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- PDB-5i3r: Crystal Structure of BMP-2-inducible kinase in complex with an In... -

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Basic information

Entry
Database: PDB / ID: 5i3r
TitleCrystal Structure of BMP-2-inducible kinase in complex with an Indazole inhibitor
ComponentsBMP-2-inducible protein kinase
KeywordsTransferase/Transferase Inhibitor / transferase / protein kinase domain / Structural Genomics / Structural Genomics Consortium / SGC / Transferase-Transferase Inhibitor Complex
Function / homology
Function and homology information


phosphatase regulator activity / regulation of clathrin-dependent endocytosis / AP-2 adaptor complex binding / regulation of bone mineralization / positive regulation of Notch signaling pathway / non-specific serine/threonine protein kinase / nuclear speck / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity ...phosphatase regulator activity / regulation of clathrin-dependent endocytosis / AP-2 adaptor complex binding / regulation of bone mineralization / positive regulation of Notch signaling pathway / non-specific serine/threonine protein kinase / nuclear speck / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
BMP-2-inducible protein kinase, C-terminal / BMP-2-inducible protein kinase C-terminus / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain ...BMP-2-inducible protein kinase, C-terminal / BMP-2-inducible protein kinase C-terminus / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-IDK / PHOSPHATE ION / BMP-2-inducible protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCounago, R.M. / Sorrell, F.J. / Krojer, T. / Savitsky, P. / Elkins, J.M. / Axtman, A. / Drewry, D. / Wells, C. / Zhang, C. / Zuercher, W. ...Counago, R.M. / Sorrell, F.J. / Krojer, T. / Savitsky, P. / Elkins, J.M. / Axtman, A. / Drewry, D. / Wells, C. / Zhang, C. / Zuercher, W. / Willson, T.M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Arruda, P. / Gileadi, O. / Structural Genomics Consortium (SGC)
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP) Brazil
CitationJournal: To Be Published
Title: Crystal Structure of BMP-2-inducible kinase in complex with an Indazole inhibitor
Authors: Counago, R.M. / Sorrell, F.J. / Krojer, T. / Elkins, J.M. / Gileadi, O. / Willson, T.M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Arruda, P.
History
DepositionFeb 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BMP-2-inducible protein kinase
B: BMP-2-inducible protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0396
Polymers68,0282
Non-polymers1,0114
Water3,459192
1
A: BMP-2-inducible protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5203
Polymers34,0141
Non-polymers5052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BMP-2-inducible protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5203
Polymers34,0141
Non-polymers5052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.433, 78.433, 255.221
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsMonomer according to Gel filtration

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Components

#1: Protein BMP-2-inducible protein kinase / BIKe


Mass: 34014.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP2K, BIKE, HRIHFB2017 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9NSY1, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-IDK / N-[6-(3-{[(cyclopropylmethyl)sulfonyl]amino}phenyl)-1H-indazol-3-yl]cyclopropanecarboxamide


Mass: 410.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H22N4O3S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG 8000; 0.2 M Ammonium chloride; 10% Ethyleneglycol; 0.1M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.4→29.55 Å / Num. obs: 32194 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 52.9 Å2 / Net I/σ(I): 9.1

