data_YYG # _chem_comp.id YYG _chem_comp.name ;4-(3-[5-O-PHOSPHONORIBOFURANOSYL]-4,6-DIMETHYL-8-OXO-4,8-DIHYDRO-3H-1,3,4,5,7A-PENTAAZA-S-INDACEN-YLAMINO-BUTYRIC ACID METHYL ESTER ; _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 "MODIFIED GUANOSINE-5'-PHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-10-04 _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 YYG _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 486D _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 YYG P P P 0 1 N N N 5.752 107.848 270.630 1.682 -0.127 -8.592 P YYG 1 YYG OP1 O1P O 0 1 N N N 6.065 106.876 269.558 2.467 1.073 -8.228 OP1 YYG 2 YYG OP2 O2P O 0 1 N N N 5.687 109.273 270.166 2.680 -1.292 -9.081 OP2 YYG 3 YYG OP3 O3P O 0 1 N Y N 4.304 107.366 271.137 0.661 0.238 -9.782 OP3 YYG 4 YYG "O5'" O5* O 0 1 N N N 6.605 107.739 271.975 0.852 -0.635 -7.310 "O5'" YYG 5 YYG "C5'" C5* C 0 1 N N N 5.889 108.177 273.172 -0.010 0.437 -6.925 "C5'" YYG 6 YYG "C4'" C4* C 0 1 N N R 6.851 107.958 274.314 -0.833 0.017 -5.705 "C4'" YYG 7 YYG "O4'" O4* O 0 1 N N N 6.553 106.734 274.962 0.036 -0.272 -4.589 "O4'" YYG 8 YYG "C3'" C3* C 0 1 N N S 8.326 107.836 273.928 -1.718 1.187 -5.222 "C3'" YYG 9 YYG "O3'" O3* O 0 1 N N N 9.008 109.081 273.707 -3.050 1.046 -5.720 "O3'" YYG 10 YYG "C2'" C2* C 0 1 N N R 8.896 107.068 275.111 -1.699 1.063 -3.681 "C2'" YYG 11 YYG "O2'" O2* O 0 1 N N N 9.114 108.003 276.148 -3.019 0.843 -3.180 "O2'" YYG 12 YYG "C1'" C1* C 0 1 N N R 7.745 106.128 275.462 -0.801 -0.166 -3.417 "C1'" YYG 13 YYG N9 N9 N 0 1 Y N N 7.972 104.855 274.853 0.018 0.048 -2.222 N9 YYG 14 YYG C8 C8 C 0 1 Y N N 7.401 104.414 273.663 1.249 0.637 -2.183 C8 YYG 15 YYG N7 N7 N 0 1 Y N N 7.788 103.193 273.326 1.683 0.660 -0.957 N7 YYG 16 YYG C5 C5 C 0 1 Y N N 8.631 102.845 274.336 0.757 0.088 -0.146 C5 YYG 17 YYG C6 C6 C 0 1 N N N 9.374 101.647 274.566 0.696 -0.154 1.248 C6 YYG 18 YYG O6 O6 O 0 1 N N N 9.364 100.662 273.793 1.619 0.181 1.968 O6 YYG 19 YYG N1 N1 N 0 1 Y N N 10.138 101.601 275.669 -0.387 -0.757 1.774 N1 YYG 20 YYG C2 C2 C 0 1 Y N N 10.153 102.655 276.498 -1.430 -1.141 0.981 C2 YYG 21 YYG N2 N2 N 0 1 Y N N 11.060 102.267 277.588 -2.342 -1.699 1.747 N2 YYG 22 YYG N3 N3 N 0 1 N N N 9.507 103.823 276.396 -1.396 -0.916 -0.380 N3 YYG 23 YYG C3 C3 C 0 1 N N N 9.636 104.811 277.335 -2.523 -1.333 -1.219 C3 YYG 24 YYG C4 C4 C 0 1 Y N N 8.762 103.835 275.272 -0.308 -0.304 -0.949 C4 YYG 25 YYG C10 C10 C 0 1 N N N 12.398 100.214 278.062 -2.675 -2.244 4.203 C10 YYG 26 YYG C11 C11 C 0 1 Y N N 11.446 101.046 277.250 -1.918 -1.695 3.021 C11 YYG 27 YYG C12 C12 C 0 1 Y N N 10.888 100.616 276.062 -0.709 -1.110 3.066 C12 YYG 28 YYG C13 C13 C 0 1 N N N 11.089 99.279 275.386 0.136 -0.890 4.294 C13 YYG 29 YYG C14 C14 C 0 1 N N N 9.858 98.449 275.661 -0.198 0.471 4.906 C14 YYG 30 YYG C15 C15 C 0 1 N N S 10.202 97.151 276.299 0.659 0.694 6.152 C15 YYG 31 YYG C16 C16 C 0 1 N N