data_Y3U # _chem_comp.id Y3U _chem_comp.name "[(2~{R},3~{S},4~{R},5~{R})-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-(4-hydroxyphenyl)propanoyl]sulfamate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H24 N4 O10 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-08-10 _chem_comp.pdbx_modified_date 2019-04-12 _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 500.480 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y3U _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 6HB7 _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 Y3U C3U C1 C 0 1 N N N -57.889 8.992 -51.317 5.254 -4.095 1.589 C3U Y3U 1 Y3U N3 N1 N 0 1 N N N -58.006 8.289 -50.026 4.331 -3.331 0.746 N3 Y3U 2 Y3U C4 C2 C 0 1 N N N -59.078 8.618 -49.183 3.387 -3.974 0.029 C4 Y3U 3 Y3U O4 O1 O 0 1 N N N -59.876 9.480 -49.532 3.299 -5.188 0.079 O4 Y3U 4 Y3U C5 C3 C 0 1 N N N -59.149 7.880 -47.941 2.500 -3.226 -0.781 C5 Y3U 5 Y3U C6 C4 C 0 1 N N N -58.223 6.946 -47.647 2.620 -1.881 -0.818 C6 Y3U 6 Y3U N1 N2 N 0 1 N N N -57.180 6.684 -48.517 3.591 -1.266 -0.076 N1 Y3U 7 Y3U "C1'" C5 C 0 1 N N R -56.113 5.703 -48.186 3.720 0.192 -0.116 "C1'" Y3U 8 Y3U "O4'" O2 O 0 1 N N N -56.657 4.402 -48.071 2.456 0.818 0.192 "O4'" Y3U 9 Y3U "C4'" C6 C 0 1 N N R -55.680 3.588 -47.373 2.552 2.155 -0.345 "C4'" Y3U 10 Y3U "C5'" C7 C 0 1 N N N -56.365 2.748 -46.321 1.157 2.748 -0.551 "C5'" Y3U 11 Y3U "O5'" O3 O 0 1 N N N -56.921 3.677 -45.323 0.528 2.937 0.718 "O5'" Y3U 12 Y3U SBI S1 S 0 1 N N N -56.741 3.350 -43.776 -0.873 3.526 0.633 SBI Y3U 13 Y3U OAD O4 O 0 1 N N N -57.220 4.476 -43.053 -1.262 3.831 1.966 OAD Y3U 14 Y3U OAE O5 O 0 1 N N N -57.316 2.065 -43.593 -0.840 4.493 -0.407 OAE Y3U 15 Y3U NAT N3 N 0 1 N N N -55.170 3.150 -43.626 -1.882 2.318 0.117 NAT Y3U 16 Y3U C C8 C 0 1 N N N -54.422 3.157 -42.483 -2.089 1.235 0.892 C Y3U 17 Y3U O O6 O 0 1 N N N -54.928 3.370 -41.383 -1.536 1.145 1.968 O Y3U 18 Y3U CA C9 C 0 1 N N S -52.977 2.798 -42.688 -3.006 0.136 0.422 CA Y3U 19 Y3U N N4 N 0 1 N N N -52.181 3.139 -41.508 -2.711 -1.098 1.162 N Y3U 20 Y3U CB C10 C 0 1 N N N -53.099 1.267 -42.839 -4.460 0.544 0.671 CB Y3U 21 Y3U CG C11 C 0 1 Y N N -51.767 0.566 -42.871 -5.381 -0.498 0.091 CG Y3U 22 Y3U CD1 C12 C 0 1 Y N N -50.840 0.845 -43.875 -5.810 -0.387 -1.219 CD1 Y3U 23 Y3U CE1 C13 C 0 1 Y N N -49.617 0.190 -43.919 -6.654 -1.342 -1.753 CE1 Y3U 24 Y3U CZ C14 C 0 1 Y N N -49.298 -0.744 -42.940 -7.070 -2.412 -0.974 CZ Y3U 25 Y3U OH O7 O 0 1 N N N -48.087 -1.368 -42.974 -7.900 -3.352 -1.498 OH Y3U 26 Y3U CE2 C15 C 0 1 Y N N -50.214 -1.031 -41.932 -6.638 -2.520 0.339 CE2 Y3U 27 Y3U CD2 C16 C 0 1 Y N N -51.430 -0.365 -41.895 -5.790 -1.566 0.867 CD2 Y3U 28 Y3U "C3'" C17 C 0 1 N N S -54.632 4.568 -46.816 3.269 1.985 -1.703 "C3'" Y3U 29 Y3U "O3'" O8 O 0 1 N N N -53.468 4.593 -47.640 4.161 3.076 -1.939 "O3'" Y3U 30 Y3U "C2'" C18 C 0 1 N N R -55.366 5.910 -46.884 4.056 0.663 -1.548 "C2'" Y3U 31 Y3U "O2'" O9 O 0 1 N N N -54.473 7.003 -46.973 5.459 0.897 -1.683 "O2'" Y3U 32 Y3U C2 C19 C 0 1 N N N -57.038 7.333 -49.733 4.425 -1.989 0.694 C2 Y3U 33 Y3U O2 O10 O 0 1 N N N -56.135 7.090 -50.521 5.278 -1.422 1.349 O2 Y3U 34 Y3U H1 H1 H 0 1 N N N -58.713 9.714 -51.418 4.827 -4.208 2.585 H1 Y3U 35 Y3U H2 H2 H 0 1 N N N -56.928 9.525 -51.358 5.418 -5.078 1.149 H2 Y3U 36 Y3U H3 H3 H 0 1 N N N -57.939 8.262 -52.138 6.205 -3.565 1.658 H3 Y3U 37 Y3U H4 H4 H 0 1 N N N -59.950 8.079 -47.244 1.738 -3.723 -1.362 H4 Y3U 38 Y3U H5 H5 H 0 1 N N N -58.296 6.395 -46.721 1.952 -1.294 -1.431 H5 Y3U 39 Y3U H6 H6 H 0 1 N N N -55.375 5.713 -49.001 4.488 0.524 0.584 H6 Y3U 40 Y3U H7 H7 H 0 1 N N N -55.181 2.918 -48.089 3.141 2.789 0.318 H7 Y3U 41 Y3U H8 H8 H 0 1 N N N -57.172 2.156 -46.777 1.241 3.708 -1.061 H8 Y3U 42 Y3U H9 H9 H 0 1 N N N -55.639 2.073 -45.845 0.558 2.067 -1.155 H9 Y3U 43 Y3U H10 H10 H 0 1 N N N -54.666 3.000 -44.477 -2.324 2.390 -0.743 H10 Y3U 44 Y3U H11 H11 H 0 1 N N N -52.574 3.253 -43.605 -2.854 -0.033 -0.643 H11 Y3U 45 Y3U H12 H12 H 0 1 N N N -52.113 4.133 -41.427 -1.777 -1.424 0.964 H12 Y3U 46 Y3U H13 H13 H 0 1 N N N -52.621 2.767 -40.690 -2.845 -0.966 2.153 H13 Y3U 47 Y3U H15 H15 H 0 1 N N N -53.631 1.050 -43.777 -4.635 0.628 1.743 H15 Y3U 48 Y3U H16 H16 H 0 1 N N N -53.679 0.877 -41.990 -4.654 1.506 0.195 H16 Y3U 49 Y3U H17 H17 H 0 1 N N N -51.077 1.581 -44.629 -5.486 0.446 -1.825 H17 Y3U 50 Y3U H18 H18 H 0 1 N N N -48.915 0.405 -44.711 -6.990 -1.255 -2.776 H18 Y3U 51 Y3U H19 H19 H 0 1 N N N -48.021 -1.972 -42.244 -7.441 -4.092 -1.918 H19 Y3U 52 Y3U H20 H20 H 0 1 N N N -49.978 -1.770 -41.181 -6.961 -3.352 0.947 H20 Y3U 53 Y3U H21 H21 H 0 1 N N N -52.126 -0.573 -41.096 -5.450 -1.653 1.888 H21 Y3U 54 Y3U H22 H22 H 0 1 N N N -54.391 4.316 -45.773 2.543 1.904 -2.511 H22 Y3U 55 Y3U H23 H23 H 0 1 N N N -52.836 5.203 -47.278 4.638 3.020 -2.778 H23 Y3U 56 Y3U H24 H24 H 0 1 N N N -56.068 6.010 -46.043 3.718 -0.070 -2.281 H24 Y3U 57 Y3U H25 H25 H 0 1 N N N -54.019 7.110 -46.145 5.725 1.196 -2.564 H25 Y3U 58 # # 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 Y3U C3U N3 SING N N 1 Y3U O2 C2 DOUB N N 2 Y3U N3 C2 SING N N 3 Y3U N3 