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- PDB-6oyw: ASK1 kinase domain in complex with Compound 11 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6oyw
TitleASK1 kinase domain in complex with Compound 11
ComponentsMitogen-activated protein kinase kinase kinase 5
KeywordsTRANSFERASE / ASK1 MAP3K5
Function / homology
Function and homology information


cellular response to reactive nitrogen species / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / IRE1-TRAF2-ASK1 complex / protein kinase complex / mitogen-activated protein kinase kinase kinase / programmed necrotic cell death / JUN kinase kinase kinase activity / endothelial cell apoptotic process / positive regulation of p38MAPK cascade / intrinsic apoptotic signaling pathway in response to oxidative stress ...cellular response to reactive nitrogen species / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / IRE1-TRAF2-ASK1 complex / protein kinase complex / mitogen-activated protein kinase kinase kinase / programmed necrotic cell death / JUN kinase kinase kinase activity / endothelial cell apoptotic process / positive regulation of p38MAPK cascade / intrinsic apoptotic signaling pathway in response to oxidative stress / p38MAPK cascade / positive regulation of JUN kinase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / MAP kinase kinase kinase activity / positive regulation of myoblast differentiation / positive regulation of cardiac muscle cell apoptotic process / stress-activated MAPK cascade / positive regulation of vascular associated smooth muscle cell proliferation / JNK cascade / cellular response to amino acid starvation / response to endoplasmic reticulum stress / response to ischemia / positive regulation of JNK cascade / apoptotic signaling pathway / cellular response to hydrogen peroxide / cellular response to tumor necrosis factor / cellular senescence / MAPK cascade / neuron apoptotic process / protein phosphatase binding / Oxidative Stress Induced Senescence / protein kinase activity / positive regulation of apoptotic process / protein domain specific binding / innate immune response / external side of plasma membrane / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / positive regulation of DNA-templated transcription / magnesium ion binding / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
MAP3K, TRAFs-binding domain / MAP3K, PH domain / MAP3K, deoxyribohydrolase domain / MAP3K, HisK-N-like globin domain / MAP3K TRAFs-binding domain / ASK kinase PH domain / HisK-N-like globin domain of the ASK signalosome / Deoxyribohydrolase (DRHyd) domain of the ASK signalosome / Sterile alpha motif/pointed domain superfamily / Phosphorylase Kinase; domain 1 ...MAP3K, TRAFs-binding domain / MAP3K, PH domain / MAP3K, deoxyribohydrolase domain / MAP3K, HisK-N-like globin domain / MAP3K TRAFs-binding domain / ASK kinase PH domain / HisK-N-like globin domain of the ASK signalosome / Deoxyribohydrolase (DRHyd) domain of the ASK signalosome / Sterile alpha motif/pointed domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-NKJ / Mitogen-activated protein kinase kinase kinase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å
AuthorsMarcotte, D.J.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Rational Design and Optimization of a Novel Class of Macrocyclic Apoptosis Signal-Regulating Kinase 1 Inhibitors.
Authors: Himmelbauer, M.K. / Xin, Z. / Jones, J.H. / Enyedy, I. / King, K. / Marcotte, D.J. / Murugan, P. / Santoro, J.C. / Hesson, T. / Spilker, K. / Johnson, J.L. / Luzzio, M.J. / Gilfillan, R. / de Turiso, F.G.
History
DepositionMay 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase 5
B: Mitogen-activated protein kinase kinase kinase 5
C: Mitogen-activated protein kinase kinase kinase 5
D: Mitogen-activated protein kinase kinase kinase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,6819
Polymers132,2594
Non-polymers1,4225
Water4,540252
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C: Mitogen-activated protein kinase kinase kinase 5
hetero molecules

A: Mitogen-activated protein kinase kinase kinase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8525
Polymers66,1292
Non-polymers7233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area1980 Å2
ΔGint-13 kcal/mol
Surface area22160 Å2
MethodPISA
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B: Mitogen-activated protein kinase kinase kinase 5
hetero molecules

