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- PDB-9q32: RIP1 kinase domain in complex with compound 1 -

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Basic information

Entry
Database: PDB / ID: 9q32
TitleRIP1 kinase domain in complex with compound 1
ComponentsReceptor-interacting serine/threonine-protein kinase 1
KeywordsTransferase/Inhibitor / kinase / inhibitor / TRANSFERASE / Transferase-Inhibitor complex
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 / JUN kinase kinase kinase activity / T cell apoptotic process / necroptotic signaling pathway / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / death-inducing signaling complex / RIP-mediated NFkB activation via ZBP1 / positive regulation of necroptotic process / 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 programmed necrotic cell death / positive regulation of extrinsic apoptotic signaling pathway / 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 / signaling adaptor activity / negative regulation of canonical NF-kappaB signal transduction / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / 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 protein phosphorylation / positive regulation of reactive oxygen species metabolic process / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / cellular response to tumor necrosis factor / Ovarian tumor domain proteases / positive regulation of neuron apoptotic process / protein autophosphorylation / response to oxidative stress / amyloid fibril formation / Potential therapeutics for SARS / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / receptor complex / 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 / cytoplasm / cytosol
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
: / Receptor-interacting serine/threonine-protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsLupardus, P. / Fong, R. / Demircioglu, F.E.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery of Clinical Candidate GDC-8264, a Novel, Potent and Selective RIP1 Inhibitor for Amelioration of Tissue Damage and the Treatment of Inflammatory Diseases.
Authors: Patel, S. / Chen, H. / Varfolomeev, E. / Kwon, Y. / Ramaswamy, S. / Kohli, P.B. / Quinn, J.G. / Webster, J.D. / Mao, J. / Chen, Y. / Fong, R. / Demircioglu, F.E. / Lupardus, P. / Stivala, C. ...Authors: Patel, S. / Chen, H. / Varfolomeev, E. / Kwon, Y. / Ramaswamy, S. / Kohli, P.B. / Quinn, J.G. / Webster, J.D. / Mao, J. / Chen, Y. / Fong, R. / Demircioglu, F.E. / Lupardus, P. / Stivala, C. / Hamilton, G.L. / Siu, M. / Sujatha-Bhaskar, S. / Mohanan, V. / Adedeji, A.O. / Santagostino, S.F. / Maher, J. / McKenzie, B. / Rothenberg, M.E. / Johnson, A. / Vucic, D.
History
DepositionAug 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 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
C: Receptor-interacting serine/threonine-protein kinase 1
D: Receptor-interacting serine/threonine-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,5928
Polymers134,4514
Non-polymers1,1414
Water3,135174
1
A: Receptor-interacting serine/threonine-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8982
Polymers33,6131
Non-polymers2851
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)33,8982
Polymers33,6131
Non-polymers2851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Receptor-interacting serine/threonine-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8982
Polymers33,6131
Non-polymers2851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Receptor-interacting serine/threonine-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8982
Polymers33,6131
Non-polymers2851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.814, 139.385, 94.074
Angle α, β, γ (deg.)90.00, 94.72, 90.00
Int Tables number4
Space group name H-MP1211

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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: 33612.855 Da / Num. of mol.: 4
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-A1CNV / methyl 1-[(2,6-dichlorophenyl)methyl]-1H-pyrazole-3-carboxylate


