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- PDB-9gty: RIPK1 in complex with AZ"320 -

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Basic information

Entry
Database: PDB / ID: 9gty
TitleRIPK1 in complex with AZ"320
ComponentsReceptor-interacting serine/threonine-protein kinase 1
KeywordsTRANSFERASE / Kinase / inhibitor
Function / homology
Function and homology information


ripoptosome assembly / positive regulation of miRNA processing / positive regulation of interleukin-6-mediated signaling pathway / ripoptosome assembly involved in necroptotic process / death domain binding / peptidyl-serine autophosphorylation / ripoptosome / Defective RIPK1-mediated regulated necrosis / Microbial modulation of RIPK1-mediated regulated necrosis / TRIF-mediated programmed cell death ...ripoptosome assembly / positive regulation of miRNA processing / positive regulation of interleukin-6-mediated signaling pathway / ripoptosome assembly involved in necroptotic process / death domain binding / peptidyl-serine autophosphorylation / ripoptosome / Defective RIPK1-mediated regulated necrosis / Microbial modulation of RIPK1-mediated regulated necrosis / TRIF-mediated programmed cell death / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TLR3-mediated TICAM1-dependent programmed cell death / TNF signaling / programmed necrotic cell death / Caspase activation via Death Receptors in the presence of ligand / SARS-CoV-1-mediated effects on programmed cell death / positive regulation of macrophage differentiation / T cell apoptotic process / JUN kinase kinase kinase activity / necroptotic signaling pathway / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / death-inducing signaling complex / positive regulation of necroptotic process / RIP-mediated NFkB activation via ZBP1 / negative regulation of necroptotic process / positive regulation of tumor necrosis factor-mediated signaling pathway / death receptor binding / positive regulation of programmed cell death / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of programmed necrotic cell death / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / TRP channels / necroptotic process / response to tumor necrosis factor / positive regulation of execution phase of apoptosis / canonical NF-kappaB signal transduction / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / tumor necrosis factor-mediated signaling pathway / extrinsic apoptotic signaling pathway / signaling adaptor activity / negative regulation of canonical NF-kappaB signal transduction / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of interleukin-8 production / positive regulation of JNK cascade / Regulation of TNFR1 signaling / protein catabolic process / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / cellular response to growth factor stimulus / Regulation of necroptotic cell death / cellular response to hydrogen peroxide / positive regulation of inflammatory response / positive regulation of reactive oxygen species metabolic process / positive regulation of tumor necrosis factor production / Ovarian tumor domain proteases / positive regulation of neuron apoptotic process / positive regulation of protein phosphorylation / cellular response to tumor necrosis factor / protein autophosphorylation / amyloid fibril formation / response to oxidative stress / Potential therapeutics for SARS / positive regulation of canonical NF-kappaB signal transduction / receptor complex / non-specific serine/threonine protein kinase / protein kinase activity / endosome membrane / Ub-specific processing proteases / intracellular signal transduction / positive regulation of apoptotic process / inflammatory response / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / positive regulation of gene expression / negative regulation of apoptotic process / protein-containing complex binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
RIP1, Death domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / : / Death-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site ...RIP1, Death domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / : / Death-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Chem-RCM / Receptor-interacting serine/threonine-protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.145 Å
AuthorsPetersen, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Chem.Biol. / Year: 2025
Title: Discovery and Validation of a Novel Class of Necroptosis Inhibitors Targeting RIPK1.
Authors: Soday, L. / Seripracharat, C. / Gray, J.L. / Luz, A.F.S. / Howard, R.T. / Singh, R. / Burden, T.J. / Bernardini, E. / Mateus-Pinheiro, M. / Petersen, J. / Gunnarsson, A. / Gunnarsson, J. / ...Authors: Soday, L. / Seripracharat, C. / Gray, J.L. / Luz, A.F.S. / Howard, R.T. / Singh, R. / Burden, T.J. / Bernardini, E. / Mateus-Pinheiro, M. / Petersen, J. / Gunnarsson, A. / Gunnarsson, J. / Aagaard, A. / Sjogren, T. / Maslen, S. / Bartlett, E.J. / Iles, A.F. / Smith, D.M. / Scott, J.S. / Skehel, M. / Davis, A.M. / Ressurreicao, A.S. / Moreira, R. / Rodrigues, C.M.P. / Shenoy, A.R. / Tate, E.W.
History
DepositionSep 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor-interacting serine/threonine-protein kinase 1
B: Receptor-interacting serine/threonine-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3207
Polymers71,1922
Non-polymers1,1285
Water1,62190
1
A: Receptor-interacting serine/threonine-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9523
Polymers35,5961
Non-polymers3562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor-interacting serine/threonine-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3684
Polymers35,5961
Non-polymers7723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.698, 93.482, 125.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Receptor-interacting serine/threonine-protein kinase 1 / Cell death protein RIP / Receptor-interacting protein 1 / RIP-1


Mass: 35595.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RIPK1, RIP, RIP1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q13546, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-RCM / (5R)-5-[(7-chloro-1H-indol-3-yl)methyl]-3-methylimidazolidine-2,4-dione


Mass: 277.706 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12ClN3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-A1IKX / 7-[4-[3-(methylsulfonylmethyl)azetidin-1-yl]sulfonylphenyl]quinoline / (2S)-2-[[N-[(4S)-4-azanyl-5-oxidanyl-5-oxidanylidene-pentyl]carbamimidoyl]amino]butanedioic acid


Mass: 416.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N2O4S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 1.97 Å3/Da / Density % sol: 37.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG 4K 21%w/v pH 0, MES 0.1M pH 6.5, NaCl 0.3M pH 0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.145→62.77 Å / Num. obs: 23604 / % possible obs: 74.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.03 / Rrim(I) all: 0.078 / Net I/σ(I): 13.3
Reflection shellResolution: 2.145→2.327 Å / % possible obs: 17.5 % / Redundancy: 7 % / Rmerge(I) obs: 1.303 / Num. measured all: 8225 / Num. unique obs: 1180 / Rpim(I) all: 0.531 / Rrim(I) all: 1.409 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022) PACIOREKrefinement
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.145→62.77 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.896 / SU R Cruickshank DPI: 0.465 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.472 / SU Rfree Blow DPI: 0.29 / SU Rfree Cruickshank DPI: 0.292
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT ELECTRON-CLOUD POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2939 1180 5 %RANDOM
Rwork0.2491 ---
obs0.2513 23604 74.8 %-
Displacement parametersBiso mean: 70.39 Å2
Baniso -1Baniso -2Baniso -3
1-2.3593 Å20 Å20 Å2
2--0.654 Å20 Å2
3----3.0133 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.145→62.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4051 0 74 90 4215
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084222HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.985706HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1481SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes699HARMONIC5
X-RAY DIFFRACTIONt_it4210HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion18.97
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion543SEMIHARMONIC5
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_contact3201SEMIHARMONIC4
LS refinement shellResolution: 2.15→2.25 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3992 -3.81 %
Rwork0.3183 455 -
all0.3211 473 -
obs--11.03 %
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)
12.6895-0.2854-0.53195.71061.97744.13990.2316-0.17250.3378-0.2183-0.04280.2271-0.1599-0.162-0.1887-0.3598-0.01790.0261-0.24540.021-0.341711.09485.677823.1519
23.20791.49-2.3155.71210.06377.4065-0.0279-0.1563-0.35990.4142-0.1379-0.18630.43930.45430.1659-0.3471-0.04610.0184-0.25420.016-0.407526.09865.193752.0125
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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