N 9.584 97.035 277.662 0.329 2.035 6.756 C16 YYG 32 YYG O17 O17 O 0 1 N N N 8.643 97.759 278.002 0.936 3.020 6.408 O17 YYG 33 YYG O18 O18 O 0 1 N N N 10.092 96.064 278.595 -0.639 2.135 7.679 O18 YYG 34 YYG C19 C19 C 0 1 N N N 10.814 96.746 279.617 -0.957 3.427 8.261 C19 YYG 35 YYG N20 N20 N 0 1 N N N 9.622 96.059 275.478 0.385 -0.361 7.130 N20 YYG 36 YYG C21 C21 C 0 1 N N N 8.333 96.087 275.209 1.352 -0.758 7.981 C21 YYG 37 YYG O22 O22 O 0 1 N N N 7.561 96.827 275.818 2.450 -0.240 7.938 O22 YYG 38 YYG O23 O23 O 0 1 N N N 7.807 95.231 274.190 1.100 -1.729 8.880 O23 YYG 39 YYG C24 C24 C 0 1 N N N 6.915 94.279 274.771 2.141 -2.157 9.797 C24 YYG 40 YYG HOP2 2HOP H 0 0 N N N 5.486 109.896 270.853 3.157 -0.948 -9.848 HOP2 YYG 41 YYG HOP3 3HOP H 0 0 N N N 4.103 107.989 271.824 0.171 -0.568 -9.988 HOP3 YYG 42 YYG "H5'" 1H5* H 0 1 N N N 5.499 109.219 273.106 -0.681 0.677 -7.750 "H5'" YYG 43 YYG "H5''" 2H5* H 0 0 N N N 4.902 107.677 273.313 0.587 1.313 -6.677 "H5''" YYG 44 YYG "H4'" H4* H 0 1 N N N 6.718 108.868 274.943 -1.448 -0.850 -5.943 "H4'" YYG 45 YYG "H3'" H3* H 0 1 N N N 8.455 107.337 272.939 -1.294 2.142 -5.535 "H3'" YYG 46 YYG "HO3'" H3T H 0 0 N Y N 9.924 109.005 273.467 -3.554 1.801 -5.388 "HO3'" YYG 47 YYG "H2'" H2* H 0 1 N N N 9.853 106.526 274.928 -1.264 1.955 -3.231 "H2'" YYG 48 YYG "HO2'" 2HO* H 0 0 N N N 9.470 107.523 276.886 -3.544 1.616 -3.428 "HO2'" YYG 49 YYG "H1'" H1* H 0 1 N N N 7.660 105.964 276.561 -1.410 -1.063 -3.303 "H1'" YYG 50 YYG H8 H8 H 0 1 N N N 6.697 104.987 273.036 1.780 1.025 -3.039 H8 YYG 51 YYG H31 1H3 H 0 1 N N N 9.097 105.783 277.250 -3.287 -1.797 -0.596 H31 YYG 52 YYG H32 2H3 H 0 1 N N N 9.384 104.370 278.327 -2.943 -0.462 -1.722 H32 YYG 53 YYG H33 3H3 H 0 1 N N N 10.723 105.033 277.446 -2.176 -2.050 -1.963 H33 YYG 54 YYG H101 1H10 H 0 0 N N N 12.723 99.186 277.777 -2.417 -3.294 4.344 H101 YYG 55 YYG H102 2H10 H 0 0 N N N 13.321 100.821 278.208 -2.410 -1.681 5.098 H102 YYG 56 YYG H103 3H10 H 0 0 N N N 11.981 100.152 279.094 -3.746 -2.155 4.022 H103 YYG 57 YYG H131 1H13 H 0 0 N N N 11.320 99.369 274.299 1.190 -0.915 4.018 H131 YYG 58 YYG H132 2H13 H 0 0 N N N 12.034 98.772 275.692 -0.067 -1.676 5.021 H132 YYG 59 YYG H141 1H14 H 0 0 N N N 9.112 99.015 276.267 -1.253 0.495 5.182 H141 YYG 60 YYG H142 2H14 H 0 0 N N N 9.253 98.300 274.736 0.005 1.256 4.179 H142 YYG 61 YYG H15 H15 H 0 1 N N N 11.312 97.086 276.378 1.714 0.670 5.877 H15 YYG 62 YYG H191 1H19 H 0 0 N N N 11.207 95.993 280.339 -1.763 3.311 8.985 H191 YYG 63 YYG H192 2H19 H 0 0 N N N 11.615 97.403 279.206 -0.075 3.829 8.760 H192 YYG 64 YYG H193 3H19 H 0 0 N N N 10.205 97.537 280.113 -1.272 4.112 7.473 H193 YYG 65 YYG HN20 HN20 H 0 0 N N N 10.125 95.263 275.085 -0.491 -0.774 7.165 HN20 YYG 66 YYG H241 1H24 H 0 0 N N N 6.505 93.612 273.977 1.754 -2.944 10.444 H241 YYG 67 YYG H242 2H24 H 0 0 N N N 7.395 93.702 275.595 2.991 -2.537 9.230 H242 YYG 68 