data_YG # _chem_comp.id YG _chem_comp.name WYBUTOSINE _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C21 H29 N6 O12 P" _chem_comp.mon_nstd_parent_comp_id G _chem_comp.pdbx_synonyms ;Y-BASE; 1H-IMIDAZO(1,2-ALPHA)PURINE-7-BUTANOIC ACID,4,9-DIHYDRO-ALPHA-((METHOXYCARBONYL)AMINO)-4,6-DIMETHYL-9-OXO-METHYL ESTER ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2020-06-17 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 588.462 _chem_comp.one_letter_code G _chem_comp.three_letter_code YG _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1EVV _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal YG N1 N1 N 0 1 Y N N 44.744 -13.942 1.252 -0.938 -0.917 1.913 N1 YG 1 YG N2 N2 N 0 1 Y N N 44.558 -15.668 2.736 -2.990 -1.594 1.713 N2 YG 2 YG C2 C2 C 0 1 Y N N 43.937 -14.598 2.123 -1.962 -1.130 1.036 C2 YG 3 YG N3 N3 N 0 1 N N N 42.650 -14.255 2.388 -1.803 -0.859 -0.308 N3 YG 4 YG C3 C3 C 0 1 N N N 41.796 -15.012 3.368 -2.910 -1.093 -1.238 C3 YG 5 YG C4 C4 C 0 1 Y N N 42.253 -13.151 1.661 -0.607 -0.372 -0.773 C4 YG 6 YG C5 C5 C 0 1 Y N N 42.998 -12.415 0.752 0.438 -0.153 0.115 C5 YG 7 YG C6 C6 C 0 1 N N N 44.362 -12.803 0.487 0.248 -0.439 1.490 C6 YG 8 YG O6 O6 O 0 1 N N N 45.175 -12.285 -0.291 1.152 -0.255 2.284 O6 YG 9 YG N7 N7 N 0 1 Y N N 42.247 -11.366 0.234 1.485 0.324 -0.605 N7 YG 10 YG C8 C8 C 0 1 Y N N 41.083 -11.473 0.822 1.140 0.406 -1.856 C8 YG 11 YG N9 N9 N 0 1 Y N N 41.016 -12.527 1.705 -0.148 -0.015 -2.004 N9 YG 12 YG C10 C10 C 0 1 N N N 46.936 -16.678 2.574 -3.564 -2.187 4.112 C10 YG 13 YG C11 C11 C 0 1 Y N N 45.847 -15.692 2.226 -2.661 -1.695 3.010 C11 YG 14 YG C12 C12 C 0 1 Y N N 45.937 -14.639 1.330 -1.393 -1.276 3.163 C12 YG 15 YG C13 C13 C 0 1 N N N 47.181 -14.328 0.528 -0.617 -1.215 4.452 C13 YG 16 YG C14 C14 C 0 1 N N N 47.458 -15.392 -0.513 -0.819 0.153 5.106 C14 YG 17 YG C15 C15 C 0 1 N N R 48.845 -16.050 -0.454 -0.031 0.214 6.416 C15 YG 18 YG C16 C16 C 0 1 N N N 49.306 -16.490 -1.848 -0.230 1.562 7.059 C16 YG 19 YG O17 O17 O 0 1 N N N 49.152 -15.747 -2.819 -1.141 1.732 7.835 O17 YG 20 YG O18 O18 O 0 1 N N N 49.854 -17.722 -1.968 0.603 2.573 6.771 O18 YG 21 YG C19 C19 C 0 1 N N N 51.257 -17.925 -2.286 0.411 3.872 7.391 C19 YG 22 YG N20 N20 N 0 1 N N N 48.845 -17.176 0.482 1.393 0.011 6.138 N20 YG 23 YG C21 C21 C 0 1 N N N 49.763 -17.348 1.434 2.184 -0.564 7.064 C21 YG 