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- PDB-9m3u: Crystal structure of human pyruvate dehydrogenase kinase isoform ... -

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Basic information

Entry
Database: PDB / ID: 9m3u
TitleCrystal structure of human pyruvate dehydrogenase kinase isoform 2 in complex with ATP competitive inhibitor 24
Components[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
KeywordsTRANSFERASE / ghkl atpase/kinase family / pyruvate dehydrogenase complex / mitochondrial kinase
Function / homology
Function and homology information


[pyruvate dehydrogenase (acetyl-transferring)] kinase / pyruvate dehydrogenase (acetyl-transferring) kinase activity / regulation of pyruvate decarboxylation to acetyl-CoA / Regulation of pyruvate dehydrogenase (PDH) complex / pyruvate dehydrogenase complex / regulation of ketone metabolic process / regulation of pH / cellular response to nutrient / Signaling by Retinoic Acid / regulation of gluconeogenesis ...[pyruvate dehydrogenase (acetyl-transferring)] kinase / pyruvate dehydrogenase (acetyl-transferring) kinase activity / regulation of pyruvate decarboxylation to acetyl-CoA / Regulation of pyruvate dehydrogenase (PDH) complex / pyruvate dehydrogenase complex / regulation of ketone metabolic process / regulation of pH / cellular response to nutrient / Signaling by Retinoic Acid / regulation of gluconeogenesis / intrinsic apoptotic signaling pathway by p53 class mediator / regulation of glucose metabolic process / regulation of calcium-mediated signaling / cellular response to reactive oxygen species / glucose metabolic process / insulin receptor signaling pathway / glucose homeostasis / protein kinase activity / mitochondrial matrix / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal / Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain superfamily / PDK/BCKDK protein kinase / Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
: / Chem-TF3 / [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsXu, Z.H. / Chen, S. / Han, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2025
Title: Discovery of ATP competitive PDHK1/2 dual inhibitors.
Authors: Xu, H. / Ding, D. / Han, X. / Miao, K. / Liang, C. / Yun, H. / Zhu, W. / Dey, F. / Zhao, D. / Wu, Y. / Reutlinger, M. / Yang, J. / Zhai, G. / Lin, Z. / Li, C. / Wu, W. / Xu, B. / Han, L. / ...Authors: Xu, H. / Ding, D. / Han, X. / Miao, K. / Liang, C. / Yun, H. / Zhu, W. / Dey, F. / Zhao, D. / Wu, Y. / Reutlinger, M. / Yang, J. / Zhai, G. / Lin, Z. / Li, C. / Wu, W. / Xu, B. / Han, L. / Chen, S. / Huang, X. / Casagrande, F. / Hilbert, M. / Strebel, Q. / Wichert, M. / Westwood, P. / Schafer, R. / Roth, D. / Heer, D. / Tian, X. / Ma, T. / Zhang, T. / Zhao, J. / Urich, E. / Xia, G. / Lassen, K. / Shen, H.C. / Zou, G.
History
DepositionMar 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1768
Polymers41,0061
Non-polymers1,1707
Water2,792155
1
A: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
hetero molecules

A: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,35116
Polymers82,0122
Non-polymers2,34014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
Buried area5170 Å2
ΔGint3 kcal/mol
Surface area32070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.630, 110.630, 84.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

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Protein , 1 types, 1 molecules A

#1: Protein [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial / Pyruvate dehydrogenase kinase isoform 2 / PDH kinase 2 / PDKII


Mass: 41005.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDK2, PDHK2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q15119, [pyruvate dehydrogenase (acetyl-transferring)] kinase

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Non-polymers , 5 types, 162 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-TF3 / N-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL)OXY]PHENYL} ACETAMIDE


Mass: 360.878 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25ClN2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-A1EQJ / 2-cyano-N-[(3R)-1-[(3S)-3-ethyl-7-(ethylamino)-5-fluoranyl-2-oxidanylidene-1H-indol-3-yl]piperidin-3-yl]-2-azaspiro[3.3]heptane-6-carboxamide


Mass: 468.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C25H33FN6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.62 Å3/Da / Density % sol: 61.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.42 M NaK tartrate, 0.1 M Na citrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.31→73 Å / Num. obs: 199622 / % possible obs: 80.3 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.109 / Net I/σ(I): 6.68
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.31-1.391.77758510.0231.861
1.39-1.491.688247070.0181.721
1.49-1.611.666337430.0181.5431
1.61-1.761.456323880.01822.1691
1.76-1.975.383292290.2175.8181
1.97-2.281.142257960.8331.2341
2.28-2.790.275218160.9880.2971
2.79-3.940.066168350.9990.0721
3.94-700.03292570.9990.0351

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Processing

Software
NameVersionClassification
PHENIX(1.19rc4_4035: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→47.9 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2134 1659 5.01 %
Rwork0.179 --
obs0.1807 33134 74.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.92→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2804 0 81 155 3040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082979
X-RAY DIFFRACTIONf_angle_d0.894033
X-RAY DIFFRACTIONf_dihedral_angle_d12.841148
X-RAY DIFFRACTIONf_chiral_restr0.053436
X-RAY DIFFRACTIONf_plane_restr0.007525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.970.715280.461123X-RAY DIFFRACTION4
1.98-2.040.3509270.3251372X-RAY DIFFRACTION11
2.04-2.110.2647630.2916987X-RAY DIFFRACTION28
2.11-2.20.33411020.24342065X-RAY DIFFRACTION59
2.2-2.30.2971750.26013203X-RAY DIFFRACTION91
2.3-2.420.28941820.22173485X-RAY DIFFRACTION99
2.42-2.570.24551930.21423499X-RAY DIFFRACTION99
2.57-2.770.22611690.19943524X-RAY DIFFRACTION99
2.77-3.040.25721750.21673517X-RAY DIFFRACTION99
3.05-3.490.22771820.17763553X-RAY DIFFRACTION100
3.49-4.390.17881800.15513547X-RAY DIFFRACTION100
4.39-47.90.18662030.15483600X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4742-0.7564-1.64323.31390.35892.83230.38950.84860.5319-0.3576-0.087-0.637-0.04210.7293-0.12280.41730.07140.12760.59710.13730.6187-34.332121.1649-39.2102
23.8865-1.45710.59311.41610.1112.69580.26440.72950.923-0.1757-0.2007-0.1346-0.33260.1925-0.12460.44940.03650.05520.47810.18080.5365-46.891126.158-37.86
33.05070.1346-1.18992.97730.20072.52460.1578-0.53120.23250.6571-0.0804-0.2515-0.18470.315-0.01920.5578-0.0142-0.1510.3985-0.07760.4265-43.407617.1825-10.3471
43.99520.5859-0.78143.1562-0.19952.2570.1675-0.35610.33460.5184-0.08850.1665-0.1955-0.03660.02340.48050.0420.00110.3189-0.06120.3058-54.318812.404-12.0209
53.17781.5654-1.32792.7111-1.27811.5305-0.00770.47630.29070.0030.16990.3796-0.0652-0.3908-0.21130.44150.0612-0.01970.43190.01990.3547-58.300211.7154-24.1756
62.1933-0.57110.53541.4702-0.25940.47670.17260.3911-0.1113-0.0118-0.2308-0.2179-0.08620.2130.01040.41130.0725-0.01020.4148-0.04890.404-45.88087.6373-27.4341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 175 )
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 241 )
4X-RAY DIFFRACTION4chain 'A' and (resid 242 through 290 )
5X-RAY DIFFRACTION5chain 'A' and (resid 291 through 349 )
6X-RAY DIFFRACTION6chain 'A' and (resid 350 through 378 )

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