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- PDB-6mny: Crystal structure of mouse BTK kinase domain in complex with comp... -

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Basic information

Entry
Database: PDB / ID: 6mny
TitleCrystal structure of mouse BTK kinase domain in complex with compound 9a
ComponentsTyrosine-protein kinase
KeywordsTRANSFERASE / kinase / drug design
Function / homology
Function and homology information


transmembrane receptor protein tyrosine kinase activity / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / adaptive immune response / intracellular signal transduction / ATP binding / metal ion binding
Similarity search - Function
Tyrosine-protein kinase BTK, SH3 domain / Zinc finger, Btk motif / BTK motif / Zinc finger Btk-type profile. / Bruton's tyrosine kinase Cys-rich motif / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain ...Tyrosine-protein kinase BTK, SH3 domain / Zinc finger, Btk motif / BTK motif / Zinc finger Btk-type profile. / Bruton's tyrosine kinase Cys-rich motif / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology 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. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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-JVP / Tyrosine-protein kinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsHan, S. / Caspers, N. / Ohren, J.O.
CitationJournal: ACS Med Chem Lett / Year: 2019
Title: Aminopyrazole Carboxamide Bruton's Tyrosine Kinase Inhibitors. Irreversible to Reversible Covalent Reactive Group Tuning.
Authors: Schnute, M.E. / Benoit, S.E. / Buchler, I.P. / Caspers, N. / Grapperhaus, M.L. / Han, S. / Hotchandani, R. / Huang, N. / Hughes, R.O. / Juba, B.M. / Kim, K.H. / Liu, E. / McCarthy, E. / ...Authors: Schnute, M.E. / Benoit, S.E. / Buchler, I.P. / Caspers, N. / Grapperhaus, M.L. / Han, S. / Hotchandani, R. / Huang, N. / Hughes, R.O. / Juba, B.M. / Kim, K.H. / Liu, E. / McCarthy, E. / Messing, D. / Miyashiro, J.S. / Mohan, S. / O'Connell, T.N. / Ohren, J.F. / Parikh, M.D. / Schmidt, M. / Selness, S.R. / Springer, J.R. / Thanabal, V. / Trujillo, J.I. / Walker, D.P. / Wan, Z.K. / Withka, J.M. / Wittwer, A.J. / Wood, N.L. / Xing, L. / Zapf, C.W. / Douhan III, J.
History
DepositionOct 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,5143
Polymers64,0752
Non-polymers4381
Water2,666148
1
A: Tyrosine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4762
Polymers32,0381
Non-polymers4381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine-protein kinase


Theoretical massNumber of molelcules
Total (without water)32,0381
Polymers32,0381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.945, 63.515, 70.005
Angle α, β, γ (deg.)76.77, 85.27, 78.13
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Tyrosine-protein kinase


Mass: 32037.719 Da / Num. of mol.: 2 / Fragment: Protein kinase domain, residues 384-659
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Btk / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q7TMU1, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-JVP / 5-amino-1-[(3R)-1-cyanopiperidin-3-yl]-3-[4-(2,4-difluorophenoxy)phenyl]-1H-pyrazole-4-carboxamide


Mass: 438.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20F2N6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% PEG 3350, 0.1 M Bis-Tris pH 6.0, 0.1 M sodium malonate

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→68.1 Å / Num. obs: 16257 / % possible obs: 96.8 % / Redundancy: 1.8 % / Biso Wilson estimate: 52.55 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 6.3
Reflection shellResolution: 2.8→2.89 Å / Rmerge(I) obs: 0.467 / Num. unique obs: 2364 / % possible all: 96.1

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
HKL-2000data reduction
SCALAdata scaling
BUSTERphasing
RefinementResolution: 2.8→68.1 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.807 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.385
RfactorNum. reflection% reflectionSelection details
Rfree0.257 742 5 %RANDOM
Rwork0.196 ---
obs0.199 14844 96.9 %-
Displacement parametersBiso mean: 30.97 Å2
Baniso -1Baniso -2Baniso -3
1-2.1537 Å2-0.5101 Å20.6425 Å2
2---5.0521 Å2-0.7585 Å2
3---2.8984 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: 1 / Resolution: 2.8→68.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4167 0 32 185 4384
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014339HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.15863HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1545SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes731HARMONIC5
X-RAY DIFFRACTIONt_it4339HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion20.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion522SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4985SEMIHARMONIC4
LS refinement shellResolution: 2.8→3.02 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.305 149 4.9 %
Rwork0.2139 2894 -
all0.2187 3043 -
obs--96.33 %
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)
11.64170.80090.17640.6954-0.13860.07870.00770.07540.1011-0.01970.046-0.00790.02520.0892-0.0537-0.0209-0.01020.0105-0.1508-0.018-0.00725.768-0.83887.899
20.6611-0.1763-0.14010.2768-0.03240.6711-0.0436-0.2877-0.07280.06150.07090.0907-0.0349-0.0599-0.0273-0.07020.0092-0.0112-0.0449-0.0061-0.02263.3339-29.447235.9758
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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