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- PDB-6bkh: BTK complex with compound 11 -

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Basic information

Entry
Database: PDB / ID: 6bkh
TitleBTK complex with compound 11
ComponentsTyrosine-protein kinase BTK
KeywordsTRANSFERASE / BTK / inhibitor / water structure / kinase
Function / homology
Function and homology information


regulation of B cell cytokine production / regulation of B cell apoptotic process / monocyte proliferation / positive regulation of interleukin-17A production / eosinophil homeostasis / proteoglycan catabolic process / positive regulation of type III hypersensitivity / B cell affinity maturation / positive regulation of synoviocyte proliferation / histamine secretion by mast cell ...regulation of B cell cytokine production / regulation of B cell apoptotic process / monocyte proliferation / positive regulation of interleukin-17A production / eosinophil homeostasis / proteoglycan catabolic process / positive regulation of type III hypersensitivity / B cell affinity maturation / positive regulation of synoviocyte proliferation / histamine secretion by mast cell / neutrophil homeostasis / positive regulation of cGAS/STING signaling pathway / cellular response to molecule of fungal origin / positive regulation of type I hypersensitivity / MyD88 deficiency (TLR2/4) / cellular response to interleukin-7 / IRAK4 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of B cell differentiation / positive regulation of immunoglobulin production / phospholipase activator activity / negative regulation of interleukin-10 production / negative regulation of B cell proliferation / positive regulation of NLRP3 inflammasome complex assembly / Fc-epsilon receptor signaling pathway / mesoderm development / phosphatidylinositol-3,4,5-trisphosphate binding / B cell activation / RHO GTPases Activate WASPs and WAVEs / phospholipase binding / cell maturation / positive regulation of B cell proliferation / FCERI mediated Ca+2 mobilization / positive regulation of phagocytosis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / peptidyl-tyrosine phosphorylation / cellular response to reactive oxygen species / B cell receptor signaling pathway / non-membrane spanning protein tyrosine kinase activity / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / apoptotic signaling pathway / calcium-mediated signaling / positive regulation of NF-kappaB transcription factor activity / Regulation of actin dynamics for phagocytic cup formation / positive regulation of interleukin-6 production / G beta:gamma signalling through BTK / positive regulation of tumor necrosis factor production / DAP12 signaling / G alpha (12/13) signalling events / T cell receptor signaling pathway / ER-Phagosome pathway / cytoplasmic vesicle / protein tyrosine kinase activity / response to lipopolysaccharide / G alpha (q) signalling events / Potential therapeutics for SARS / adaptive immune response / positive regulation of canonical NF-kappaB signal transduction / intracellular signal transduction / membrane raft / innate immune response / perinuclear region of cytoplasm / zinc ion binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
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 ...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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-DVD / Tyrosine-protein kinase BTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.792 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 8, 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
Revision 1.3Apr 2, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)34,7916
Polymers33,8791
Non-polymers9125
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)108.213, 108.213, 41.794
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DVD / N-[2-(hydroxymethyl)-3-{5-[(5-methyl-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrazin-2-yl)amino]-6-oxo-1,6-dihydropyridazin-3-yl}phenyl]-1-benzothiophene-2-carboxamide


Mass: 527.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H25N7O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.01 %
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: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7902→50 Å / Num. obs: 26407 / % possible obs: 99.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 20.17 Å2 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.034 / Rrim(I) all: 0.076 / Χ2: 0.969 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.834.30.61413280.670.330.6990.59599.6
1.83-1.864.50.56812920.7020.2970.6420.62399.9
1.86-1.94.50.47313210.7960.2470.5350.6399.8
1.9-1.944.60.39413160.8680.2030.4450.65499.8
1.94-1.984.60.32312850.9020.1670.3650.69599.8
1.98-2.034.70.27413150.9270.1410.3090.71699.8
2.03-2.084.80.2413300.9470.1220.2690.77999.9
2.08-2.134.80.18912920.970.0960.2120.76299.5
2.13-2.24.80.16113180.9780.0810.1810.78199.8
2.2-2.2750.14612880.9820.0720.1630.84899.8
2.27-2.354.90.12413270.9880.0620.1390.83799.8
2.35-2.445.10.10813050.9910.0520.120.84699.9
2.44-2.555.10.08913210.9930.0430.0990.83199.8
2.55-2.695.20.07413290.9960.0350.0820.828100
2.69-2.865.30.06213250.9970.0290.0690.871100
2.86-3.085.20.05413230.9970.0260.061.09699.8
3.08-3.395.30.05113210.9980.0240.0561.65299.8
3.39-3.885.20.04613480.9980.0220.0512.26499.6
3.88-4.8850.03113270.9990.0150.0351.48899.7
4.88-505.30.02613960.9990.0120.0291.13699.7