YYG H243 3H24 H 0 0 N N N 6.108 94.768 275.365 2.460 -1.311 10.406 H243 YYG 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 YYG P OP1 DOUB N N 1 YYG P OP2 SING N N 2 YYG P OP3 SING N N 3 YYG P "O5'" SING N N 4 YYG OP2 HOP2 SING N N 5 YYG OP3 HOP3 SING N N 6 YYG "O5'" "C5'" SING N N 7 YYG "C5'" "C4'" SING N N 8 YYG "C5'" "H5'" SING N N 9 YYG "C5'" "H5''" SING N N 10 YYG "C4'" "O4'" SING N N 11 YYG "C4'" "C3'" SING N N 12 YYG "C4'" "H4'" SING N N 13 YYG "O4'" "C1'" SING N N 14 YYG "C3'" "O3'" SING N N 15 YYG "C3'" "C2'" SING N N 16 YYG "C3'" "H3'" SING N N 17 YYG "O3'" "HO3'" SING N N 18 YYG "C2'" "O2'" SING N N 19 YYG "C2'" "C1'" SING N N 20 YYG "C2'" "H2'" SING N N 21 YYG "O2'" "HO2'" SING N N 22 YYG "C1'" N9 SING N N 23 YYG "C1'" "H1'" SING N N 24 YYG N9 C8 SING Y N 25 YYG N9 C4 SING Y N 26 YYG C8 N7 DOUB Y N 27 YYG C8 H8 SING N N 28 YYG N7 C5 SING Y N 29 YYG C5 C6 SING N N 30 YYG C5 C4 DOUB Y N 31 YYG C6 O6 DOUB N N 32 YYG C6 N1 SING N N 33 YYG N1 C2 SING Y N 34 YYG N1 C12 SING Y N 35 YYG C2 N2 DOUB Y N 36 YYG C2 N3 SING N N 37 YYG N2 C11 SING Y N 38 YYG N3 C3 SING N N 39 YYG N3 C4 SING N N 40 YYG C3 H31 SING N N 41 YYG C3 H32 SING N N 42 YYG C3 H33 SING N N 43 YYG C10 C11 SING N N 44 YYG C10 H101 SING N N 45 YYG C10 H102 SING N N 46 YYG C10 H103 SING N N 47 YYG C11 C12 DOUB Y N 48 YYG C12 C13 SING N N 49 YYG C13 C14 SING N N 50 YYG C13 H131 SING N N 51 YYG C13 H132 SING N N 52 YYG C14 C15 SING N N 53 YYG C14 H141 SING N N 54 YYG C14 H142 SING N N 55 YYG C15 C16 SING N N 56 YYG C15 N20 SING N N 57 YYG C15 H15 SING N N 58 YYG C16 O17 DOUB N N 59 YYG C16 O18 SING N N 60 YYG O18 C19 SING N N 61 YYG C19 H191 SING N N 62 YYG C19 H192 SING N N 63 YYG C19 H193 SING N N 64 YYG N20 C21 SING N N 65 YYG N20 HN20 SING N N 66 YYG C21 O22 DOUB N N 67 YYG C21 O23 SING N N 68 YYG O23 C24 SING N N 69 YYG C24 H241 SING N N 70 YYG C24 H242 SING N N 71 YYG C24 H243 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 YYG 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" YYG 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" YYG 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" YYG 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" YYG 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" YYG 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+/m0/s1" YYG InChIKey InChI 1.03 WOMRPCAFQVCGCI-QHOAOGIMSA-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 YYG "SYSTEMATIC NAME" ACDLabs 10.04 "7-{(3S)-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" YYG "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "methyl (2S)-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 YYG "Create component" 1999-10-04 EBI YYG "Modify descriptor" 2011-06-04 RCSB YYG "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id YYG _pdbx_chem_comp_synonyms.name "MODIFIED GUANOSINE-5'-PHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##