24 YG O22 O22 O 0 1 N N N 50.637 -16.503 1.658 1.717 -0.915 8.129 O22 YG 25 YG O23 O23 O 0 1 N N N 49.718 -18.480 2.178 3.493 -0.750 6.809 O23 YG 26 YG C24 C24 C 0 1 N N N 50.557 -18.696 3.340 4.346 -1.371 7.807 C24 YG 27 YG "C1'" C1* C 0 1 N N R 39.868 -12.898 2.535 -0.901 -0.074 -3.259 "C1'" YG 28 YG "C2'" C2* C 0 1 N N R 40.093 -12.669 4.036 -1.614 1.270 -3.523 "C2'" YG 29 YG "O2'" O2* O 0 1 N N N 39.528 -13.723 4.791 -2.984 1.204 -3.121 "O2'" YG 30 YG "C3'" C3* C 0 1 N N S 39.388 -11.338 4.253 -1.507 1.456 -5.054 "C3'" YG 31 YG "O3'" O3* O 0 1 N N N 38.968 -11.194 5.600 -2.807 1.508 -5.645 "O3'" YG 32 YG "C4'" C4* C 0 1 N N R 38.194 -11.472 3.333 -0.746 0.200 -5.533 "C4'" YG 33 YG "O4'" O4* O 0 1 N N N 38.766 -12.092 2.154 -0.002 -0.243 -4.377 "O4'" YG 34 YG "C5'" C5* C 0 1 N N N 37.541 -10.173 2.951 0.208 0.556 -6.675 "C5'" YG 35 YG "O5'" O5* O 0 1 N N N 38.443 -9.380 2.192 0.953 -0.602 -7.053 "O5'" YG 36 YG P P P 0 1 N N N 37.928 -8.086 1.424 1.930 -0.157 -8.252 P YG 37 YG OP1 O1P O 0 1 N N N 39.097 -7.469 0.736 2.833 0.915 -7.779 OP1 YG 38 YG OP2 O2P O 0 1 N N N 37.108 -7.272 2.363 2.805 -1.422 -8.729 OP2 YG 39 YG OP3 O3P O 0 1 N Y N 36.937 -8.673 0.301 1.052 0.384 -9.487 OP3 YG 40 YG H31 1H3 H 0 1 N N N 40.739 -14.730 3.585 -3.770 -1.478 -0.690 H31 YG 41 YG H32 2H3 H 0 1 N N N 41.802 -16.084 3.061 -3.179 -0.156 -1.725 H32 YG 42 YG H33 3H3 H 0 1 N N N 42.343 -15.040 4.339 -2.604 -1.819 -1.992 H33 YG 43 YG H8 H8 H 0 1 N N N 40.264 -10.766 0.602 1.777 0.755 -2.656 H8 YG 44 YG H101 1H10 H 0 0 N N N 47.972 -16.697 2.163 -3.452 -3.266 4.219 H101 YG 45 YG H102 2H10 H 0 0 N N N 47.041 -16.645 3.683 -3.294 -1.699 5.048 H102 YG 46 YG H103 3H10 H 0 0 N N N 46.509 -17.690 2.386 -4.600 -1.952 3.865 H103 YG 47 YG H131 1H13 H 0 0 N N N 47.124 -13.314 0.067 0.442 -1.366 4.246 H131 YG 48 YG H132 2H13 H 0 0 N N N 48.063 -14.169 1.191 -0.970 -1.995 5.126 H132 YG 49 YG H141 1H14 H 0 0 N N N 46.666 -16.175 -0.472 -1.879 0.303 5.312 H141 YG 50 YG H142 2H14 H 0 0 N N N 47.279 -14.978 -1.532 -0.466 0.933 4.432 H142 YG 51 YG H15 H15 H 0 1 N N N 49.572 -15.291 -0.081 -0.384 -0.565 7.090 H15 YG 52 YG H191 1H19 H 0 0 N N N 51.708 -18.939 -2.384 1.178 4.561 7.038 H191 YG 53 YG H192 2H19 H 0 0 N N N 51.472 -17.367 -3.227 -0.573 4.259 7.127 H192 YG 54 YG H193 3H19 H 0 0 N N N 51.857 -17.361 -1.534 0.483 3.772 8.474 H193 YG 55 