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Structure paper

TitleSelectively Disrupting m6A-Dependent Protein-RNA Interactions with Fragments.
Journal, issue, pagesAcs Chem. Biol., Vol. 15, Page 618-625, Year 2020
Publish dateOct 1, 2019 (structure data deposition date)
AuthorsBedi, R.K. / Huang, D. / Wiedmer, L. / Li, Y. / Dolbois, A. / Wojdyla, J.A. / Sharpe, M.E. / Caflisch, A. / Sledz, P.
External linksAcs Chem. Biol. / PubMed:32101404
MethodsX-ray diffraction
Resolution1.1 - 2.4 Å
Structure data

PDB-6syz:
Crystal structure of YTHDC1 with fragment 1 (DHU_DC1_141)
Method: X-RAY DIFFRACTION / Resolution: 2.28 Å

PDB-6sz1:
Crystal structure of YTHDC1 with fragment 2 (DHU_DC1_140)
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-6sz2:
Crystal structure of YTHDC1 with fragment 3 (DHU_DC1_149)
Method: X-RAY DIFFRACTION / Resolution: 1.52 Å

PDB-6sz3:
Crystal structure of YTHDC1 with fragment 4 (DHU_DC1_158)
Method: X-RAY DIFFRACTION / Resolution: 1.28 Å

PDB-6sz7:
Crystal structure of YTHDC1 with fragment 5 (DHU_DC1_066)
Method: X-RAY DIFFRACTION / Resolution: 2.31 Å

PDB-6sz8:
Crystal structure of YTHDC1 with fragment 6 (DHU_DC1_034)
Method: X-RAY DIFFRACTION / Resolution: 1.47 Å

PDB-6szl:
Crystal structure of YTHDC1 with fragment 7 (DHU_DC1_021)
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-6szn:
Crystal structure of YTHDC1 with fragment 8 (DHU_DC1_006)
Method: X-RAY DIFFRACTION / Resolution: 1.47 Å

PDB-6szr:
Crystal structure of YTHDC1 with fragment 9 (DHU_DC1_107)
Method: X-RAY DIFFRACTION / Resolution: 1.64 Å

PDB-6szt:
Crystal structure of YTHDC1 with fragment 10 (DHU_DC1_076)
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-6szx:
Crystal structure of YTHDC1 with fragment 11 (DHU_DC1_128)
Method: X-RAY DIFFRACTION / Resolution: 1.17 Å

PDB-6szy:
Crystal structure of YTHDC1 with fragment 12 (DHU_DC1_150)
Method: X-RAY DIFFRACTION / Resolution: 1.79 Å

PDB-6t01:
Crystal structure of YTHDC1 with fragment 13 (DHU_DC1_153)
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-6t02:
Crystal structure of YTHDC1 with fragment 15 (DHU_DC1_169)
Method: X-RAY DIFFRACTION / Resolution: 1.1 Å

PDB-6t03:
Crystal structure of YTHDC1 with fragment 16 (DHU_DC1_017)
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-6t04:
Crystal structure of YTHDC1 with fragment 17 (DHU_DC1_042)
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-6t05:
Crystal structure of YTHDC1 with fragment 18 (DHU_DC1_048)
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-6t06:
Crystal structure of YTHDC1 with fragment 19 (DHU_DC1_045)
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-6t07:
Crystal structure of YTHDC1 with fragment 20 (DHU_DC1_134)
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-6t08:
Crystal structure of YTHDC1 with fragment 21 (DHU_DC1_131)
Method: X-RAY DIFFRACTION / Resolution: 1.41 Å

PDB-6t09:
Crystal structure of YTHDC1 with fragment 24 (PSI_DC1_003)
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-6t0a:
Crystal structure of YTHDC1 with fragment 25 (PSI_DC1_005)
Method: X-RAY DIFFRACTION / Resolution: 2.02 Å

PDB-6t0c:
Crystal structure of YTHDC1 with fragment 26 (DHU_DC1_198)
Method: X-RAY DIFFRACTION / Resolution: 2.03 Å

PDB-6t0d:
Crystal structure of YTHDC1 with fragment 27 (DHU_DC1_256)
Method: X-RAY DIFFRACTION / Resolution: 1.43 Å

