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- PDB-9ix2: Crystal structure of the mouse RIP3 kinase domain in complexed wi... -

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Basic information

Entry
Database: PDB / ID: 9ix2
TitleCrystal structure of the mouse RIP3 kinase domain in complexed with TAK-632
ComponentsReceptor-interacting serine/threonine-protein kinase 3
KeywordsTRANSFERASE / Mouse RIP3 kinase domain / inhibitor / complex
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 / Regulation of necroptotic cell death / IKK complex recruitment mediated by RIP1 / regulation of adaptive immune response / regulation of activated T cell proliferation ...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 / Regulation of necroptotic cell death / IKK complex recruitment mediated by RIP1 / regulation of adaptive immune response / regulation of activated T cell proliferation / regulation of type II interferon production / programmed necrotic cell death / necroptotic signaling pathway / TRP channels / activation of protein kinase activity / positive regulation of necroptotic process / non-canonical NF-kappaB signal transduction / regulation of reactive oxygen species metabolic process / T cell homeostasis / 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 / regulation of apoptotic process / defense response to virus / amyloid fibril formation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / protein-containing complex binding / protein-containing complex / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RHIM domain / RIP homotypic interaction motif / : / 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. ...RHIM domain / RIP homotypic interaction motif / : / 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
Similarity search - Domain/homology
Chem-1SU / Receptor-interacting serine/threonine-protein kinase 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsXie, H. / Su, H.X. / Li, M.J. / Xu, Y.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Structure-based design of potent and selective inhibitors targeting RIPK3 for eliminating on-target toxicity in vitro.
Authors: Su, H. / Chen, G. / Xie, H. / Li, W. / Xiong, M. / He, J. / Hu, H. / Zhao, W. / Shao, Q. / Li, M. / Zhao, Q. / Xu, Y.
History
DepositionJul 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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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)72,9813
Polymers72,4272
Non-polymers5551
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.771, 54.870, 102.724
Angle α, β, γ (deg.)90.00, 130.78, 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 / RIP-3 / mRIP3


Mass: 36213.328 Da / Num. of mol.: 2
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-1SU / N-{7-cyano-6-[4-fluoro-3-({[3-(trifluoromethyl)phenyl]acetyl}amino)phenoxy]-1,3-benzothiazol-2-yl}cyclopropanecarboxamide


Mass: 554.515 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C27H18F4N4O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 43.12 %
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: SSRF / Beamline: BL02U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.39→77.79 Å / Num. obs: 24180 / % possible obs: 98.3 % / Redundancy: 3.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.051 / Rrim(I) all: 0.102 / Χ2: 0.93 / Net I/σ(I): 9.9 / Num. measured all: 94731
Reflection shellResolution: 2.39→2.52 Å / % possible obs: 97.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.634 / Num. measured all: 14175 / Num. unique obs: 3470 / CC1/2: 0.823 / Rpim(I) all: 0.358 / Rrim(I) all: 0.73 / Χ2: 0.86 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M66

4m66


Resolution: 2.39→38.89 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2761 1157 4.79 %
Rwork0.2277 --
obs0.23 24151 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→38.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3833 0 39 10 3882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053964
X-RAY DIFFRACTIONf_angle_d0.9315430
X-RAY DIFFRACTIONf_dihedral_angle_d10.66578
X-RAY DIFFRACTIONf_chiral_restr0.054640
X-RAY DIFFRACTIONf_plane_restr0.007694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.50.39391490.30612812X-RAY DIFFRACTION97
2.5-2.630.35431570.28982827X-RAY DIFFRACTION97
2.63-2.80.31671510.26262821X-RAY DIFFRACTION98
2.8-3.020.31661450.24432858X-RAY DIFFRACTION98
3.02-3.320.31941270.25522893X-RAY DIFFRACTION98
3.32-3.80.25831460.22932889X-RAY DIFFRACTION98
3.8-4.780.21691620.1972892X-RAY DIFFRACTION99
4.79-38.890.27011200.20613002X-RAY DIFFRACTION98

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