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- PDB-6bkw: BTK complex with compound 12 -

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Basic information

Entry
Database: PDB / ID: 6bkw
TitleBTK complex with compound 12
ComponentsTyrosine-protein kinase BTK
KeywordsTRANSFERASE / BTK / inhibitor / water structure / kinase
Function / homology
Function and homology information


regulation of B cell cytokine production / proteoglycan catabolic process / monocyte proliferation / positive regulation of interleukin-17A production / regulation of B cell apoptotic process / eosinophil homeostasis / positive regulation of type III hypersensitivity / B cell affinity maturation / histamine secretion by mast cell / positive regulation of synoviocyte proliferation ...regulation of B cell cytokine production / proteoglycan catabolic process / monocyte proliferation / positive regulation of interleukin-17A production / regulation of B cell apoptotic process / eosinophil homeostasis / positive regulation of type III hypersensitivity / B cell affinity maturation / histamine secretion by mast cell / positive regulation of synoviocyte proliferation / neutrophil homeostasis / cellular response to molecule of fungal origin / positive regulation of type I hypersensitivity / cellular response to interleukin-7 / MyD88 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of B cell differentiation / positive regulation of NLRP3 inflammasome complex assembly / phospholipase activator activity / negative regulation of interleukin-10 production / B cell activation / negative regulation of B cell proliferation / Fc-epsilon receptor signaling pathway / phosphatidylinositol-3,4,5-trisphosphate binding / phospholipase binding / mesoderm development / positive regulation of immunoglobulin production / RHO GTPases Activate WASPs and WAVEs / positive regulation of phagocytosis / positive regulation of B cell proliferation / cell maturation / FCERI mediated Ca+2 mobilization / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calcium-mediated signaling / apoptotic signaling pathway / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / G beta:gamma signalling through BTK / Regulation of actin dynamics for phagocytic cup formation / cellular response to reactive oxygen species / positive regulation of interleukin-6 production / peptidyl-tyrosine phosphorylation / G alpha (12/13) signalling events / positive regulation of tumor necrosis factor production / DAP12 signaling / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / T cell receptor signaling pathway / cytoplasmic vesicle / G alpha (q) signalling events / protein tyrosine kinase activity / Potential therapeutics for SARS / response to lipopolysaccharide / adaptive immune response / intracellular signal transduction / membrane raft / protein phosphorylation / innate immune response / perinuclear region of cytoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
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-DXM / triphenylphosphane / Tyrosine-protein kinase BTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å
AuthorsKiefer, J.R. / Eigenbrot, C. / Yu, C.L.
CitationJournal: J. Comput. Aided Mol. Des. / Year: 2019
Title: Water molecules in protein-ligand interfaces. Evaluation of software tools and SAR comparison.
Authors: Nittinger, E. / Gibbons, P. / Eigenbrot, C. / Davies, D.R. / Maurer, B. / Yu, C.L. / Kiefer, J.R. / Kuglstatter, A. / Murray, J. / Ortwine, D.F. / Tang, Y. / Tsui, V.
History
DepositionNov 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase BTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1248
Polymers33,8791
Non-polymers1,2457
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.765, 108.765, 41.863
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Tyrosine-protein kinase BTK / Agammaglobulinemia tyrosine kinase / ATK / B-cell progenitor kinase / BPK / Bruton tyrosine kinase


Mass: 33878.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTK, AGMX1, ATK, BPK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q06187, non-specific protein-tyrosine kinase

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Non-polymers , 5 types, 210 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DXM / N-(3-{5-[(1,5-dimethyl-1H-pyrazol-3-yl)amino]-1-methyl-6-oxo-1,6-dihydropyridazin-3-yl}-2,6-difluorophenyl)-4,5,6,7-tetrahydro-1-benzothiophene-2-carboxamide


Mass: 510.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H24F2N6O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FPZ / triphenylphosphane / Triphenylphosphine