C4 SING N N 4 Y3U C2 N1 SING N N 5 Y3U O4 C4 DOUB N N 6 Y3U C4 C5 SING N N 7 Y3U N1 "C1'" SING N N 8 Y3U N1 C6 SING N N 9 Y3U "C1'" "O4'" SING N N 10 Y3U "C1'" "C2'" SING N N 11 Y3U "O4'" "C4'" SING N N 12 Y3U C5 C6 DOUB N N 13 Y3U "O3'" "C3'" SING N N 14 Y3U "C4'" "C3'" SING N N 15 Y3U "C4'" "C5'" SING N N 16 Y3U "O2'" "C2'" SING N N 17 Y3U "C2'" "C3'" SING N N 18 Y3U "C5'" "O5'" SING N N 19 Y3U "O5'" SBI SING N N 20 Y3U CE1 CD1 DOUB Y N 21 Y3U CE1 CZ SING Y N 22 Y3U CD1 CG SING Y N 23 Y3U SBI NAT SING N N 24 Y3U SBI OAE DOUB N N 25 Y3U SBI OAD DOUB N N 26 Y3U NAT C SING N N 27 Y3U OH CZ SING N N 28 Y3U CZ CE2 DOUB Y N 29 Y3U CG CB SING N N 30 Y3U CG CD2 DOUB Y N 31 Y3U CB CA SING N N 32 Y3U CA C SING N N 33 Y3U CA N SING N N 34 Y3U C O DOUB N N 35 Y3U CE2 CD2 SING Y N 36 Y3U C3U H1 SING N N 37 Y3U C3U H2 SING N N 38 Y3U C3U H3 SING N N 39 Y3U C5 H4 SING N N 40 Y3U C6 H5 SING N N 41 Y3U "C1'" H6 SING N N 42 Y3U "C4'" H7 SING N N 43 Y3U "C5'" H8 SING N N 44 Y3U "C5'" H9 SING N N 45 Y3U NAT H10 SING N N 46 Y3U CA H11 SING N N 47 Y3U N H12 SING N N 48 Y3U N H13 SING N N 49 Y3U CB H15 SING N N 50 Y3U CB H16 SING N N 51 Y3U CD1 H17 SING N N 52 Y3U CE1 H18 SING N N 53 Y3U OH H19 SING N N 54 Y3U CE2 H20 SING N N 55 Y3U CD2 H21 SING N N 56 Y3U "C3'" H22 SING N N 57 Y3U "O3'" H23 SING N N 58 Y3U "C2'" H24 SING N N 59 Y3U "O2'" H25 SING N N 60 # # 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 Y3U InChI InChI 1.03 "InChI=1S/C19H24N4O10S/c1-22-14(25)6-7-23(19(22)29)18-16(27)15(26)13(33-18)9-32-34(30,31)21-17(28)12(20)8-10-2-4-11(24)5-3-10/h2-7,12-13,15-16,18,24,26-27H,8-9,20H2,1H3,(H,21,28)/t12-,13+,15+,16+,18+/m0/s1" Y3U InChIKey InChI 1.03 JZICRHJSYJTEMP-IQNGCQKYSA-N Y3U SMILES_CANONICAL CACTVS 3.385 "CN1C(=O)C=CN([C@@H]2O[C@H](CO[S](=O)(=O)NC(=O)[C@@H](N)Cc3ccc(O)cc3)[C@@H](O)[C@H]2O)C1=O" Y3U SMILES CACTVS 3.385 "CN1C(=O)C=CN([CH]2O[CH](CO[S](=O)(=O)NC(=O)[CH](N)Cc3ccc(O)cc3)[CH](O)[CH]2O)C1=O" Y3U SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CN1C(=O)C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COS(=O)(=O)NC(=O)[C@H](Cc3ccc(cc3)O)N)O)O" Y3U SMILES "OpenEye OEToolkits" 2.0.6 "CN1C(=O)C=CN(C1=O)C2C(C(C(O2)COS(=O)(=O)NC(=O)C(Cc3ccc(cc3)O)N)O)O" # _pdbx_chem_comp_identifier.comp_id Y3U _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},4~{R},5~{R})-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-(4-hydroxyphenyl)propanoyl]sulfamate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site Y3U "Create component" 2018-08-10 EBI Y3U "Initial release" 2019-04-17 RCSB ##