0.109 / SU Rfree Cruickshank DPI: 0.104
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 2709 5.09 %RANDOM
Rwork0.1632 ---
obs0.1646 53262 93.8 %-
Displacement parametersBiso mean: 21.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.4236 Å20 Å20 Å2
2--0.0677 Å20 Å2
3---0.356 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.838→35.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3901 0 96 534 4531
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084132HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.895627HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1446SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes750HARMONIC5
X-RAY DIFFRACTIONt_it4114HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.21
X-RAY DIFFRACTIONt_other_torsion14.18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion555SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4131SEMIHARMONIC4
LS refinement shellResolution: 1.84→1.85 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.1836 -5.72 %
Rwork0.1946 1005 -
all0.1939 1066 -
obs--72.89 %

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