Mass: 285.126 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H10Cl2N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M Na Bromide; 0.1M Bis Tris Propane, pH 6.5; 20% PEG 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→35 Å / Num. obs: 40127 / % possible obs: 99.4 % / Redundancy: 4 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.081 / Rrim(I) all: 0.168 / Χ2: 0.957 / Net I/σ(I): 7.4 / Num. measured all: 162133
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.49-2.532.70.6718800.4370.780.4740.8240.47895.7
2.53-2.582.90.67319350.5050.8190.4550.8160.50796.7
2.58-2.633.10.66920260.5680.8510.4290.7980.597.8
2.63-2.683.40.71319640.5650.850.4350.8380.54898.7
2.68-2.743.80.67719630.6580.8910.3910.7840.54399.5
2.74-2.840.63720670.7220.9160.3560.7310.5699.9
2.8-2.874.20.55419690.7810.9370.3050.6330.56299.9
2.87-2.954.30.49420230.8430.9560.2680.5630.541100
2.95-3.044.30.38720280.8910.9710.210.4410.597100
3.04-3.144.30.32519960.920.9790.1750.370.653100
3.14-3.254.40.2620480.9480.9870.1380.2950.756100
3.25-3.384.40.19419990.970.9920.1030.220.85100
3.38-3.534.40.1620020.980.9950.0840.1810.98100
3.53-3.724.50.13120430.9810.9950.070.1491.148100
3.72-3.954.40.11319870.9860.9960.060.1281.28699.9
3.95-4.264.40.09220270.990.9980.0480.1041.422100
4.26-4.684.40.07320280.9930.9980.0390.0831.481100
4.68-5.364.40.06820400.9940.9990.0360.0771.522100
5.36-6.744.30.0720430.9940.9990.0380.081.584100
6.74-354.10.05720590.9960.9990.0320.0661.71499.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→34.85 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 1262 3.16 %
Rwork0.1876 --
obs0.1891 39915 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.49→34.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8185 0 72 174 8431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028423
X-RAY DIFFRACTIONf_angle_d0.51611356
X-RAY DIFFRACTIONf_dihedral_angle_d4.9421099
X-RAY DIFFRACTIONf_chiral_restr0.0421261
X-RAY DIFFRACTIONf_plane_restr0.0041431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.590.29391300.27064112X-RAY DIFFRACTION96
2.59-2.710.29461370.23694225X-RAY DIFFRACTION98
2.71-2.850.26591410.21934322X-RAY DIFFRACTION100
2.85-3.030.29641170.22334337X-RAY DIFFRACTION100
3.03-3.260.29711380.21074322X-RAY DIFFRACTION100
3.26-3.590.2211340.17654328X-RAY DIFFRACTION100
3.59-4.110.20791620.16124314X-RAY DIFFRACTION100
4.11-5.170.19821480.15624321X-RAY DIFFRACTION100
5.17-34.850.21581550.18194372X-RAY DIFFRACTION100
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)
12.3707-0.4556-0.37381.6996-0.10163.764-0.19920.3605-0.1572-0.4570.02170.32410.1797-0.45230.21130.5032-0.08950.01870.3706-0.10920.3736-17.553955.137898.9496
20.42530.4011-0.57664.3503-1.54561.26410.14090.13330.6760.5481-0.18060.47660.1974-0.3178-0.01360.246-0.04860.04250.268-0.05220.3277-13.049570.451108.3
32.2860.490.08923.5943-0.39832.8652-0.025-0.012-0.18140.7983-0.13610.61310.338-0.22290.03450.4558-0.13580.14050.3193-0.06510.351-18.915956.3536114.9054
40.85960.5428-0.94611.08240.65653.53160.0259-0.21090.04260.30880.0182-0.0870.19640.0353-0.10540.4534-0.0314-0.06380.40710.07920.39876.586542.980970.7157
52.6828-0.6233-0.94952.0596-0.04293.208-0.0785-0.0972-0.03830.3197-0.0206-0.6028-0.29390.45640.03780.3388-0.0295-0.22690.2822-0.03960.360817.091452.35662.6987
60.0416-0.06390.06972.6656-1.00091.85220.05910.0571-0.04050.18770.0889-0.0752-0.051-0.0282-0.12790.1823-0.0133-0.00510.27490.01110.337310.23751.805649.3484
