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- PDB-9m3r: Crystal structure of human pyruvate dehydrogenase kinase isoform ... -

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Basic information

Entry
Database: PDB / ID: 9m3r
TitleCrystal structure of human pyruvate dehydrogenase kinase isoform 1 in complex with ATP competitive inhibitor 29
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: 2.14 Å
AuthorsXu, Z.H. / Chen, S.
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)44,1327
Polymers42,9791
Non-polymers1,1536
Water2,270126
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)88,26314
Polymers85,9582
Non-polymers2,30512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
Buried area7180 Å2
ΔGint-77 kcal/mol
Surface area31620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.800, 109.800, 84.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-347-

PHE

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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: 42978.977 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 , 6 types, 132 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Chemical ChemComp-A1EQH / 3-[4-[4-(ethylamino)-6-fluoranyl-2-oxidanylidene-3H-benzimidazol-1-yl]phenoxy]benzenesulfonyl fluoride


Mass: 445.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17F2N3O4S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.16 Å3/Da / Density % sol: 61.14 %
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: Nov 18, 2019
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: 2.14→47.54 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2149 1571 4.91 %
Rwork0.1819 --
obs0.1835 31973 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.14→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2877 0 75 126 3078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083100
X-RAY DIFFRACTIONf_angle_d0.8414195
X-RAY DIFFRACTIONf_dihedral_angle_d12.8581180
X-RAY DIFFRACTIONf_chiral_restr0.051446
X-RAY DIFFRACTIONf_plane_restr0.007544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.210.25281290.23622756X-RAY DIFFRACTION100
2.21-2.290.27371520.22292756X-RAY DIFFRACTION100
2.29-2.380.27431490.21372737X-RAY DIFFRACTION100
2.38-2.490.24411670.19592725X-RAY DIFFRACTION100
2.49-2.620.23851390.19862756X-RAY DIFFRACTION100
2.62-2.780.25081320.20872739X-RAY DIFFRACTION100
2.78-30.27191470.21732771X-RAY DIFFRACTION100
3-3.30.23821310.1962788X-RAY DIFFRACTION100
3.3-3.780.22821400.17922778X-RAY DIFFRACTION100
3.78-4.760.17321550.14972759X-RAY DIFFRACTION100
4.76-47.540.18741300.17522837X-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)
14.8879-0.52940.28921.28010.27391.95440.20090.83480.949-0.2613-0.1338-0.2897-0.26610.4365-0.04940.49820.02760.09750.60890.20770.682-40.958925.5274-39.3612
22.28380.2009-0.45822.1574-0.19892.17560.0635-0.1780.26210.436-0.0367-0.1223-0.1860.1366-0.04710.4520.0306-0.0480.2984-0.03280.4118-47.832716.207-16.1319
33.09450.35110.022.2916-0.51030.97830.0720.48220.1702-0.1202-0.00170.0908-0.1014-0.0951-0.10370.38130.0761-0.01540.3430.00480.3033-54.12389.5756-26.1287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 144 )
2X-RAY DIFFRACTION2chain 'A' and (resid 145 through 282 )
3X-RAY DIFFRACTION3chain 'A' and (resid 283 through 394 )

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