Mass: 262.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H15P
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7 / Details: PEG 10000, Li2SO4, pH 7.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 1.499→35 Å / Num. obs: 43469 / % possible obs: 95.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 16.58 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.044 / Rrim(I) all: 0.089 / Χ2: 1.093 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.531.50.54314280.4490.4930.7360.36663.5
1.53-1.551.70.49716930.4830.4450.670.40674
1.55-1.581.90.44819140.6270.3780.590.41985.5
1.58-1.622.10.38620780.7180.3030.4940.42390.7
1.62-1.652.40.35121580.7820.2560.4370.47396.5
1.65-1.692.90.30822550.8520.2050.3730.48699.3
1.69-1.733.40.2822750.9110.1690.3290.58299.7
1.73-1.784.40.24522430.9470.1290.2780.637100
1.78-1.835.10.20322810.970.0980.2260.699100
1.83-1.895.10.1722740.9770.0810.1880.811100
1.89-1.965.10.14222600.9840.0690.1580.888100
1.96-2.045.10.11422650.9880.0550.1270.997100
2.04-2.1350.09822790.990.0480.111.106100
2.13-2.244.90.08522870.9930.0420.0961.199100
2.24-2.384.90.08122960.9930.040.0911.309100
2.38-2.564.80.07522720.9930.0380.0851.437100
2.56-2.824.60.0722940.9930.0370.081.51399.9
2.82-3.234.10.06423040.9930.0360.0741.80999.7
3.23-4.073.60.05622960.9920.0350.0671.89999.5
4.07-353.50.05223170.9950.0330.0621.87396.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.499→31.289 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.19
RfactorNum. reflection% reflection
Rfree0.1895 2200 5.07 %
Rwork0.1625 --
obs0.1638 43393 95.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.16 Å2 / Biso mean: 25.8452 Å2 / Biso min: 9.82 Å2
Refinement stepCycle: final / Resolution: 1.499→31.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2159 0 133 208 2500
Biso mean--34.64 30.9 -
Num. residues----266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072344
X-RAY DIFFRACTIONf_angle_d1.1133173
X-RAY DIFFRACTIONf_chiral_restr0.073324
X-RAY DIFFRACTIONf_plane_restr0.005397
X-RAY DIFFRACTIONf_dihedral_angle_d24.688865
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4992-1.53180.314990.26481712181164
1.5318-1.56750.2522940.24922083217778
1.5675-1.60670.25411310.22422390252189
1.6067-1.65010.23981330.20072557269095
1.6501-1.69870.19421430.18272681282499
1.6987-1.75350.18361490.171626862835100
1.7535-1.81610.19161530.157426902843100
1.8161-1.88890.17961300.154727042834100
1.8889-1.97480.20111670.160626642831100
1.9748-2.07890.16941370.149227202857100
2.0789-2.20910.19141410.148826902831100
2.2091-2.37960.18751440.148127122856100
2.3796-2.6190.19171260.153227272853100
2.619-2.99770.17121680.16327002868100
2.9977-3.77580.19851500.156827352885100
3.7758-31.29580.16991350.15982742287798
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)
10.04340.04550.00760.07090.02990.01840.01940.0731-0.0554-0.0512-0.0289-0.10760.10380.0671-00.169-0.025-0.03360.18640.0120.244654.6208-8.27729.4246
20.19650.2340.04940.26910.06870.07-0.09460.11620.0344-0.08680.1073-0.1703-0.0708-0.00980.00110.1646-0.02920.01510.136-0.01210.223150.5315-14.25493.6723
30.00140.0007-0-0.00270.0013-0.00130.0273-0.01760.096-0.052-0.0487-0.0590.00160.0246-0.00010.1472-0.01340.00230.14030.02250.178946.5854-9.62531.8836
40.1526-0.03330.1740.0047-0.03920.1983-0.0408-0.0628-0.01190.13690.0343-0.1055-0.0078-0.0513-0.00590.1508-0.0176-0.01350.13250.00040.141133.6299-18.748312.8588
50.0536-0.02390.01190.07010.01530.0125-0.01660.05940.0421-0.0968-0.03850.0428-0.1171-0.0966-0.00940.1621-0.0039-0.00180.15430.01290.123327.2139-12.99470.3612
60.34540.20470.08370.28660.14560.45260.01810.1023-0.0404-0.02030.0263-0.1165-0.0465-0.00630.01730.1194-0.01860.00010.1426-0.01170.126636.3921-24.1335-3.1817
70.51130.1766-0.18250.2753-0.12090.6003-0.01790.0857-0.0688-0.0785-0.05720.06520.0557-0.1617-0.13290.1052-0.0127-0.01430.162-0.0150.100922.5095-26.8365-3.4644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 393 through 407 )A393 - 407
2X-RAY DIFFRACTION2chain 'A' and (resid 408 through 451 )A408 - 451
3X-RAY DIFFRACTION3chain 'A' and (resid 452 through 470 )A452 - 470
4X-RAY DIFFRACTION4chain 'A' and (resid 471 through 494 )A471 - 494
5X-RAY DIFFRACTION5chain 'A' and (resid 495 through 515 )A495 - 515
6X-RAY DIFFRACTION6chain 'A' and (resid 516 through 591 )A516 - 591
7X-RAY DIFFRACTION7chain 'A' and (resid 592 through 658 )A592 - 658

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