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- PDB-6u09: Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking -

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Basic information

Entry
Database: PDB / ID: 6u09
TitleDiscovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking
ComponentsEukaryotic translation initiation factor 4E
KeywordsTRANSLATION/INHIBITOR / cap-binding site / anti-neoplastic / inhibitor / translation initiation blocking / TRANSLATION-INHIBITOR complex
Function / homology
Function and homology information


Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Deadenylation of mRNA / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ISG15 antiviral mechanism / mTORC1-mediated signalling / L13a-mediated translational silencing of Ceruloplasmin expression ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Deadenylation of mRNA / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ISG15 antiviral mechanism / mTORC1-mediated signalling / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / eukaryotic initiation factor 4G binding / regulation of translation at postsynapse, modulating synaptic transmission / chromatoid body / eukaryotic translation initiation factor 4F complex / mRNA cap binding / RNA 7-methylguanosine cap binding / RISC complex / nuclear export / postsynaptic cytosol / stem cell population maintenance / behavioral fear response / negative regulation of neuron differentiation / mRNA export from nucleus / translation initiation factor activity / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / translational initiation / P-body / neuron differentiation / cytoplasmic stress granule / G1/S transition of mitotic cell cycle / regulation of translation / DNA-binding transcription factor binding / postsynapse / negative regulation of translation / nuclear body / nuclear speck / translation / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / nucleus / cytosol / cytoplasm
Similarity search - Function
RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. / Translation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EI9 / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsWan, X.B. / Shoichet, B.K. / Taunton, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R35 GM122481 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking.
Authors: Wan, X. / Yang, T. / Cuesta, A. / Pang, X. / Balius, T.E. / Irwin, J.J. / Shoichet, B.K. / Taunton, J.
History
DepositionAug 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E
B: Eukaryotic translation initiation factor 4E
C: Eukaryotic translation initiation factor 4E
D: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4748
Polymers88,5804
Non-polymers1,8944
Water4,378243
1
A: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6192
Polymers22,1451
Non-polymers4731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6192
Polymers22,1451
Non-polymers4731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6192
Polymers22,1451
Non-polymers4731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6192
Polymers22,1451
Non-polymers4731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.100, 38.240, 147.790
Angle α, β, γ (deg.)95.500, 87.280, 101.850
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Eukaryotic translation initiation factor 4E / mRNA cap-binding protein / eIF-4F 25 kDa subunit


Mass: 22145.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: covalent lysine inhibitor / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Eif4e / Production host: Escherichia coli (E. coli) / References: UniProt: P63073
#2: Chemical
ChemComp-EI9 / 3-{(1-oxo-1,2-dihydroisoquinolin-7-yl)[(pyridin-4-yl)methyl]sulfamoyl}benzene-1-sulfonyl fluoride


Mass: 473.497 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H16FN3O5S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 7.2 / Details: HEPES, MPD, PEG 6K, NDSB-256

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.12011 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12011 Å / Relative weight: 1
ReflectionResolution: 1.13→146.99 Å / Num. obs: 202752 / % possible obs: 66.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 28.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.044 / Rrim(I) all: 0.082 / Net I/σ(I): 5.3 / Num. measured all: 674897 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allNet I/σ(I) obs% possible allCC1/2
1.13-1.151.72.2932701581.9813.0470.41
6.17-146.993.80.027682718160.0160.03132.897.40.999

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Processing

Software
NameVersionClassification
PHENIXphenix-1.13-2998refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DT6

