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- PDB-3h0z: Aurora A in complex with a bisanilinopyrimidine -

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Basic information

Entry
Database: PDB / ID: 3h0z
TitleAurora A in complex with a bisanilinopyrimidine
ComponentsSerine/threonine-protein kinase 6Serine/threonine-specific protein kinase
KeywordsTRANSFERASE / Protein:Inhibitor complex Aurora-A / Cell cycle / Serine/threonine / protein kinase / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase
Function / homology
Function and homology information


Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / meiotic spindle / mitotic centrosome separation / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / positive regulation of mitochondrial fission / spindle organization / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / centriole / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic cell cycle / AURKA Activation by TPX2 / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of mitotic nuclear division / ciliary basal body / negative regulation of protein binding / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / molecular function activator activity / liver regeneration / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / regulation of protein stability / mitotic spindle / spindle / kinetochore / response to wounding / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / proteasome-mediated ubiquitin-dependent protein catabolic process / basolateral plasma membrane / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / microtubule / postsynaptic density / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / cell division / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Aurora kinase A / Aurora kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Aurora kinase A / Aurora kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-45B / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsWiesmann, C. / Ultsch, M.H. / Cochran, A.G.
CitationJournal: J.Med.Chem. / Year: 2009
Title: A class of 2,4-bisanilinopyrimidine Aurora A inhibitors with unusually high selectivity against Aurora B.
Authors: Aliagas-Martin, I. / Burdick, D. / Corson, L. / Dotson, J. / Drummond, J. / Fields, C. / Huang, O.W. / Hunsaker, T. / Kleinheinz, T. / Krueger, E. / Liang, J. / Moffat, J. / Phillips, G. / ...Authors: Aliagas-Martin, I. / Burdick, D. / Corson, L. / Dotson, J. / Drummond, J. / Fields, C. / Huang, O.W. / Hunsaker, T. / Kleinheinz, T. / Krueger, E. / Liang, J. / Moffat, J. / Phillips, G. / Pulk, R. / Rawson, T.E. / Ultsch, M. / Walker, L. / Wiesmann, C. / Zhang, B. / Zhu, B.Y. / Cochran, A.G.
History
DepositionApr 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase 6
B: Serine/threonine-protein kinase 6
C: Serine/threonine-protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9496
Polymers93,1433
Non-polymers1,8063
Water0
1
A: Serine/threonine-protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6502
Polymers31,0481
Non-polymers6021
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6502
Polymers31,0481
Non-polymers6021
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Serine/threonine-protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6502
Polymers31,0481
Non-polymers6021
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.712, 86.875, 122.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine/threonine-protein kinase 6 / Serine/threonine-specific protein kinase / Aurora kinase A / Aurora-A / Serine/threonine kinase 15 / Aurora/IPL1-related kinase 1 / Aurora- ...Aurora kinase A / Aurora-A / Serine/threonine kinase 15 / Aurora/IPL1-related kinase 1 / Aurora-related kinase 1 / hARK1 / Breast tumor-amplified kinase


Mass: 31047.723 Da / Num. of mol.: 3 / Fragment: Kinase domain (UNP residues 124-391) / Mutation: K124A, T287A, T288A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AURKA, AIK, ARK1, AURA, BTAK, STK15, STK6 / Production host: Escherichia coli (E. coli)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-45B / 4-{[2-({4-[2-(4-acetylpiperazin-1-yl)-2-oxoethyl]phenyl}amino)-5-fluoropyrimidin-4-yl]amino}-N-(2-chlorophenyl)benzamide


Mass: 602.058 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C31H29ClFN7O3

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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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 3350, 0.2 M Ammonium sulfate, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 14, 2006 / Details: Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.92→50 Å / Num. all: 20042 / Num. obs: 19992 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.066
Reflection shellResolution: 2.92→3.02 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.405 / % possible all: 99.8

