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- PDB-3vs5: Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhi... -

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Basic information

Entry
Database: PDB / ID: 3vs5
TitleCrystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor 7-(1-methylpiperidin-4-yl)-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine
ComponentsTyrosine-protein kinase HCK
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


regulation of DNA-templated transcription
Similarity search - Function
PRD domain protein, EF0829/AHA3910 / PRD domain / PRD domain superfamily / PRD domain profile. / SH2 domain / SHC Adaptor Protein / SH3 Domains / SH3 domain / SH2 domain / SH3 type barrels. ...PRD domain protein, EF0829/AHA3910 / PRD domain / PRD domain superfamily / PRD domain profile. / SH2 domain / SHC Adaptor Protein / SH3 Domains / SH3 domain / SH2 domain / SH3 type barrels. / Protein tyrosine and serine/threonine kinase / Roll / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-VSG / PRD domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.851 Å
AuthorsKuratani, M. / Tomabechi, Y. / Handa, N. / Yokoyama, S.
CitationJournal: Sci Transl Med / Year: 2013
Title: A Pyrrolo-Pyrimidine Derivative Targets Human Primary AML Stem Cells in Vivo
Authors: Saito, Y. / Yuki, H. / Kuratani, M. / Hashizume, Y. / Takagi, S. / Honma, T. / Tanaka, A. / Shirouzu, M. / Mikuni, J. / Handa, N. / Ogahara, I. / Sone, A. / Najima, Y. / Tomabechi, Y. / ...Authors: Saito, Y. / Yuki, H. / Kuratani, M. / Hashizume, Y. / Takagi, S. / Honma, T. / Tanaka, A. / Shirouzu, M. / Mikuni, J. / Handa, N. / Ogahara, I. / Sone, A. / Najima, Y. / Tomabechi, Y. / Wakiyama, M. / Uchida, N. / Tomizawa-Murasawa, M. / Kaneko, A. / Tanaka, S. / Suzuki, N. / Kajita, H. / Aoki, Y. / Ohara, O. / Shultz, L.D. / Fukami, T. / Goto, T. / Taniguchi, S. / Yokoyama, S. / Ishikawa, F.
History
DepositionApr 21, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase HCK
B: Tyrosine-protein kinase HCK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8806
Polymers104,0002
Non-polymers8794
Water68538
1
A: Tyrosine-protein kinase HCK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4403
Polymers52,0001
Non-polymers4402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine-protein kinase HCK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4403
Polymers52,0001
Non-polymers4402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.489, 94.826, 179.982
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 Tyrosine-protein kinase HCK / Hematopoietic cell kinase / Hemopoietic cell kinase / p59-HCK/p60-HCK / p59Hck / p61Hck


Mass: 52000.227 Da / Num. of mol.: 2 / Fragment: UNP residues 81-526 / Mutation: Q528E, Q529E, Q530I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P08631, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-VSG / 7-(1-methylpiperidin-4-yl)-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine


Mass: 399.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25N5O
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.01 Å3/Da / Density % sol: 59.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris, 0.1M calcium acetate, 20% glycerol, 21% PEG6000, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 22, 2011
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.851→50 Å / Num. all: 29389 / Num. obs: 28831 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 48.57 Å2
Reflection shellResolution: 2.9→3 Å / % possible all: 97.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VRZ

3vrz


Resolution: 2.851→48.803 Å / Occupancy max: 1 / Occupancy min: 0.83 / SU ML: 0.41 / σ(F): 0.06 / Phase error: 34.32 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3094 1993 7.45 %random
Rwork0.2552 ---
all0.3094 28831 --
obs0.2592 26756 88.87 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 12.715 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso max: 116.43 Å2 / Biso mean: 53.1675 Å2 / Biso min: 20.53 Å2
Baniso -1Baniso -2Baniso -3
1--4.8505 Å20 Å2-0 Å2
2--21.9777 Å2-0 Å2
3----17.1272 Å2
Refinement stepCycle: LAST / Resolution: 2.851→48.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6927 0 62 38 7027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077161
X-RAY DIFFRACTIONf_angle_d1.0969678
X-RAY DIFFRACTIONf_chiral_restr0.071025
X-RAY DIFFRACTIONf_plane_restr0.0051228
X-RAY DIFFRACTIONf_dihedral_angle_d17.9682700
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8507-2.9220.426810.34311003108452
2.922-3.0010.40481250.33251560168579
3.001-3.08930.35371330.31981636176983
3.0893-3.1890.37011330.29321668180185
3.189-3.30290.3431390.28551716185588
3.3029-3.43520.29851430.27331768191190
3.4352-3.59140.31671440.27621790193492
3.5914-3.78070.33451480.26241830197893
3.7807-4.01750.32831510.25711884203595
4.0175-4.32750.31540.22811925207996
4.3275-4.76270.26431550.21321938209398
4.7627-5.45110.27871580.24311963212197
5.4511-6.86470.27691610.25231981214298
6.8647-48.81050.29231680.23132101226998

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