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- PDB-6oko: Crystal structure of mRIPK3 complexed with N-(3-fluoro-4-{1H-pyrr... -

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Basic information

Entry
Database: PDB / ID: 6oko
TitleCrystal structure of mRIPK3 complexed with N-(3-fluoro-4-{1H-pyrrolo[2,3-b]pyridin-4-yloxy}phenyl)-1-(4-fluorophenyl)-2-oxo-1,2-dihydropyridine-3-carboxamide
ComponentsReceptor-interacting serine/threonine-protein kinase 3
KeywordsTRANSFERASE / kinase / RIPK3 / RIP3
Function / homology
Function and homology information


RIPK1-mediated regulated necrosis / regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / TRIF-mediated programmed cell death / execution phase of necroptosis / regulation of T cell mediated cytotoxicity / IKK complex recruitment mediated by RIP1 / regulation of activated T cell proliferation / regulation of adaptive immune response / Regulation of necroptotic cell death ...RIPK1-mediated regulated necrosis / regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / TRIF-mediated programmed cell death / execution phase of necroptosis / regulation of T cell mediated cytotoxicity / IKK complex recruitment mediated by RIP1 / regulation of activated T cell proliferation / regulation of adaptive immune response / Regulation of necroptotic cell death / regulation of type II interferon production / programmed necrotic cell death / necroptotic signaling pathway / TRP channels / positive regulation of necroptotic process / regulation of reactive oxygen species metabolic process / T cell homeostasis / activation of protein kinase activity / non-canonical NF-kappaB signal transduction / necroptotic process / lymph node development / positive regulation of intrinsic apoptotic signaling pathway / spleen development / reactive oxygen species metabolic process / thymus development / cellular response to hydrogen peroxide / positive regulation of reactive oxygen species metabolic process / T cell differentiation in thymus / defense response to virus / regulation of apoptotic process / amyloid fibril formation / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / protein-containing complex binding / signal transduction / protein-containing complex / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RHIM domain / RIP homotypic interaction motif / 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, ATP binding site / Protein kinases ATP-binding region signature. ...RHIM domain / RIP homotypic interaction motif / 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, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1FN / Receptor-interacting serine/threonine-protein kinase 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPokross, M.E.
CitationJournal: Acs Med.Chem.Lett. / Year: 2020
Title: Identification of RIPK3 Type II Inhibitors Using High-Throughput Mechanistic Studies in Hit Triage.
Authors: Hart, A.C. / Abell, L. / Guo, J. / Mertzman, M.E. / Padmanabha, R. / Macor, J.E. / Chaudhry, C. / Lu, H. / O'Malley, K. / Shaw, P.J. / Weigelt, C. / Pokross, M. / Kish, K. / Kim, K.S. / ...Authors: Hart, A.C. / Abell, L. / Guo, J. / Mertzman, M.E. / Padmanabha, R. / Macor, J.E. / Chaudhry, C. / Lu, H. / O'Malley, K. / Shaw, P.J. / Weigelt, C. / Pokross, M. / Kish, K. / Kim, K.S. / Cornelius, L. / Douglas, A.E. / Calambur, D. / Zhang, P. / Carpenter, B. / Pitts, W.J.
History
DepositionApr 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor-interacting serine/threonine-protein kinase 3
B: Receptor-interacting serine/threonine-protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3434
Polymers72,4272
Non-polymers9172
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint3 kcal/mol
Surface area22820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.760, 52.750, 103.750
Angle α, β, γ (deg.)90.00, 130.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Receptor-interacting serine/threonine-protein kinase 3 / RIP-like protein kinase 3 / Receptor-interacting protein 3 / mRIP3


Mass: 36213.328 Da / Num. of mol.: 2 / Fragment: UNP residues 1-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ripk3, Rip3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9QZL0, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-1FN / 1-(4-fluorophenyl)-N-[3-fluoro-4-(1H-pyrrolo[2,3-b]pyridin-4-yloxy)phenyl]-2-oxo-1,2-dihydropyridine-3-carboxamide


Mass: 458.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H16F2N4O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.07 Å3/Da / Density % sol: 40.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 18-22% w/v PEG3350, 10-15 mM L-proline

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2014 / Details: ???
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→47.53 Å / Num. obs: 34398 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 46.98 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 19.2
Reflection shellResolution: 2.1→2.35 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 9702 / % possible all: 99.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
BUSTER2.11.5refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→39.26 Å / Cor.coef. Fo:Fc: 0.9555 / Cor.coef. Fo:Fc free: 0.9501 / SU R Cruickshank DPI: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.186 / SU Rfree Blow DPI: 0.145 / SU Rfree Cruickshank DPI: 0.147
RfactorNum. reflection% reflectionSelection details
Rfree0.1984 1807 5.25 %RANDOM
Rwork0.1798 ---
obs0.1808 34396 98.55 %-
Displacement parametersBiso mean: 61.87 Å2
Baniso -1Baniso -2Baniso -3
1-3.8252 Å20 Å20.383 Å2
2---9.8567 Å20 Å2
3---6.0314 Å2
Refine analyzeLuzzati coordinate error obs: 0.317 Å
Refinement stepCycle: LAST / Resolution: 2.1→39.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3994 0 68 202 4264
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094197HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.015754HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1362SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes88HARMONIC2
X-RAY DIFFRACTIONt_gen_planes708HARMONIC5
X-RAY DIFFRACTIONt_it4197HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.57
X-RAY DIFFRACTIONt_other_torsion17.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion516SEMIHARMONIC5
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_contact4720SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.17 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2359 168 6.12 %
Rwork0.2135 2575 -
all0.2148 2743 -
obs--98.55 %
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)
12.37440.65560.30840.8876-0.13412.46370.05630.0193-0.09860.0086-0.1894-0.04770.0115-0.15230.1332-0.11380.0072-0.0179-0.1103-0.0177-0.16993.86856.8243-25.0882
24.73430.1993-0.50941.8344-0.14232.3464-0.0550.0422-0.0340.1436-0.0434-0.4775-0.01340.6980.0985-0.2803-0.034-0.07470.08290.1092-0.172331.46658.0065-15.1864
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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