YG HN2 HN2 H 0 1 N N N 48.137 -17.910 0.469 1.766 0.292 5.288 HN2 YG 56 YG H241 1H24 H 0 0 N N N 50.520 -19.627 3.952 5.364 -1.437 7.424 H241 YG 57 YG H242 2H24 H 0 0 N N N 51.614 -18.550 3.019 4.338 -0.770 8.716 H242 YG 58 YG H243 3H24 H 0 0 N N N 50.396 -17.836 4.031 3.976 -2.372 8.029 H243 YG 59 YG "H1'" H1* H 0 1 N N N 39.696 -13.988 2.375 -1.625 -0.888 -3.229 "H1'" YG 60 YG "H2'" H2* H 0 1 N N N 41.161 -12.648 4.355 -1.103 2.080 -3.003 "H2'" YG 61 YG "HO2'" *HO2 H 0 0 N N N 39.667 -13.581 5.720 -3.388 2.048 -3.366 "HO2'" YG 62 YG "H3'" H3* H 0 1 N N N 40.029 -10.449 4.047 -0.944 2.358 -5.292 "H3'" YG 63 YG "HO3'" *HO3 H 0 0 N Y N 38.527 -10.363 5.735 -3.234 2.309 -5.311 "HO3'" YG 64 YG "H4'" H4* H 0 1 N N N 37.378 -12.043 3.833 -1.447 -0.570 -5.852 "H4'" YG 65 YG "H5'" 1H5* H 0 1 N N N 36.574 -10.332 2.418 -0.366 0.914 -7.530 "H5'" YG 66 YG "H5''" 2H5* H 0 0 N N N 37.149 -9.625 3.839 0.893 1.337 -6.346 "H5''" YG 67 YG HOP2 2HOP H 0 0 N N N 36.800 -6.499 1.904 3.375 -1.113 -9.446 HOP2 YG 68 YG HOP3 3HOP H 0 0 N N N 36.629 -7.900 -0.157 0.479 -0.344 -9.764 HOP3 YG 69 # # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal YG N1 C2 SING Y N 1 YG N1 C6 SING N N 2 YG N1 C12 SING Y N 3 YG N2 C2 DOUB Y N 4 YG N2 C11 SING Y N 5 YG C2 N3 SING N N 6 YG N3 C3 SING N N 7 YG N3 C4 SING N N 8 YG C3 H31 SING N N 9 YG C3 H32 SING N N 10 YG C3 H33 SING N N 11 YG C4 C5 DOUB Y N 12 YG C4 N9 SING Y N 13 YG C5 C6 SING N N 14 YG C5 N7 SING Y N 15 YG C6 O6 DOUB N N 16 YG N7 C8 DOUB Y N 17 YG C8 N9 SING Y N 18 YG C8 H8 SING N N 19 YG N9 "C1'" SING N N 20 YG C10 C11 SING N N 21 YG C10 H101 SING N N 22 YG C10 H102 SING N N 23 YG C10 H103 SING N N 24 YG C11 C12 DOUB Y N 25 YG C12 C13 SING N N 26 YG C13 C14 SING N N 27 YG C13 H131 SING N N 28 YG C13 H132 SING N N 29 YG C14 C15 SING N N 30 YG C14 H141 SING N N 31 YG C14 H142 SING N N 32 YG C15 C16 SING N N 33 YG C15 N20 SING N N 34 YG C15 H15 SING N N 35 YG C16 O17 DOUB N N 36 YG C16 O18 SING N N 37 YG O18 C19 SING N N 38 YG C19 H191 SING N N 39 YG C19 H192 SING N N 40 YG C19 H193 SING N N 41 YG N20 C21 SING N N 42 YG N20 HN2 SING N N 43 YG C21 O22 DOUB N N 44 YG C21 O23 SING N N 45 YG O23 C24 SING N N 46 YG C24 H241 SING N N 47 YG C24 H242 SING N N 48 YG C24 H243 SING N N 49 YG "C1'" "C2'" SING N N 50 YG "C1'" "O4'" SING N N 51 YG "C1'" "H1'" SING N N 52 YG "C2'" "O2'" SING