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Structure paper

TitleStructure-based design of ligands of the m6A-RNA reader YTHDC1
Journal, issue, pagesEur J Med Chem Rep, Vol. 5, Page 100057-, Year 2022
Publish dateApr 6, 2020 (structure data deposition date)
AuthorsLi, Y. / Bedi, R.K. / Nai, F. / von Roten, V. / Dolbois, A. / Zalesak, F. / Nachawati, R. / Huang, D. / Caflisch, A.
External linksEur J Med Chem Rep / Search PubMed
MethodsX-ray diffraction
Resolution1.1 - 1.9 Å
Structure data

PDB-6yke:
Crystal structure of YTHDC1 with compound DHU_DC1_038
Method: X-RAY DIFFRACTION / Resolution: 1.52 Å

PDB-6yki:
Crystal structure of YTHDC1 with compound DHU_DC1_092
Method: X-RAY DIFFRACTION / Resolution: 1.3 Å

PDB-6ykj:
Crystal structure of YTHDC1 with compound DHU_DC1_125
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-6ykz:
Crystal structure of YTHDC1 with compound DHU_DC1_234
Method: X-RAY DIFFRACTION / Resolution: 1.2 Å

PDB-6yl8:
Crystal structure of YTHDC1 with compound DHU_DC1_011
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-6yl9:
Crystal structure of YTHDC1 with compound DHU_DC1_085
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-6yni:
Crystal structure of YTHDC1 with compound DHU_DC1_036
Method: X-RAY DIFFRACTION / Resolution: 1.36 Å

PDB-6ynj:
Crystal structure of YTHDC1 with compound DHU_DC1_046
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-6ynk:
Crystal structure of YTHDC1 with compound DHU_DC1_068
Method: X-RAY DIFFRACTION / Resolution: 1.3 Å

PDB-6ynl:
Crystal structure of YTHDC1 with compound DHU_DC1_078
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-6ynm:
Crystal structure of YTHDC1 with compound DHU_DC1_096
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-6ynp:
Crystal structure of YTHDC1 with compound T96C1
Method: X-RAY DIFFRACTION / Resolution: 1.1 Å

PDB-6yoq:
Crystal structure of YTHDC1 with compound VVR_DC1_002
Method: X-RAY DIFFRACTION / Resolution: 1.3 Å

PDB-7p87:
Crystal structure of YTHDC1 with compound YLI_DC1_001
Method: X-RAY DIFFRACTION / Resolution: 1.3 Å

PDB-7p88:
Crystal structure of YTHDC1 with compound YLI_DC1_002
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-7p8a:
Crystal structure of YTHDC1 with compound YLI_DC1_003
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-7p8b:
Crystal structure of YTHDC1 with compound YLI_DC1_006
Method: X-RAY DIFFRACTION / Resolution: 1.2 Å

PDB-7p8f:
Crystal structure of YTHDC1 with compound YLI_DC1_008
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-7pj7:
Crystal structure of YTHDC1 with compound DHU_DC1_222
Method: X-RAY DIFFRACTION / Resolution: 1.41 Å

PDB-7pj8:
Crystal structure of YTHDC1 with compound DHU_DC1_225
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7pj9:
Crystal structure of YTHDC1 with compound DHU_DC1_232
Method: X-RAY DIFFRACTION / Resolution: 1.72 Å

PDB-7pja:
Crystal structure of YTHDC1 with compound PSI_DC1_002
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-7pjb:
Crystal structure of YTHDC1 with compound PSI_DC1_004
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-7pjp:
Crystal structure of YTHDC1 with compound DHU_DC1_226
Method: X-RAY DIFFRACTION / Resolution: 1.61 Å

PDB-7pjq:
Crystal structure of YTHDC1 with compound T96
Method: X-RAY DIFFRACTION / Resolution: 1.2 Å

Chemicals

ChemComp-SO4:
SULFATE ION

ChemComp-OUQ:
(2~{R})-2-(3-fluorophenyl)-5,5-dimethyl-morpholine

ChemComp-HOH:
WATER

ChemComp-OUZ:
~{N}-ethyl-2-[(2~{S},5~{R})-5-methyl-2-phenyl-morpholin-4-yl]ethanamine

ChemComp-OUW:
~{N}-methyl-4-(methylamino)pyridine-2-carboxamide

ChemComp-OW8:
~{N}-methyl-1,4,5,6-tetrahydrocyclopenta[c]pyrazole-3-carboxamide

ChemComp-OWZ:
(2~{R},5~{S})-2-(2-chlorophenyl)-5-methyl-morpholine

ChemComp-OXB:
3-[(2~{R},5~{S})-2-(2,5-dimethylphenyl)-5-methyl-morpholin-4-yl]propane-1-sulfonamide

ChemComp-P0Q:
(2~{R},3~{R})-2-(3-chlorophenyl)-3,5,5-trimethyl-morpholine

ChemComp-P0N:
(2~{R})-2-(2-chlorophenyl)-5,5-dimethyl-morpholine

ChemComp-P0K:
6-[[furan-2-ylmethyl(methyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-P0Z:
3-[(2~{R})-5,5-dimethyl-2-phenyl-morpholin-4-yl]-~{N}-(methylcarbamoyl)propanamide

ChemComp-P1Q:
1-[(2~{R},5~{S})-2-(3-chlorophenyl)-5-methyl-morpholin-4-yl]-3-methoxy-propan-2-ol

ChemComp-PJH:
~{N}-methylpyridine-3-carboxamide

ChemComp-CL:
Unknown entry

ChemComp-P5H:
6-methyl-~{N}-[2-(methylsulfonylamino)ethyl]-2-oxidanylidene-3~{H}-pyridine-3-carboxamide

ChemComp-ID0:
N-methyl-4,5,6,7-tetrahydro-1H-indazole-3-carboxamide

ChemComp-OYN:
2-chloranyl-~{N}-methyl-9~{H}-purin-6-amine

ChemComp-OYK:
~{N},9-dimethylpurin-6-amine

ChemComp-OYT:
9-cyclopropyl-~{N}-methyl-purin-6-amine

ChemComp-5ZK:
~{N},3-dimethyl-1~{H}-pyrazolo[4,3-d]pyrimidin-7-amine

ChemComp-7RN:
N-methyl-3-(5-methylthiophen-2-yl)-1H-pyrazole-5-carboxamide

ChemComp-7RT:
N-methyl-1H-indole-4-carboxamide

ChemComp-7RI:
5-bromanyl-N-methyl-1H-indazole-3-carboxamide

ChemComp-7RE:
6-methyl-3H-pyridin-2-one

ChemComp-GOL:
GLYCEROL

ChemComp-7RX:
(R)-homoproline

ChemComp-7SL:
5-(furan-2-yl)-N-methyl-1H-pyrazole-3-carboxamide

ChemComp-OWH:
~{N}-methylpyridine-3-carbothioamide

Source
  • homo sapiens (human)
KeywordsRNA BINDING PROTEIN / YTHDC1 / m6A / complex / inhibitor

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