D: Mitogen-activated protein kinase kinase kinase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8284
Polymers66,1292
Non-polymers6992
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_644-x+1,y-1/2,-z-1/21
Buried area1770 Å2
ΔGint-8 kcal/mol
Surface area22270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.987, 130.415, 137.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 671 or (resid 672 and (name...
21(chain B and (resid 671 or (resid 672 and (name...
31(chain C and (resid 671 through 712 or (resid 713...
41(chain D and (resid 671 through 679 or (resid 680...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULEULEU(chain A and (resid 671 or (resid 672 and (name...AA67114
12GLUGLUGLUGLU(chain A and (resid 671 or (resid 672 and (name...AA67215
13LEULEULYSLYS(chain A and (resid 671 or (resid 672 and (name...AA671 - 93914 - 282
14LEULEULYSLYS(chain A and (resid 671 or (resid 672 and (name...AA671 - 93914 - 282
15LEULEULYSLYS(chain A and (resid 671 or (resid 672 and (name...AA671 - 93914 - 282
16LEULEULYSLYS(chain A and (resid 671 or (resid 672 and (name...AA671 - 93914 - 282
21LEULEULEULEU(chain B and (resid 671 or (resid 672 and (name...BB67114
22GLUGLUGLUGLU(chain B and (resid 671 or (resid 672 and (name...BB67215
23LEULEUVALVAL(chain B and (resid 671 or (resid 672 and (name...BB671 - 94014 - 283
24LEULEUVALVAL(chain B and (resid 671 or (resid 672 and (name...BB671 - 94014 - 283
25LEULEUVALVAL(chain B and (resid 671 or (resid 672 and (name...BB671 - 94014 - 283
26LEULEUVALVAL(chain B and (resid 671 or (resid 672 and (name...BB671 - 94014 - 283
31LEULEUPROPRO(chain C and (resid 671 through 712 or (resid 713...CC671 - 71214 - 55
32GLUGLUGLNGLN(chain C and (resid 671 through 712 or (resid 713...CC713 - 72056 - 63
33LEULEULYSLYS(chain C and (resid 671 through 712 or (resid 713...CC671 - 93914 - 282
34LEULEULYSLYS(chain C and (resid 671 through 712 or (resid 713...CC671 - 93914 - 282
35LEULEULYSLYS(chain C and (resid 671 through 712 or (resid 713...CC671 - 93914 - 282
36LEULEULYSLYS(chain C and (resid 671 through 712 or (resid 713...CC671 - 93914 - 282
41LEULEUGLUGLU(chain D and (resid 671 through 679 or (resid 680...DD671 - 67914 - 22
42ASNASNASNASN(chain D and (resid 671 through 679 or (resid 680...DD68023
43LEULEULYSLYS(chain D and (resid 671 through 679 or (resid 680...DD671 - 93914 - 282
44LEULEULYSLYS(chain D and (resid 671 through 679 or (resid 680...DD671 - 93914 - 282
45LEULEULYSLYS(chain D and (resid 671 through 679 or (resid 680...DD671 - 93914 - 282
46LEULEULYSLYS(chain D and (resid 671 through 679 or (resid 680...DD671 - 93914 - 282

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Components

#1: Protein
Mitogen-activated protein kinase kinase kinase 5 / Apoptosis signal-regulating kinase 1 / ASK-1 / MAPK/ERK kinase kinase 5 / MEKK 5


Mass: 33064.676 Da / Num. of mol.: 4 / Mutation: T838E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K5, ASK1, MAPKKK5, MEKK5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q99683, mitogen-activated protein kinase kinase kinase
#2: Chemical
ChemComp-NKJ / (19S)-19-methyl-16,17,18,19-tetrahydro-8,4-(azeno)[1,2,4]triazolo[4,3-f][1,6,13]benzoxadiazacyclohexadecin-10(9H)-one


Mass: 349.386 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H19N5O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M BisTRIS pH 5.5, 0.2M MgCl2, 10mM Na cholate and 12% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 42652 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.988 / Rmerge(I) obs: 0.187 / Net I/σ(I): 7.2
Reflection shellResolution: 2.6→2.74 Å / Rmerge(I) obs: 0.747 / Num. unique obs: 6142 / CC1/2: 0.677 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BF2