N N 53 YG "C2'" "C3'" SING N N 54 YG "C2'" "H2'" SING N N 55 YG "O2'" "HO2'" SING N N 56 YG "C3'" "O3'" SING N N 57 YG "C3'" "C4'" SING N N 58 YG "C3'" "H3'" SING N N 59 YG "O3'" "HO3'" SING N N 60 YG "C4'" "O4'" SING N N 61 YG "C4'" "C5'" SING N N 62 YG "C4'" "H4'" SING N N 63 YG "C5'" "O5'" SING N N 64 YG "C5'" "H5'" SING N N 65 YG "C5'" "H5''" SING N N 66 YG "O5'" P SING N N 67 YG P OP1 DOUB N N 68 YG P OP2 SING N N 69 YG P OP3 SING N N 70 YG OP2 HOP2 SING N N 71 YG OP3 HOP3 SING N N 72 # # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor YG SMILES ACDLabs 10.04 "O=C(OC)C(NC(=O)OC)CCc3c(nc4N(c1c(ncn1C2OC(C(O)C2O)COP(=O)(O)O)C(=O)n34)C)C" YG SMILES_CANONICAL CACTVS 3.341 "COC(=O)N[C@H](CCc1n2C(=O)c3ncn([C@@H]4O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]4O)c3N(C)c2nc1C)C(=O)OC" YG SMILES CACTVS 3.341 "COC(=O)N[CH](CCc1n2C(=O)c3ncn([CH]4O[CH](CO[P](O)(O)=O)[CH](O)[CH]4O)c3N(C)c2nc1C)C(=O)OC" YG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1c(n2c(n1)N(c3c(ncn3[C@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(O)O)O)O)C2=O)C)CC[C@H](C(=O)OC)NC(=O)OC" YG SMILES "OpenEye OEToolkits" 1.5.0 "Cc1c(n2c(n1)N(c3c(ncn3C4C(C(C(O4)COP(=O)(O)O)O)O)C2=O)C)CCC(C(=O)OC)NC(=O)OC" YG InChI InChI 1.03 "InChI=1S/C21H29N6O12P/c1-9-11(6-5-10(19(31)36-3)24-21(32)37-4)27-17(30)13-16(25(2)20(27)23-9)26(8-22-13)18-15(29)14(28)12(39-18)7-38-40(33,34)35/h8,10,12,14-15,18,28-29H,5-7H2,1-4H3,(H,24,32)(H2,33,34,35)/t10-,12-,14-,15-,18-/m1/s1" YG InChIKey InChI 1.03 WOMRPCAFQVCGCI-DPHITLOKSA-N # # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier YG "SYSTEMATIC NAME" ACDLabs 10.04 "7-{(3R)-4-methoxy-3-[(methoxycarbonyl)amino]-4-oxobutyl}-4,6-dimethyl-3-(5-O-phosphono-beta-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one" YG "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "methyl (2R)-4-[3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]-4,6-dimethyl-9-oxo-imidazo[3,2-a]purin-7-yl]-2-(methoxycarbonylamino)butanoate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YG "Create component" 1999-07-08 PDBJ YG "Modify descriptor" 2011-06-04 RCSB YG "Modify synonyms" 2020-06-05 PDBE # # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 YG Y-BASE ? ? 2 YG "1H-IMIDAZO(1,2-ALPHA)PURINE-7-BUTANOIC ACID,4,9-DIHYDRO-ALPHA-((METHOXYCARBONYL)AMINO)-4,6-DIMETHYL-9-OXO-METHYL ESTER" ? ? ##