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- PDB-9gtg: RIPK1 in complex with AZ"902 -

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Basic information

Entry
Database: PDB / ID: 9gtg
TitleRIPK1 in complex with AZ"902
ComponentsReceptor-interacting serine/threonine-protein kinase 1
KeywordsTRANSFERASE / RIPK1 / 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 / positive regulation of macrophage differentiation / SARS-CoV-1-mediated effects on programmed cell death / 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 / extrinsic apoptotic signaling pathway / TICAM1, RIP1-mediated IKK complex recruitment / signaling adaptor activity / IKK complex recruitment mediated by RIP1 / negative regulation of canonical NF-kappaB signal transduction / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / tumor necrosis factor-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of interleukin-8 production / positive regulation of JNK cascade / Regulation of necroptotic cell death / 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 / cellular response to hydrogen peroxide / positive regulation of protein phosphorylation / Ovarian tumor domain proteases / positive regulation of inflammatory response / positive regulation of reactive oxygen species metabolic process / positive regulation of tumor necrosis factor production / cellular response to tumor necrosis factor / positive regulation of neuron apoptotic process / protein autophosphorylation / response to oxidative stress / amyloid fibril formation / Potential therapeutics for SARS / endosome membrane / receptor complex / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / inflammatory response / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / apoptotic process / 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: 2.25 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 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Jul 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)72,5946
Polymers71,1922
Non-polymers1,4024
Water25214
1
A: Receptor-interacting serine/threonine-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2973
Polymers35,5961
Non-polymers7012
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)36,2973
Polymers35,5961
Non-polymers7012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.084, 96.491, 129.002
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: isolated from a natural source / Formula: C13H12ClN3O2
#3: Chemical ChemComp-A1IPG / ~{N}-[[(3~{S})-1-ethanoylpyrrolidin-3-yl]methyl]-~{N}-methyl-4-quinolin-7-yl-benzenesulfonamide


Mass: 423.528 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H25N3O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG4000, 0.3 M NaCl, 0.1 M MES pH 6.5.

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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 200K / 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: 2.25→77.27 Å / Num. obs: 24404 / % possible obs: 85.6 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.046 / Rrim(I) all: 0.119 / Net I/σ(I): 9
Reflection shellResolution: 2.255→2.395 Å / % possible obs: 26.4 % / Redundancy: 7 % / Rmerge(I) obs: 1.459 / Num. measured all: 8545 / Num. unique obs: 1220 / Rpim(I) all: 0.591 / Rrim(I) all: 1.576 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→77.27 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.634 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.428 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29485 1161 4.8 %RANDOM
Rwork0.21725 ---
obs0.22118 23243 85.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.063 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0 Å2
2---0.1 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.25→77.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4113 0 98 14 4225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124302
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163993
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.6685803
X-RAY DIFFRACTIONr_angle_other_deg0.4751.5569311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4355511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.5851018
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98910791
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024743
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02783
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.5057.1142065
X-RAY DIFFRACTIONr_mcbond_other6.5037.1142065
X-RAY DIFFRACTIONr_mcangle_it9.17710.6482569
X-RAY DIFFRACTIONr_mcangle_other9.17610.6482570
X-RAY DIFFRACTIONr_scbond_it6.6477.462237
X-RAY DIFFRACTIONr_scbond_other6.5967.4662184
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.55210.9613156
X-RAY DIFFRACTIONr_long_range_B_refined12.29593.8534756
X-RAY DIFFRACTIONr_long_range_B_other12.29294.024680
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.255→2.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 8 -
Rwork0.406 159 -
obs--8.18 %

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