4bf2


Resolution: 2.603→29.962 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2552 2087 4.9 %
Rwork0.2078 40489 -
obs0.21 42576 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.33 Å2 / Biso mean: 41.6527 Å2 / Biso min: 11.19 Å2
Refinement stepCycle: final / Resolution: 2.603→29.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8008 0 105 252 8365
Biso mean--26.63 36.49 -
Num. residues----1037
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2984X-RAY DIFFRACTION7.52TORSIONAL
12B2984X-RAY DIFFRACTION7.52TORSIONAL
13C2984X-RAY DIFFRACTION7.52TORSIONAL
14D2984X-RAY DIFFRACTION7.52TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6028-2.66330.35351440.300226502794100
2.6633-2.72990.33191410.266426492790100
2.7299-2.80360.30711490.252626582807100
2.8036-2.8860.28151590.249226422801100
2.886-2.97910.27931220.250726582780100
2.9791-3.08550.29591260.240327022828100
3.0855-3.20890.27951440.240826842828100
3.2089-3.35480.29091590.23326522811100
3.3548-3.53140.27241240.217826892813100
3.5314-3.75220.27561210.194627142835100
3.7522-4.04130.23241120.178427312843100
4.0413-4.44680.18941270.163327312858100
4.4468-5.08760.18081380.154727392877100
5.0876-6.39950.26141690.208727292898100
6.3995-29.96410.23221520.1972861301399
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)
13.29952.4293-1.17934.6621-1.78924.05240.5645-0.6415-0.27720.8454-0.4613-0.5145-0.22770.7571-0.13760.4435-0.114-0.130.3448-0.02310.447641.016.585432.9625
21.7137-0.143-0.61162.39160.35733.0303-0.0193-0.0060.01880.1364-0.0043-0.01050.1032-0.18980.03430.2001-0.0364-0.01990.20010.00480.304333.98027.690318.5311
34.94482.2488-1.36775.9888-0.43944.5130.09330.25460.5975-0.2044-0.0560.4451-0.9283-0.5682-0.0680.44930.0832-0.04950.3088-0.09260.365830.961217.976613.1018
42.6346-0.6165-1.81724.2586-1.05633.75810.05230.2256-0.1464-0.3548-0.03440.07550.0365-0.29180.01780.2911-0.0374-0.06730.2846-0.01410.193436.699111.1021-1.0523
58.46351.9973-5.49644.7488-1.33023.6358-0.51320.5377-0.6928-0.7752-0.05940.37210.4668-0.5210.48810.37370.1322-0.0560.5197-0.09180.357226.129912.8505-50.2907
63.458-0.603-0.80094.90652.62894.94030.06180.09980.0313-0.3964-0.47810.24-0.6907-0.06510.42210.32610.06080.00190.2470.00240.239332.356520.6909-45.8383
72.6987-1.64191.41994.2137-1.47164.16720.05420.23450.0689-0.10580.08340.11140.00140.0423-0.10730.2530.02320.07950.2498-0.04550.235540.683218.554-41.0597
81.1858-0.6097-0.1512.54810.75636.3479-0.0198-0.06930.18710.170.1838-0.162-0.30940.5105-0.13330.20670.0112-0.01430.3243-0.04260.286647.884721.2356-25.2051
97.6947-2.5652-3.91962.74952.44433.9392-0.5413-0.2393-0.52280.27930.342-0.81420.62511.7899-0.01670.31190.23920.07130.936-0.23980.331461.492314.5446-26.5787
100.52730.47241.08161.48941.35322.3645-0.10180.08860.1177-0.2867-0.23630.626-0.2579-0.2199-0.19020.70950.1188-0.58020.3771-0.28871.0541-8.67618.6586-53.5928
112.4205-1.9144-0.12294.43783.05213.9267-0.3860.0510.1916-1.0954-0.16641.1411-0.7109-0.1340.33230.3241-0.0138-0.15720.22630.00650.611-1.916420.1377-49.3859
122.5807-0.8276-1.77591.7276-0.88252.6755-0.07940.06580.8111-0.62810.01470.3491-0.9098-0.646-0.11580.71110.1321-0.23380.24480.01960.8785-0.891527.2987-49.3114
133.6956-1.4960.58293.6527-1.64124.0053-0.340.1371.0708-0.61190.00270.2985-0.62180.22210.17790.5896-0.0139-0.13960.23810.03850.58927.385425.4424-49.1026
142.43711.12570.33344.09051.07713.11440.0633-0.16430.01480.2916-0.13260.47630.324-0.03960.01230.24670.00880.05130.1803-0.02670.30968.343715.4638-33.504
154.0862-1.212-2.4917.8649-1.42518.44230.41790.41420.23730.1820.17610.459-1.0235-0.1112-0.59040.32710.0463-0.07820.2956-0.00610.3869.749132.7154-30.9915