4dt6


Resolution: 1.79→73.525 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 25.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2383 3466 4.83 %
Rwork0.1908 68306 -
obs0.193 71772 93.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.01 Å2 / Biso mean: 43.6788 Å2 / Biso min: 15.69 Å2
Refinement stepCycle: final / Resolution: 1.79→73.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5896 0 124 243 6263
Biso mean--79.58 41.74 -
Num. residues----730
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.79-1.81460.3871310.3269273991
1.8146-1.84050.35921120.3149262591
1.8405-1.8680.34191440.3036261991
1.868-1.89710.33161310.2784276092
1.8971-1.92820.28261400.2758265192
1.9282-1.96150.30271430.2561262592
1.9615-1.99720.25631510.2407276993
1.9972-2.03560.30731610.2307262393
2.0356-2.07710.25311140.217269192
2.0771-2.12230.25141100.216285494
2.1223-2.17170.2571490.2091263793
2.1717-2.2260.2621300.21277894
2.226-2.28620.23021310.1978274094
2.2862-2.35350.24421450.1945269794
2.3535-2.42940.23651520.1925274895
2.4294-2.51630.25771720.1982273094
2.5163-2.6170.27751390.1948272195
2.617-2.73610.24831650.1895278895
2.7361-2.88040.24881170.1954277295
2.8804-3.06080.25091180.1828275895
3.0608-3.29720.22861370.1807279095
3.2972-3.6290.20971280.1734277495
3.629-4.15410.21211560.1592280596
4.1541-5.23350.1941410.1592277396
5.2335-73.5250.22711490.1812283997
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)
15.06710.6992-2.89525.35860.33642.8957-0.1680.1108-0.3446-0.35740.2635-0.67120.07370.7708-0.10530.32270.0873-0.01710.3752-0.10610.418724.5491-11.82627.3469
29.9529-1.3575-1.3020.61360.41430.6321-0.07950.3886-0.2459-0.0264-0.1280.38180.0518-0.44150.17260.2571-0.0021-0.01210.3276-0.06280.4325-3.8139-2.89315.039
37.701-0.4524-4.27710.06810.19662.61720.07240.51020.11240.0256-0.24370.5583-0.2958-0.67030.23360.2618-0.041-0.03370.2528-0.1360.54621.1537-6.985212.0786
42.7375-0.6995-0.93482.7050.30243.1442-0.02390.1708-0.1545-0.1525-0.01730.262-0.1462-0.17520.02660.2002-0.0199-0.03050.1627-0.02470.24688.64930.479310.4727
56.78690.6974-2.03223.55750.56782.264-0.0637-0.0713-0.51680.5930.01110.28950.5426-0.68250.04210.38240.01440.07660.24660.03280.30312.6443-10.914725.8141
61.7089-0.1894-0.50322.5913-0.09763.0777-0.0204-0.22420.06180.32780.0439-0.0015-0.12440.1253-0.00730.2114-0.0033-0.01020.1449-0.03090.21912.22173.841225.5615
70.93282.382-0.03556.17390.6124.24330.2501-0.49910.84360.8388-0.35871.1292-0.276-0.822-0.05970.41240.01380.1160.3081-0.06250.40495.17751.046335.9222
84.6655-0.93821.67495.229-3.43894.25090.4116-0.1168-0.320.1198-0.6095-0.49520.70030.3775-0.15210.2895-0.004-0.10230.36930.04220.425338.99644.464668.9868
91.3897-2.033-0.29876.4344-0.20360.503-0.00110.13810.46270.2073-0.2131-0.2212-0.3133-0.11660.23670.25980.0051-0.06270.2907-0.0050.42427.09728.400562.5589
103.0392-0.01390.29752.3097-0.76583.4112-0.0197-0.29060.03160.2151-0.01610.1042-0.269-0.190.04720.1573-0.0009-0.03140.212-0.02370.228724.176817.055766.2749
112.33841.00070.15224.4343-0.9729.2359-0.15960.13620.3971-0.0980.0726-0.2308-0.9928-0.0480.1210.2602-0.06340.01140.27420.04750.34333.876524.938550.7605
122.877-0.1511-1.78660.80520.04972.48740.02260.16650.3615-0.18430.00450.4807-0.113-0.5353-0.03670.2072-0.0405-0.03320.4155-0.0230.358412.629816.16953.5291
132.00440.13470.04472.7173-0.40793.198-0.00420.23440.0166-0.2628-0.0616-0.06130.1143-0.02560.07640.1421-0.0144-0.0150.2127-0.00220.224125.1914.195553.1952
147.6240.2778-2.7954.7504-0.40035.21260.10180.9028-0.2673-0.3838-0.09180.05590.4299-0.53360.09170.3272-0.0161-0.02680.2756-0.0920.225.13487.10345.1771
154.33322.5929-0.82053.2929-0.94673.6627-0.19060.67370.2436-0.52190.34380.26470.0998-0.172-0.18260.2781-0.0381-0.05780.3824-0.00010.302919.652215.677242.6426
163.19950.2425-0.24523.0754-0.07453.97470.316-0.6775-0.34920.2408-0.25430.0221-0.01290.4154-0.03570.20290.0645-0.04190.41520.02070.312314.17719.879681.1133
173.92843.07130.65128.12360.32480.81030.0348-0.2623-1.03910.0986-0.22310.13080.57160.44630.10670.33450.10520.03920.57830.06120.582210.4216-2.087183.5981
181.97530.2588-0.31252.017-0.77162.7335-0.0127-0.1053-0.3974-0.07180.14150.08590.2448-0.2298-0.11440.2099-0.028-0.01860.47440.05910.29455.03728.1281.0677
