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- PDB-9lfu: Crystal structure of human RIP3 kinase domain complexed with LK01003 -

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Basic information

Entry
Database: PDB / ID: 9lfu
TitleCrystal structure of human RIP3 kinase domain complexed with LK01003
ComponentsReceptor-interacting serine/threonine-protein kinase 3
KeywordsTRANSFERASE / Human RIP3 kinase domain / inhibitor / complex
Function / homology
Function and homology information


regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / execution phase of necroptosis / regulation of T cell mediated cytotoxicity / regulation of adaptive immune response / regulation of activated T cell proliferation / TRIF-mediated programmed cell death / Microbial modulation of RIPK1-mediated regulated necrosis / TLR3-mediated TICAM1-dependent programmed cell death / regulation of type II interferon production ...regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / execution phase of necroptosis / regulation of T cell mediated cytotoxicity / regulation of adaptive immune response / regulation of activated T cell proliferation / TRIF-mediated programmed cell death / Microbial modulation of RIPK1-mediated regulated necrosis / TLR3-mediated TICAM1-dependent programmed cell death / regulation of type II interferon production / programmed necrotic cell death / SARS-CoV-1-mediated effects on programmed cell death / necroptotic signaling pathway / activation of protein kinase activity / positive regulation of necroptotic process / RIP-mediated NFkB activation via ZBP1 / non-canonical NF-kappaB signal transduction / RIPK1-mediated regulated necrosis / TRP channels / T cell homeostasis / necroptotic process / lymph node development / positive regulation of intrinsic apoptotic signaling pathway / spleen development / reactive oxygen species metabolic process / TICAM1, RIP1-mediated IKK complex recruitment / thymus development / IKK complex recruitment mediated by RIP1 / apoptotic signaling pathway / protein modification process / Regulation of necroptotic cell death / cellular response to hydrogen peroxide / positive regulation of reactive oxygen species metabolic process / positive regulation of NF-kappaB transcription factor activity / SARS-CoV-1 activates/modulates innate immune responses / T cell differentiation in thymus / regulation of apoptotic process / defense response to virus / amyloid fibril formation / eukaryotic translation initiation factor 2alpha kinase activity / transcription coactivator 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 / 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 / : / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsXie, H. / Su, H.X. / Li, M.J. / Xu, Y.C.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
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
DepositionJan 9, 2025Deposition 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)78,1374
Polymers77,2342
Non-polymers9032
Water00
1
A: Receptor-interacting serine/threonine-protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0682
Polymers38,6171
Non-polymers4521
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor-interacting serine/threonine-protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0682
Polymers38,6171
Non-polymers4521
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.203, 129.203, 79.429
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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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


Mass: 38616.758 Da / Num. of mol.: 2 / Mutation: C3S, C110A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RIPK3, RIP3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Y572, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1D97 / 2-cyclopentyl-~{N}-(6-propan-2-ylsulfonylquinolin-4-yl)-1,3-benzothiazol-5-amine


Mass: 451.604 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25N3O2S2
Has ligand of interestN
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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M magnesium chloride, 22.5% (w/v) polyethylene glycol 3350, 0.1 M Tris, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.93→111.89 Å / Num. obs: 16341 / % possible obs: 100 % / Redundancy: 20.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.046 / Rrim(I) all: 0.206 / Χ2: 0.94 / Net I/σ(I): 11.4 / Num. measured all: 333886
Reflection shellResolution: 2.93→3.09 Å / % possible obs: 100 % / Redundancy: 20.9 % / Rmerge(I) obs: 4.233 / Num. measured all: 49225 / Num. unique obs: 2356 / CC1/2: 0.504 / Rpim(I) all: 0.946 / Rrim(I) all: 4.338 / Χ2: 0.88 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.93→55.95 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3186 810 4.98 %
Rwork0.2584 --
obs0.2613 16250 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.93→55.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4478 0 62 0 4540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044647
X-RAY DIFFRACTIONf_angle_d0.7956315
X-RAY DIFFRACTIONf_dihedral_angle_d12.4091776
X-RAY DIFFRACTIONf_chiral_restr0.047703
X-RAY DIFFRACTIONf_plane_restr0.005810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.93-3.120.42521270.35782528X-RAY DIFFRACTION99
3.12-3.360.38631350.32572559X-RAY DIFFRACTION100
3.36-3.690.3571210.29092593X-RAY DIFFRACTION100
3.69-4.230.3251370.25862579X-RAY DIFFRACTION100
4.23-5.330.30211730.25162538X-RAY DIFFRACTION100
5.33-55.950.29211170.23032643X-RAY DIFFRACTION99

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