161.7245-0.47820.39194.35790.8263.3232-0.0659-0.51930.38111.1036-0.06680.8697-0.1126-0.26360.06380.4893-0.02370.13580.307-0.07470.47797.159926.9766-21.2755
176.71160.1753-1.866.2559-2.7896.8621-0.0604-0.27480.03531.42090.2258-0.45290.47440.034-0.06770.48210.0073-0.0730.2671-0.0110.247316.648617.463-19.2308
184.20453.96724.41298.5438-0.18758.5849-0.42040.4568-0.1556-1.65970.063-0.84750.06170.60910.34940.91020.04950.24630.4917-0.0860.532438.165856.0263-39.1434
195.044-1.16491.49054.4918-0.53683.20650.01610.408-0.2678-0.9813-0.0345-0.5360.16570.64220.06370.4271-0.0710.06840.2788-0.02660.281633.323652.9108-32.0838
202.12531.38341.62534.6851.77454.7687-0.00330.1201-0.1944-0.47550.0647-0.0001-0.0140.0922-0.06330.2511-0.0360.02070.23880.03960.311930.693754.5388-23.072
211.21480.81650.97823.2830.51622.29540.1114-0.2448-0.09880.4009-0.02790.412-0.0329-0.0805-0.07820.1971-0.04010.0630.28580.06410.308430.047159.4672-12.2034
226.56076.25-3.01377.3292-0.94085.0281-0.4905-0.0735-0.47780.0046-0.058-0.03591.2205-0.15740.43020.5037-0.05510.05060.2277-0.04070.443928.057444.6793-14.0133
236.4185-0.09690.37316.4636-0.52064.52710.1296-0.3306-0.4510.1527-0.1258-0.17960.74310.43970.07750.3310.01160.01160.28770.05150.260334.654448.7241-4.5351
245.4602-0.031-0.57282.1122-1.89727.9352-0.03230.1341-0.76640.42790.0296-0.92270.83331.07360.04970.45620.1133-0.1180.51540.03830.819945.548344.7528-3.2588
255.2215-1.42240.41417.24551.8145.9893-0.0836-0.3806-0.18151.57150.2486-0.62320.38090.0482-0.0990.5903-0.1081-0.08820.47050.08460.286638.996857.67694.0806
265.9204-0.04671.17474.171-1.07095.64180.0685-0.7078-0.03410.819-0.00530.98320.3293-0.629-0.01810.427-0.02160.18830.4830.03160.359727.138456.69042.4168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 671 through 703 )A671 - 703
2X-RAY DIFFRACTION2chain 'A' and (resid 704 through 817 )A704 - 817
3X-RAY DIFFRACTION3chain 'A' and (resid 818 through 840 )A818 - 840
4X-RAY DIFFRACTION4chain 'A' and (resid 841 through 939 )A841 - 939
5X-RAY DIFFRACTION5chain 'B' and (resid 671 through 684 )B671 - 684
6X-RAY DIFFRACTION6chain 'B' and (resid 685 through 718 )B685 - 718
7X-RAY DIFFRACTION7chain 'B' and (resid 719 through 776 )B719 - 776
8X-RAY DIFFRACTION8chain 'B' and (resid 777 through 928 )B777 - 928
9X-RAY DIFFRACTION9chain 'B' and (resid 929 through 940 )B929 - 940
10X-RAY DIFFRACTION10chain 'C' and (resid 671 through 684 )C671 - 684
11X-RAY DIFFRACTION11chain 'C' and (resid 685 through 703 )C685 - 703
12X-RAY DIFFRACTION12chain 'C' and (resid 704 through 719 )C704 - 719
13X-RAY DIFFRACTION13chain 'C' and (resid 720 through 755 )C720 - 755
14X-RAY DIFFRACTION14chain 'C' and (resid 756 through 825 )C756 - 825
15X-RAY DIFFRACTION15chain 'C' and (resid 826 through 847 )C826 - 847
16X-RAY DIFFRACTION16chain 'C' and (resid 848 through 897 )C848 - 897
17X-RAY DIFFRACTION17chain 'C' and (resid 898 through 939 )C898 - 939
18X-RAY DIFFRACTION18chain 'D' and (resid 671 through 684 )D671 - 684
19X-RAY DIFFRACTION19chain 'D' and (resid 685 through 715 )D685 - 715
20X-RAY DIFFRACTION20chain 'D' and (resid 716 through 776 )D716 - 776
21X-RAY DIFFRACTION21chain 'D' and (resid 777 through 820 )D777 - 820
22X-RAY DIFFRACTION22chain 'D' and (resid 821 through 842 )D821 - 842
23X-RAY DIFFRACTION23chain 'D' and (resid 843 through 876 )D843 - 876
24X-RAY DIFFRACTION24chain 'D' and (resid 877 through 897 )D877 - 897
25X-RAY DIFFRACTION25chain 'D' and (resid 898 through 919 )D898 - 919
26X-RAY DIFFRACTION26chain 'D' and (resid 920 through 939 )D920 - 939

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