72.5194-1.3802-0.30792.6212-0.672.04670.07540.11320.0966-0.6793-0.1561-0.64050.26420.28730.03490.28970.03020.12520.3552-0.0210.377618.603849.189437.3915
80.40380.83590.33842.87820.94150.5781-0.63730.4138-0.378-0.74320.15420.1008-0.4642-0.30160.33331.1878-0.1774-0.01330.92060.00370.6592-15.07414.767725.8202
91.95660.2691-0.6491.91791.78223.1452-1.06090.5397-0.3661-0.67150.0550.63020.5375-0.67620.21890.8962-0.1905-0.31580.6605-0.00950.5588-22.509712.997333.4552
100.70510.61870.21093.80341.50083.3992-0.40830.74690.3097-1.0120.1641-0.39120.12290.74190.11450.559-0.12480.02740.44150.01620.2974-0.938722.7443.0133
112.47580.1474-0.06141.25070.40773.256-0.41170.28980.0829-0.90860.18040.5091-0.11640.02770.21430.3864-0.0162-0.10730.24630.00370.3359-14.458619.168946.2577
121.24720.66010.63611.24610.78420.6031-0.46370.1753-0.2657-0.41070.26620.0530.0875-0.17310.11220.3144-0.00170.03680.239-0.02670.2491-14.60924.687655.7921
133.03330.9107-0.52244.5016-0.41013.01240.1474-0.16290.11630.5495-0.1859-0.0646-0.26870.13450.16860.2973-0.0069-0.01590.276-0.02580.1916-6.594715.131861.5184
142.19932.9816-1.15294.6359-2.22681.35920.1193-0.39740.55660.5135-0.19580.5232-0.9105-0.32050.0940.58470.0797-0.05880.3639-0.15590.6098-13.861432.123758.6252
151.9993-0.27540.36851.199-0.39292.67530.1305-0.55770.05640.35350.2166-0.34860.3653-0.0915-0.28670.738-0.1517-0.01710.64660.00970.4835-3.975931.1483116.0207
161.3283-0.51691.28441.3127-0.18522.1935-0.0059-0.23170.08810.3107-0.128-0.2995-0.35850.27090.03610.568-0.08850.00890.4536-0.02480.3195-1.56632.0802108.8031
171.9233-0.47730.66862.03010.23733.29770.0034-0.32060.02310.3838-0.11120.2340.3512-0.37560.02320.4438-0.06520.10910.3421-0.01830.2783-10.38924.1432105.1021
180.34340.3326-0.04622.44040.91492.07930.0459-0.1084-0.03310.3243-0.0448-0.14740.02470.15860.00210.1914-0.014-0.01030.311-0.01430.2718-5.02322.750791.0885
192.1296-0.7617-0.47132.89080.55061.6242-0.11530.2359-0.0511-0.12-0.02440.4812-0.1188-0.32260.13180.2110.0099-0.01460.3511-0.03060.2565-15.224625.315378.8109
201.3698-0.6142-0.60063.4568-0.0461.9263-0.08620.57820.2743-0.3456-0.00030.2199-0.15030.0090.04360.6888-0.1951-0.04410.6194-0.02550.3741-11.366461.43582.8751
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 93 through 168 )
2X-RAY DIFFRACTION2chain 'B' and (resid 169 through 206 )
3X-RAY DIFFRACTION3chain 'B' and (resid 207 through 294 )
4X-RAY DIFFRACTION4chain 'C' and (resid 6 through 83 )
5X-RAY DIFFRACTION5chain 'C' and (resid 84 through 111 )
6X-RAY DIFFRACTION6chain 'C' and (resid 112 through 242 )
7X-RAY DIFFRACTION7chain 'C' and (resid 243 through 293 )
8X-RAY DIFFRACTION8chain 'D' and (resid 8 through 55 )
9X-RAY DIFFRACTION9chain 'D' and (resid 56 through 92 )
10X-RAY DIFFRACTION10chain 'D' and (resid 93 through 111 )
11X-RAY DIFFRACTION11chain 'D' and (resid 112 through 167 )
12X-RAY DIFFRACTION12chain 'D' and (resid 168 through 206 )
13X-RAY DIFFRACTION13chain 'D' and (resid 207 through 277 )
14X-RAY DIFFRACTION14chain 'D' and (resid 278 through 294 )
15X-RAY DIFFRACTION15chain 'A' and (resid 6 through 31 )
16X-RAY DIFFRACTION16chain 'A' and (resid 32 through 77 )
17X-RAY DIFFRACTION17chain 'A' and (resid 78 through 111 )
18X-RAY DIFFRACTION18chain 'A' and (resid 112 through 242 )
19X-RAY DIFFRACTION19chain 'A' and (resid 243 through 293 )
20X-RAY DIFFRACTION20chain 'B' and (resid 8 through 92 )

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