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- PDB-9ix3: Crystal structure of the mouse RIP3 kinase domain in complexed wi... -

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Basic information

Entry
Database: PDB / ID: 9ix3
TitleCrystal structure of the mouse RIP3 kinase domain in complexed with compound 18
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
: / Receptor-interacting serine/threonine-protein kinase 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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)73,4524
Polymers72,4272
Non-polymers1,0252
Water1,17165
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)144.200, 54.161, 104.034
Angle α, β, γ (deg.)90.00, 130.99, 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-A1EAA / ~{N}-[4-[2-(cyclopropylcarbonylamino)pyridin-4-yl]oxy-2,3-dimethyl-phenyl]-1-(4-fluorophenyl)-2-oxidanylidene-pyridine-3-carboxamide / Ripk3-IN-1


Mass: 512.532 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H25FN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4 / Details: 10% PEG1500, 50 mM BICINE, 17.1% PEG300, pH 8.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.07→78.53 Å / Num. obs: 37230 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.042 / Rrim(I) all: 0.108 / Χ2: 0.89 / Net I/σ(I): 9 / Num. measured all: 244097
Reflection shellResolution: 2.07→2.12 Å / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 1.094 / Num. measured all: 18042 / Num. unique obs: 2718 / CC1/2: 0.834 / Rpim(I) all: 0.455 / Rrim(I) all: 1.187 / Χ2: 0.89 / Net I/σ(I) obs: 1.7

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Processing

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

4m66


Resolution: 2.07→54.42 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2604 1696 4.56 %
Rwork0.2282 --
obs0.2296 37166 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→54.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3901 0 76 65 4042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034079
X-RAY DIFFRACTIONf_angle_d0.5815560
X-RAY DIFFRACTIONf_dihedral_angle_d12.6311510
X-RAY DIFFRACTIONf_chiral_restr0.042624
X-RAY DIFFRACTIONf_plane_restr0.005709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.130.37321250.32172941X-RAY DIFFRACTION100
2.13-2.20.34771460.30122920X-RAY DIFFRACTION100
2.2-2.280.37491340.28742921X-RAY DIFFRACTION100
2.28-2.370.32481350.27942945X-RAY DIFFRACTION100
2.37-2.480.27041090.25372985X-RAY DIFFRACTION100
2.48-2.610.27811220.25532949X-RAY DIFFRACTION100
2.61-2.770.28891390.24872960X-RAY DIFFRACTION100
2.77-2.990.27141790.24392903X-RAY DIFFRACTION100
2.99-3.290.2671810.23832918X-RAY DIFFRACTION100
3.29-3.760.27291330.21672991X-RAY DIFFRACTION100
3.76-4.740.2031780.19172942X-RAY DIFFRACTION100
4.74-54.420.23271150.20083095X-RAY DIFFRACTION100

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