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.92→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.875 / SU B: 42.848 / SU ML: 0.372 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.486 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28581 1014 5.1 %RANDOM
Rwork0.21789 ---
all0.221 18945 --
obs0.22131 18896 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.999 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---2.25 Å20 Å2
3---2.29 Å2
Refinement stepCycle: LAST / Resolution: 2.92→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6057 0 129 0 6186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226343
X-RAY DIFFRACTIONr_bond_other_d0.0010.024471
X-RAY DIFFRACTIONr_angle_refined_deg1.0651.9938574
X-RAY DIFFRACTIONr_angle_other_deg0.859310793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4455727
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18122.899307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.028151116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7331556
X-RAY DIFFRACTIONr_chiral_restr0.0950.2909
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026913
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021379
X-RAY DIFFRACTIONr_nbd_refined0.1920.21317
X-RAY DIFFRACTIONr_nbd_other0.1740.24384
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23025
X-RAY DIFFRACTIONr_nbtor_other0.0820.23366
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2113
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1510.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9052.54771
X-RAY DIFFRACTIONr_mcbond_other0.2452.51467
X-RAY DIFFRACTIONr_mcangle_it2.55655932
X-RAY DIFFRACTIONr_scbond_it1.2692.53189
X-RAY DIFFRACTIONr_scangle_it1.94352642
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.92→2.979 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.396 54 -
Rwork0.279 1065 -
obs--98.94 %
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)
110.28260.4921-3.86884.97880.20746.57130.04910.43720.995-0.3574-0.12790.0555-0.4634-0.34240.0788-0.2273-0.0037-0.029-0.13880.0963-0.26337.249439.000356.6119
26.35322.2967-1.11534.09820.51721.36290.17390.31660.0733-0.047-0.1057-0.1911-0.09240.154-0.0682-0.32650.0228-0.0118-0.10550.0793-0.305926.252327.829567.3819
34.34412.23720.2055.4844-0.49794.43050.00640.31880.448-0.0899-0.00210.42960.0682-0.3125-0.0043-0.43640.02880.0262-0.04350.1206-0.217211.874223.433364.416
45.27450.48482.66386.1751.02168.4659-0.1782-0.946-0.09890.2583-0.22680.097-0.4169-0.66450.4051-0.2615-0.0293-0.0507-0.14020.1004-0.103213.338755.324241.5694
55.87542.10723.29568.8774-0.24062.932-0.1427-0.33030.4727-0.5204-0.01020.4683-0.07860.10680.153-0.1840.0158-0.0124-0.30820.0245-0.17856.932643.881727.4913
65.45461.6228-0.33738.4617-3.50167.54080.0674-0.0881-0.0888-0.5330.10080.30840.5985-0.1674-0.1682-0.1060.0105-0.0805-0.4035-0.0349-0.14062.773528.930828.8698
74.00522.46730.11299.42573.9616.0850.1102-0.2852-0.3291-0.15220.3438-1.57450.2691.6194-0.45410.06650.15690.0380.16670.11490.278458.875950.500728.5893
85.80660.8156-2.44498.1395-0.64954.7950.09490.2790.21370.0583-0.00670.2088-0.43130.0031-0.08820.14110.1632-0.0749-0.21060.0552-0.292544.056239.232822.879
95.88390.29050.68775.50030.26825.96380.21610.4453-0.3826-0.4644-0.15230.31930.4563-0.3957-0.06380.00760.0823-0.139-0.3018-0.0652-0.19542.630724.236725.8374
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A128 - 212
2X-RAY DIFFRACTION2A213 - 274
3X-RAY DIFFRACTION3A292 - 388
4X-RAY DIFFRACTION4B126 - 212
5X-RAY DIFFRACTION5B213 - 274
6X-RAY DIFFRACTION6B292 - 388
7X-RAY DIFFRACTION7C126 - 212
8X-RAY DIFFRACTION8C213 - 274
9X-RAY DIFFRACTION9C292 - 388

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