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- PDB-3cjo: Crystal structure of KSP in complex with inhibitor 30 -

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Basic information

Entry
Database: PDB / ID: 3cjo
TitleCrystal structure of KSP in complex with inhibitor 30
ComponentsKinesin-like protein KIF11
KeywordsMOTOR PROTEIN / KSP / KSP-inhibitor complex / ATP-binding / Cell cycle / Cell division / Coiled coil / Microtubule / Mitosis / Nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


spindle elongation / regulation of mitotic centrosome separation / Kinesins / mitotic centrosome separation / plus-end-directed microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / spindle organization / kinesin complex / microtubule-based movement ...spindle elongation / regulation of mitotic centrosome separation / Kinesins / mitotic centrosome separation / plus-end-directed microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / spindle organization / kinesin complex / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / mitotic spindle / spindle pole / spindle / mitotic cell cycle / microtubule binding / microtubule / cell division / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain / Kinesin / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. ...Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain / Kinesin / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-K30 / Kinesin-like protein KIF11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.28 Å
AuthorsYan, Y.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Kinesin spindle protein (KSP) inhibitors. 9. Discovery of (2S)-4-(2,5-difluorophenyl)-n-[(3R,4S)-3-fluoro-1-methylpiperidin-4-yl]-2-(hydroxymethyl)-N-methyl-2-phenyl-2,5-dihydro-1H-pyrrole-1- ...Title: Kinesin spindle protein (KSP) inhibitors. 9. Discovery of (2S)-4-(2,5-difluorophenyl)-n-[(3R,4S)-3-fluoro-1-methylpiperidin-4-yl]-2-(hydroxymethyl)-N-methyl-2-phenyl-2,5-dihydro-1H-pyrrole-1-carboxamide (MK-0731) for the treatment of taxane-refractory cancer.
Authors: Cox, C.D. / Coleman, P.J. / Breslin, M.J. / Whitman, D.B. / Garbaccio, R.M. / Fraley, M.E. / Buser, C.A. / Walsh, E.S. / Hamilton, K. / Schaber, M.D. / Lobell, R.B. / Tao, W. / Davide, J.P. ...Authors: Cox, C.D. / Coleman, P.J. / Breslin, M.J. / Whitman, D.B. / Garbaccio, R.M. / Fraley, M.E. / Buser, C.A. / Walsh, E.S. / Hamilton, K. / Schaber, M.D. / Lobell, R.B. / Tao, W. / Davide, J.P. / Diehl, R.E. / Abrams, M.T. / South, V.J. / Huber, H.E. / Torrent, M. / Prueksaritanont, T. / Li, C. / Slaughter, D.E. / Mahan, E. / Fernandez-Metzler, C. / Yan, Y. / Kuo, L.C. / Kohl, N.E. / Hartman, G.D.
History
DepositionMar 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinesin-like protein KIF11
B: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6718
Polymers81,8492
Non-polymers1,8226
Water5,819323
1
A: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8354
Polymers40,9241
Non-polymers9113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8354
Polymers40,9241
Non-polymers9113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.758, 79.374, 158.853
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 Kinesin-like protein KIF11 / Kinesin-related motor protein Eg5 / Kinesin-like spindle protein HKSP / Thyroid receptor- ...Kinesin-related motor protein Eg5 / Kinesin-like spindle protein HKSP / Thyroid receptor-interacting protein 5 / TRIP-5 / Kinesin-like protein 1


Mass: 40924.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF11, EG5, KNSL1, TRIP5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P52732
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-K30 / (2S)-4-(2,5-difluorophenyl)-N-[(3R,4S)-3-fluoro-1-methylpiperidin-4-yl]-2-(hydroxymethyl)-N-methyl-2-phenyl-2,5-dihydro-1H-pyrrole-1-carboxamide


Mass: 459.504 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H28F3N3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG3350, Potassium Phosphate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 1, 2003 / Details: mirror
RadiationMonochromator: yale Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.28→70.31 Å / Num. obs: 30737 / % possible obs: 76 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 43.082 Å2 / Rsym value: 0.1 / Net I/σ(I): 10.3
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 3098 / Rsym value: 0.785 / % possible all: 78.5

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Processing

Software
NameVersionClassification
BUSTER-TNT2.1.1refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1Q0B

1q0b


Resolution: 2.28→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2607 1527 4.97 %RANDOM
Rwork0.1812 ---
obs0.1851 30723 75.74 %-
Displacement parametersBiso mean: 43.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.64565657 Å20 Å20 Å2
2--2.55525304 Å20 Å2
3----1.90959647 Å2
Refinement stepCycle: LAST / Resolution: 2.28→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5188 0 122 323 5633
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0153962
X-RAY DIFFRACTIONt_angle_deg1.30872942
X-RAY DIFFRACTIONt_dihedral_angle_d24.80411200
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0111642
X-RAY DIFFRACTIONt_gen_planes0.0167765
X-RAY DIFFRACTIONt_it1.828539620
X-RAY DIFFRACTIONt_nbd0.0511185
LS refinement shellResolution: 2.28→2.42 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2941 245 4.92 %
Rwork0.2134 4733 -
all21.71 4978 -
obs--75.74 %

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