PDB-6t0o:
Crystal structure of YTHDC1 with fragment 14 (ACA_DC1_004)
Method: X-RAY DIFFRACTION / Resolution: 1.71 Å

PDB-6t0x:
Crystal structure of YTHDC1 with fragment 22 (ACA_DC1_001)
Method: X-RAY DIFFRACTION / Resolution: 1.36 Å

PDB-6t0z:
Crystal structure of YTHDC1 with fragment 23 (ACA_DC1_005)
Method: X-RAY DIFFRACTION / Resolution: 1.43 Å

PDB-6t10:
Crystal structure of YTHDC1 with fragment 28 (DHU_DC1_176)
Method: X-RAY DIFFRACTION / Resolution: 1.48 Å

PDB-6t11:
Crystal structure of YTHDC1 with fragment 29 (DHU_DC1_218)
Method: X-RAY DIFFRACTION / Resolution: 1.49 Å

PDB-6t12:
Crystal structure of YTHDC1 with fragment 30 (DHU_DC1_220)
Method: X-RAY DIFFRACTION / Resolution: 1.46 Å

Chemicals

ChemComp-M1E:
~{N}-methylthieno[3,2-d]pyrimidin-4-amine

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-HOH:
WATER / Water

ChemComp-M0W:
~{N}-methylquinazolin-4-amine

ChemComp-M0Q:
~{N}-methyl-1,6-naphthyridin-4-amine

ChemComp-M1H:
~{N}-methyl-5,6,7,8-tetrahydroquinolin-4-amine

ChemComp-M1Q:
5,6,7,8-tetrahydro-4~{a}~{H}-quinazoline-2,4-dione

ChemComp-M1Z:
6-pyrrolidin-1-yl-5~{H}-pyrimidine-2,4-dione

ChemComp-M3E:
6-phenyl-1~{H}-pyrimidine-2,4-dione

ChemComp-YZM:
N-carbamoylbenzamide

ChemComp-M3Z:
6-[[methyl-(phenylmethyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione

ChemComp-M4Q:
6-[[methyl(thiophen-3-ylmethyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione

ChemComp-M4K:
6-[[cyclopropyl-(phenylmethyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione

ChemComp-M5N:
4-propan-2-yl-5,6,7,8-tetrahydro-4~{a}~{H}-quinazolin-2-one

ChemComp-M4B:
6-methyl-5-nitro-4-phenyl-1~{H}-pyrimidin-2-one

ChemComp-M5E:
(~{S})-phenyl-[(2~{S})-pyrrolidin-2-yl]methanol

ChemComp-MZY:
1,3-dihydroimidazole-2-thione / 2-Imidazolidinethione

ChemComp-M3H:
2-phenyl-4,5-dihydro-1~{H}-imidazole

ChemComp-M6H:
2-(phenylmethyl)imidazolidine

ChemComp-M5H:
3-imidazolidin-2-yl-2~{H}-indazole

ChemComp-M45:
~{N}-[(2~{S})-pyrrolidin-2-yl]-1~{H}-1,2,4-triazol-5-amine

ChemComp-M5B:
~{N}-(1~{H}-imidazol-2-yl)thiophene-2-sulfonamide

ChemComp-M4T:
~{N}-pyridin-3-ylethanamide

ChemComp-M58:
(~{R})-azanyl(pyridin-3-yl)methanethiol

ChemComp-M4E:
~{N}-methyl-2~{H}-indazole-3-carboxamide

ChemComp-M4N:
~{N}-methyl-3-phenyl-1~{H}-pyrazole-5-carboxamide

ChemComp-M6N:
2-methyl-3~{H}-pyrido[3,4-d]pyrimidin-4-one

ChemComp-M6W:
(3~{S})-~{N}-methylpyrrolidine-3-carboxamide

ChemComp-M75:
~{N}-cyclopropyl-1~{H}-imidazole-4-sulfonamide

ChemComp-M6Z:
5-iodanyl-~{N}-methyl-1~{H}-indazole-3-carboxamide

ChemComp-O2A:
N-methyl-1H-indole-7-carboxamide

ChemComp-M78:
~{N},2,3-trimethyl-1~{H}-indole-5-carboxamide

Source
  • homo sapiens (human)
KeywordsRNA BINDING PROTEIN / Fragment / Complex / YTHDC1 / Epitranscriptomic

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