192.5189-0.3807-2.23015.3271-0.89012.24580.0458-0.4857-0.25090.5227-0.0418-0.12170.64930.295-0.00140.4211-0.0251-0.09130.78410.16850.386615.04390.193696.9479
205.9403-1.29194.22391.9836-1.32754.02080.1644-0.5103-0.16440.19520.07240.50750.2005-0.4491-0.29130.3441-0.02220.04460.81750.07510.4068-6.35519.052693.7887
211.878-0.1419-0.52352.8261-0.50633.16720.0981-0.7535-0.13440.363-0.00990.0447-0.4569-0.1591-0.04810.2866-0.00210.02990.59540.0390.24537.340914.165892.0456
223.1110.06510.81122.5303-0.37713.0891-0.0035-0.83670.05360.6861-0.05160.3257-0.0578-0.2020.01250.3669-0.02550.06470.70480.0420.27773.388810.5511101.8306
234.91790.2496-3.01654.3571-2.71993.8756-0.2420.122-0.2818-0.39610.28530.12150.4918-0.7926-0.1140.4536-0.0561-0.08080.3409-0.02890.24244.39653.1499-1.3727
247.73133.44150.09445.68750.07053.6736-0.06650.38940.2832-0.75330.0037-1.25040.16960.9601-0.04540.38350.07240.16580.41020.0290.59826.184222.5711-8.31
252.2120.6417-0.72633.5645-0.59852.25290.0687-0.19490.1012-0.1408-0.1031-0.2487-0.09890.20260.01660.43150.04720.01460.2053-0.00850.245514.588919.8476-4.165
265.9314-0.2981-0.53831.58430.30631.9329-0.07240.51050.2771-0.84590.1649-0.74930.3541.0318-0.09210.78120.04710.21540.4446-0.03290.474323.098412.9088-20.2626
270.79860.023-0.37121.08270.04012.03210.25890.11970.3174-0.5652-0.2768-0.0837-0.4064-0.1768-0.10140.88450.04260.04720.2510.02450.39059.933531.9026-17.0371
282.9628-0.50840.28730.89730.89813.69130.01470.3445-0.0685-1.15780.0811-0.12020.1657-0.4826-0.01260.6556-0.0422-0.010.2537-0.00440.21557.947717.6526-15.199
293.0667-0.660.1320.17320.0531.1176-0.00440.54740.472-1.3599-0.1763-0.49210.11770.3307-0.43931.13410.00050.22210.33150.05720.137915.746222.6354-21.2309
303.3410.5137-1.70631.69981.09762.20020.58050.69490.1021-1.46060.13160.7640.4041-0.90050.07320.98450.0633-0.18990.47290.06550.22883.004621.7069-24.4959
313.7547-2.56771.97883.3841-0.21961.94490.31960.59020.2187-1.0686-0.346-0.7139-0.21860.77230.03871.03550.0480.1080.58840.08830.25916.042122.7317-29.7538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 42 )A30 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 56 )A43 - 56
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 66 )A57 - 66
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 95 )A67 - 95
5X-RAY DIFFRACTION5chain 'A' and (resid 96 through 110 )A96 - 110
6X-RAY DIFFRACTION6chain 'A' and (resid 111 through 195 )A111 - 195
7X-RAY DIFFRACTION7chain 'A' and (resid 196 through 217 )A196 - 217
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 42 )B31 - 42
9X-RAY DIFFRACTION9chain 'B' and (resid 43 through 66 )B43 - 66
10X-RAY DIFFRACTION10chain 'B' and (resid 67 through 95 )B67 - 95
11X-RAY DIFFRACTION11chain 'B' and (resid 96 through 110 )B96 - 110
12X-RAY DIFFRACTION12chain 'B' and (resid 111 through 125 )B111 - 125
13X-RAY DIFFRACTION13chain 'B' and (resid 126 through 172 )B126 - 172
14X-RAY DIFFRACTION14chain 'B' and (resid 173 through 186 )B173 - 186
15X-RAY DIFFRACTION15chain 'B' and (resid 187 through 217 )B187 - 217
16X-RAY DIFFRACTION16chain 'C' and (resid 28 through 55 )C28 - 55
17X-RAY DIFFRACTION17chain 'C' and (resid 56 through 66 )C56 - 66
18X-RAY DIFFRACTION18chain 'C' and (resid 67 through 95 )C67 - 95
19X-RAY DIFFRACTION19chain 'C' and (resid 96 through 110 )C96 - 110
20X-RAY DIFFRACTION20chain 'C' and (resid 111 through 125 )C111 - 125
21X-RAY DIFFRACTION21chain 'C' and (resid 126 through 155 )C126 - 155
22X-RAY DIFFRACTION22chain 'C' and (resid 156 through 217 )C156 - 217
23X-RAY DIFFRACTION23chain 'D' and (resid 29 through 42 )D29 - 42
24X-RAY DIFFRACTION24chain 'D' and (resid 43 through 60 )D43 - 60
25X-RAY DIFFRACTION25chain 'D' and (resid 61 through 95 )D61 - 95
26X-RAY DIFFRACTION26chain 'D' and (resid 96 through 110 )D96 - 110
27X-RAY DIFFRACTION27chain 'D' and (resid 111 through 125 )D111 - 125
28X-RAY DIFFRACTION28chain 'D' and (resid 126 through 155 )D126 - 155
29X-RAY DIFFRACTION29chain 'D' and (resid 156 through 172 )D156 - 172
30X-RAY DIFFRACTION30chain 'D' and (resid 173 through 195 )D173 - 195
31X-RAY DIFFRACTION31chain 'D' and (resid 196 through 217 )D196 - 217

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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