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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: 1.792→38.17 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.37
RfactorNum. reflection% reflection
Rfree0.2008 1319 5 %
Rwork0.1524 --
obs0.1547 26394 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.8 Å2 / Biso mean: 28.6707 Å2 / Biso min: 8.99 Å2
Refinement stepCycle: final / Resolution: 1.792→38.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 0 59 205 2400
Biso mean--30.3 33.62 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012293
X-RAY DIFFRACTIONf_angle_d1.0993110
X-RAY DIFFRACTIONf_chiral_restr0.056321
X-RAY DIFFRACTIONf_plane_restr0.007397
X-RAY DIFFRACTIONf_dihedral_angle_d19.0161349
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7917-1.86340.26411270.2192680280796
1.8634-1.94830.22761440.19527752919100
1.9483-2.0510.23111540.165827602914100
2.051-2.17950.21221520.155427822934100
2.1795-2.34770.19931590.147527712930100
2.3477-2.58390.19191550.145927902945100
2.5839-2.95770.20981680.150627752943100
2.9577-3.72590.22211320.142428412973100
3.7259-38.17890.15081280.143229013029100
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)
10.1825-0.23110.07090.2599-0.08920.06860.0339-0.09590.1103-0.0468-0.0379-0.24240.02460.0039-0.00170.11620.0055-0.00780.141-0.01310.1982106.2265107.4022-9.717
20.00930.0085-0.00230.007-0.00960.015-0.11940.1148-0.1052-0.0382-0.0412-0.00890.11770.136900.11840.01390.03070.1765-0.01470.159394.472101.3529-0.7662
30.0281-0.02950.03050.0346-0.04250.04030.07830.0071-0.1207-0.1062-0.053-0.04420.07550.083300.12440.0140.02640.1617-0.00740.1771104.3767105.8025-8.2259
40.02530.008-0.02230.0033-0.00230.0314-0.00570.1806-0.0051-0.08370.0331-0.0665-0.0281-0.047-00.16250.00430.00710.1781-0.00690.127580.2546115.2125-17.1946
50.1983-0.1776-0.12760.41640.08530.53380.0075-0.10890.01480.02120.0243-0.07090.029-0.04320.08710.09860.0141-0.00230.131-0.01990.104988.1295114.83370.2448
60.0250.02110.01380.0593-0.04760.06750.0463-0.08290.046-0.0222-0.077-0.056-0.0933-0.0635-00.15640.0255-0.00790.1681-0.02260.153382.435130.476-2.2302
70.25610.0188-0.04660.10510.05270.10810.0076-0.15920.04260.0925-0.09650.137-0.0049-0.2599-0.09430.11840.00660.02860.2215-0.02560.137973.3017115.62582.6187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 396 through 444 )A396 - 444
2X-RAY DIFFRACTION2chain 'A' and (resid 445 through 459 )A445 - 459
3X-RAY DIFFRACTION3chain 'A' and (resid 460 through 480 )A460 - 480
4X-RAY DIFFRACTION4chain 'A' and (resid 482 through 494 )A482 - 494
5X-RAY DIFFRACTION5chain 'A' and (resid 495 through 591 )A495 - 591
6X-RAY DIFFRACTION6chain 'A' and (resid 592 through 611 )A592 - 611
7X-RAY DIFFRACTION7chain 'A' and (resid 612 through 658 )A612 - 658

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