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- PDB-5h0h: Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhi... -

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Basic information

Entry
Database: PDB / ID: 5h0h
TitleCrystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor (S)-2-(((1r,4S)-4-(4-amino-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)cyclohexyl)amino)-N,N,4-trimethylpentanamide
ComponentsTyrosine-protein kinase HCK
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


leukocyte degranulation / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / regulation of podosome assembly / regulation of phagocytosis / FLT3 signaling through SRC family kinases / Nef and signal transduction / regulation of DNA-binding transcription factor activity / positive regulation of actin filament polymerization ...leukocyte degranulation / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / regulation of podosome assembly / regulation of phagocytosis / FLT3 signaling through SRC family kinases / Nef and signal transduction / regulation of DNA-binding transcription factor activity / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / mesoderm development / FCGR activation / localization / type II interferon-mediated signaling pathway / Signaling by CSF3 (G-CSF) / transport vesicle / lipopolysaccharide-mediated signaling pathway / negative regulation of inflammatory response to antigenic stimulus / extrinsic component of cytoplasmic side of plasma membrane / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / cell projection / caveola / integrin-mediated signaling pathway / Regulation of signaling by CBL / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Inactivation of CSF3 (G-CSF) signaling / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of cell shape / regulation of inflammatory response / protein tyrosine kinase activity / protein autophosphorylation / cell differentiation / lysosome / cytoskeleton / cell adhesion / intracellular signal transduction / inflammatory response / signaling receptor binding / protein phosphorylation / focal adhesion / innate immune response / intracellular membrane-bounded organelle / lipid binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / Golgi apparatus / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Tyrosine-protein kinase HCK, SH2 domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...Tyrosine-protein kinase HCK, SH2 domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, 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
Similarity search - Domain/homology
Chem-OOV / Tyrosine-protein kinase HCK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsTomabechi, Y. / Kukimoto-Niino, M. / Shirouzu, M.
CitationJournal: Bioorg. Med. Chem. / Year: 2017
Title: Activity cliff for 7-substituted pyrrolo-pyrimidine inhibitors of HCK explained in terms of predicted basicity of the amine nitrogen.
Authors: Yuki, H. / Kikuzato, K. / Koda, Y. / Mikuni, J. / Tomabechi, Y. / Kukimoto-Niino, M. / Tanaka, A. / Shirai, F. / Shirouzu, M. / Koyama, H. / Honma, T.
History
DepositionOct 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5412
Polymers52,0001
Non-polymers5411
Water7,080393
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.113, 85.623, 129.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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.: 1 / Fragment: UNP RESIDUES 81-526 / Mutation: Q523E, Q524E, Q525I
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-OOV / (2~{S})-2-[[4-[4-azanyl-5-(4-phenoxyphenyl)pyrrolo[2,3-d]pyrimidin-7-yl]cyclohexyl]amino]-~{N},~{N},4-trimethyl-pentanamide


Mass: 540.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H40N6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.22-0.25 M ammonium formate, 12-22 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 51602 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 22.17 Å2 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.027 / Rrim(I) all: 0.073 / Χ2: 1.132 / Net I/av σ(I): 34.653 / Net I/σ(I): 9.3 / Num. measured all: 375872
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.72-1.756.50.55824790.8610.2340.6070.66599
1.75-1.787.30.51225420.9120.2030.5510.659100
1.78-1.827.30.43425350.9320.170.4670.66399.7
1.82-1.857.40.3625340.9520.1410.3880.678100
1.85-1.897.40.30825440.9660.1210.3310.70299.9
1.89-1.947.40.24225590.9770.0950.260.728100
1.94-1.997.40.2125550.9830.0820.2260.746100
1.99-2.047.40.16525690.9880.0650.1780.769100
2.04-2.17.40.13925340.990.0540.1490.831100
2.1-2.177.40.12225720.9930.0480.1310.854100
2.17-2.247.40.10625440.9940.0420.1140.893100
2.24-2.337.40.09325760.9950.0360.10.932100
2.33-2.447.40.08225690.9960.0320.0890.959100
2.44-2.577.40.07425870.9960.0290.0791.028100
2.57-2.737.40.06925870.9970.0270.0741.155100
2.73-2.947.40.06825870.9970.0270.0731.5100
2.94-3.247.20.07126080.9960.0280.0762.418100
3.24-3.7170.06526370.9960.0270.0713.086100
3.71-4.677.20.04526720.9980.0180.0482.049100
4.67-506.80.03228120.9990.0130.0351.26899.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.15 Å42.81 Å
Translation7.15 Å42.81 Å

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Processing

Software
NameVersionClassification
DENZOdata collection
HKL-2000data scaling
PHASER2.5.6phasing
PHENIX1.9_1690refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VS3

3vs3


Resolution: 1.72→42.812 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.81
RfactorNum. reflection% reflection
Rfree0.2239 2000 3.88 %
Rwork0.185 --
obs0.1865 51531 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.98 Å2 / Biso mean: 37.3881 Å2 / Biso min: 11.22 Å2
Refinement stepCycle: final / Resolution: 1.72→42.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3613 0 40 393 4046
Biso mean--21.23 37.4 -
Num. residues----447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073744
X-RAY DIFFRACTIONf_angle_d0.9965062
X-RAY DIFFRACTIONf_chiral_restr0.042534
X-RAY DIFFRACTIONf_plane_restr0.005645
X-RAY DIFFRACTIONf_dihedral_angle_d13.2191406
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 (%)
1.7205-1.76350.28891380.2373418355699
1.7635-1.81120.26541410.214534853626100
1.8112-1.86450.25821420.213335183660100
1.8645-1.92470.25771390.209134683607100
1.9247-1.99340.241430.197535133656100
1.9934-2.07330.22231410.188634873628100
2.0733-2.16760.24861420.185735333675100
2.1676-2.28190.23141420.185335143656100
2.2819-2.42480.21341420.183435153657100
2.4248-2.6120.21111420.184835243666100
2.612-2.87490.23431450.199435933738100
2.8749-3.29070.20961450.186335623707100
3.2907-4.14540.21521440.168436103754100
4.1454-42.82470.21111540.174337913945100

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