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W9W

4w9w


Resolution: 2.4→21.71 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.904 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.305 / SU Rfree Blow DPI: 0.221 / SU Rfree Cruickshank DPI: 0.218
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1550 4.83 %RANDOM
Rwork0.185 ---
obs0.188 32097 99.8 %-
Displacement parametersBiso mean: 59.66 Å2
Baniso -1Baniso -2Baniso -3
1--8.7631 Å20 Å20 Å2
2---8.7631 Å20 Å2
3---17.5263 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→21.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4735 0 68 192 4995
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014910HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.096669HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2278SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes737HARMONIC5
X-RAY DIFFRACTIONt_it4910HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion2.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion641SEMIHARMONIC5
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_contact5590SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.48 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.251 146 5.06 %
Rwork0.212 2739 -
obs--99.52 %
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)
15.33671.7574-0.13781.01440.16322.22560.0406-0.03280.11130.1130.0917-0.329-0.08320.3864-0.1322-0.02760.0598-0.02750.21240.0473-0.094617.075745.234131.4109
22.1291.8373-1.07791.98130.86484.23350.0182-0.1216-0.06440.09720.0192-0.25340.13680.483-0.0374-0.17820.0204-0.05720.10740.0268-0.168315.664847.755229.0241
32.32590.3319-0.25690.7858-1.29053.50430.2049-0.32970.40110.3175-0.12850.045-0.47110.3848-0.0764-0.0336-0.03170.04090.0856-0.0258-0.07796.458754.542629.4174
41.0231-0.1353-0.95254.5010.10590-0.03190.0867-0.19610.11970-0.2810.21490.06450.0318-0.12590.152-0.03680.11240.0162-0.043514.430641.90038.366
51.71620.94890.54432.64270.44481.58250.0182-0.01950.2290.17960.02960.1506-0.0249-0.0758-0.0478-0.05330.02840.00060.04070.0294-0.04291.223549.54512.1232
60.85261.4777-0.02682.44920.42150.4197-0.0604-0.29190.46830.134-0.03810.2892-0.27150.08850.0985-0.01090.0479-0.0175-0.0625-0.03460.08093.550569.607416.9951
72.13341.16440.19532.2470.50971.6001-0.24810.3120.4235-0.23810.0950.3874-0.2563-0.04960.1532-0.08420.0477-0.0851-0.02180.0903-0.04030.41857.76810.4319
82.58111.4527-0.19111.0574-1.37271.8655-0.06170.2198-0.3909-0.41450.2860.13040.2216-0.4466-0.22430.0044-0.0701-0.0811-0.020.0671-0.087725.568868.440.0669
91.8962-0.78330.49030.7565-1.218500.0127-0.04090.1495-0.11920.17480.1649-0.1879-0.1413-0.18750.09170.1063-0.05470.00210.082-0.02124.964485.84791.6193
100.42440.9168-1.7072.22770.85953.1527-0.01240.3120.1278-0.1740.13840.3473-0.1286-0.3153-0.12610.0334-0.0293-0.037-0.00010.0861-0.098626.667477.4760.2666
110.7312-1.4210.127402.62110.4812-0.0114-0.0499-0.2495-0.03720.03460.1170.0181-0.0862-0.02320.0253-0.0294-0.09530.0260.1032-0.094827.860266.590322.7088
121.3676-1.00592.41851.9349-2.24283.532-0.0230.07720.0769-0.10070.053-0.1286-0.5436-0.1605-0.02990.05910.0370.0113-0.00210.0469-0.137832.358781.076319.1351
133.2531-0.39240.67140.65-1.56150-0.04110.10770.2114-0.13-0.04190.0646-0.2806-0.21040.08310.13520.152-0.07330.08550.106-0.176917.331394.067612.7376
140.99831.3961-0.20890-0.86711.3118-0.05320.04150.2526-0.02950.07820.2559-0.2944-0.3152-0.0250.09960.152-0.0265-0.03490.0205-0.090320.440989.080724.6535
152.52760.14640.15731.7455-0.34883.3402-0.0721-0.330.39670.16030.05690.2618-0.5442-0.43940.01520.08220.0813-0.0019-0.0774-0.0215-0.15429.06587.315532.843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|42 - 62}
2X-RAY DIFFRACTION2{A|63 - 85}
3X-RAY DIFFRACTION3{A|86 - 131}
4X-RAY DIFFRACTION4{A|132 - 151}
5X-RAY DIFFRACTION5{A|152 - 196}
6X-RAY DIFFRACTION6{A|197 - 224}
7X-RAY DIFFRACTION7{A|225 - 343}
8X-RAY DIFFRACTION8{B|42 - 85}
9X-RAY DIFFRACTION9{B|86 - 102}
10X-RAY DIFFRACTION10{B|103 - 131}
11X-RAY DIFFRACTION11{B|132 - 151}
12X-RAY DIFFRACTION12{B|152 - 196}
13X-RAY DIFFRACTION13{B|197 - 224}
14X-RAY DIFFRACTION14{B|225 - 261}
15X-RAY DIFFRACTION15{B|262 - 343}

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