data_87Z # _chem_comp.id 87Z _chem_comp.name "[(2~{R},3~{R},4~{S},5~{R},6~{R})-4-acetamido-6-methyl-3,5-bis(oxidanyl)oxan-2-yl] [[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H29 N3 O15 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-09-09 _chem_comp.pdbx_modified_date 2021-09-17 _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 589.381 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 87Z _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 7S42 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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 87Z C2 C1 C 0 1 N N N 23.115 -10.486 25.668 5.975 0.605 0.812 C2 87Z 1 87Z O3 O1 O 0 1 N N N 29.604 -15.032 33.010 -4.400 2.443 -2.718 O3 87Z 2 87Z C3 C2 C 0 1 N N N 30.631 -14.467 32.858 -5.344 3.060 -2.271 C3 87Z 3 87Z C3M C3 C 0 1 N N N 31.630 -14.978 31.821 -6.024 4.109 -3.111 C3M 87Z 4 87Z N3Q N1 N 0 1 N N N 30.999 -13.387 33.543 -5.783 2.806 -1.022 N3Q 87Z 5 87Z C3Q C4 C 0 1 N N S 30.015 -12.526 34.185 -5.122 1.786 -0.206 C3Q 87Z 6 87Z C4Q C5 C 0 1 N N R 30.318 -12.226 35.658 -5.343 2.094 1.278 C4Q 87Z 7 87Z O4Q O2 O 0 1 N N N 31.601 -11.588 35.814 -6.745 2.165 1.547 O4Q 87Z 8 87Z C2Q C6 C 0 1 N N R 29.896 -11.192 33.424 -5.715 0.410 -0.524 C2Q 87Z 9 87Z O2Q O3 O 0 1 N N N 29.528 -11.450 32.071 -5.451 0.080 -1.889 O2Q 87Z 10 87Z C1Q C7 C 0 1 N N R 28.885 -10.335 34.092 -5.074 -0.638 0.389 C1Q 87Z 11 87Z O5Q O4 O 0 1 N N N 29.073 -10.126 35.478 -5.291 -0.274 1.754 O5Q 87Z 12 87Z C5Q C8 C 0 1 N N R 29.202 -11.368 36.223 -4.716 0.981 2.122 C5Q 87Z 13 87Z C6Q C9 C 0 1 N N N 29.426 -10.963 37.682 -4.985 1.251 3.604 C6Q 87Z 14 87Z O3B O5 O 0 1 N N N 27.620 -10.961 33.837 -3.670 -0.701 0.130 O3B 87Z 15 87Z PB P1 P 0 1 N N N 26.214 -10.150 33.666 -2.803 -2.044 0.317 PB 87Z 16 87Z O1B O6 O 0 1 N N N 25.633 -9.666 35.004 -3.298 -3.154 -0.739 O1B 87Z 17 87Z O2B O7 O 0 1 N N N 25.339 -11.034 32.782 -2.982 -2.559 1.694 O2B 87Z 18 87Z O3A O8 O 0 1 N N N 26.782 -8.915 32.734 -1.247 -1.719 0.064 O3A 87Z 19 87Z PA P2 P 0 1 N N N 26.089 -7.495 32.372 0.125 -2.500 0.379 PA 87Z 20 87Z O1A O9 O 0 1 N N N 24.991 -7.114 33.359 0.453 -2.395 1.952 O1A 87Z 21 87Z O2A O10 O 0 1 N N N 27.267 -6.541 32.207 -0.019 -3.923 -0.001 O2A 87Z 22 87Z "O5'" O11 O 0 1 N N N 25.346 -7.764 30.955 1.326 -1.838 -0.464 "O5'" 87Z 23 87Z "C5'" C10 C 0 1 N N N 26.092 -8.134 29.764 2.651 -2.371 -0.482 "C5'" 87Z 24 87Z "C4'" C11 C 0 1 N N R 25.589 -9.551 29.492 3.538 -1.505 -1.378 "C4'" 87Z 25 87Z "O4'" O12 O 0 1 N N N 24.271 -9.472 28.962 3.750 -0.207 -0.781 "O4'" 87Z 26 87Z "C3'" C12 C 0 1 N N S 26.342 -10.177 28.368 4.966 -2.100 -1.472 "C3'" 87Z 27 87Z "O3'" O13 O 0 1 N N N 27.491 -10.910 28.822 5.043 -3.079 -2.511 "O3'" 87Z 28 87Z "C2'" C13 C 0 1 N N N 25.346 -11.196 27.817 5.815 -0.854 -1.823 "C2'" 87Z 29 87Z "C1'" C14 C 0 1 N N R 24.014 -10.447 27.966 4.942 0.338 -1.372 "C1'" 87Z 30 87Z N1 N2 N 0 1 N N N 23.684 -9.743 26.699 5.666 1.140 -0.384 N1 87Z 31 87Z O2 O14 O 0 1 N N N 22.921 -11.641 25.841 5.649 -0.540 1.058 O2 87Z 32 87Z N3 N3 N 0 1 N N N 22.931 -9.918 24.485 6.645 1.318 1.736 N3 87Z 33 87Z C6 C15 C 0 1 N N N 24.021 -8.418 26.491 6.022 2.427 -0.684 C6 87Z 34 87Z C5 C16 C 0 1 N N N 23.733 -7.826 25.270 6.690 3.166 0.227 C5 87Z 35 87Z C5M C17 C 0 1 N N N 24.070 -6.302 25.061 7.090 4.585 -0.086 C5M 87Z 36 87Z C4 C18 C 0 1 N N N 23.210 -8.627 24.254 7.014 2.589 1.479 C4 87Z 37 87Z O4 O15 O 0 1 N N N 22.978 -8.163 23.137 7.620 3.235 2.315 O4 87Z 38 87Z H1 H1 H 0 1 N N N 31.220 -15.869 31.324 -5.533 4.172 -4.082 H1 87Z 39 87Z H2 H2 H 0 1 N N N 31.815 -14.193 31.073 -7.071 3.841 -3.250 H2 87Z 40 87Z H3 H3 H 0 1 N N N 32.575 -15.239 32.320 -5.960 5.075 -2.609 H3 87Z 41 87Z H4 H4 H 0 1 N N N 31.970 -13.162 33.618 -6.538 3.300 -0.664 H4 87Z 42 87Z H5 H5 H 0 1 N N N 29.034 -13.021 34.141 -4.053 1.782 -0.421 H5 87Z 43 87Z H6 H6 H 0 1 N N N 30.323 -13.181 36.203 -4.876 3.048 1.526 H6 87Z 44 87Z H7 H7 H 0 1 N N N 31.760 -11.415 36.735 -6.959 2.358 2.470 H7 87Z 45 87Z H8 H8 H 0 1 N N N 30.873 -10.687 33.456 -6.792 0.431 -0.356 H8 87Z 46 87Z H9 H9 H 0 1 N N N 30.187 -11.999 31.662 -5.795 -0.782 -2.159 H9 87Z 47 87Z H10 H10 H 0 1 N N N 28.893 -9.357 33.588 -5.523 -1.612 0.197 H10 87Z 48 87Z H11 H11 H 0 1 N N N 28.260 -11.932 36.160 -3.641 0.955 1.947 H11 87Z 49 87Z H12 H12 H 0 1 N N N 29.532 -11.866 38.302 -6.061 1.277 3.779 H12 87Z 50 87Z H13 H13 H 0 1 N N N 30.341 -10.357 37.758 -4.539 0.458 4.204 H13 87Z 51 87Z H14 H14 H 0 1 N N N 28.566 -10.375 38.035 -4.548 2.209 3.884 H14 87Z 52 87Z H15 H15 H 0 1 N N N 24.751 -10.004 35.107 -3.210 -2.884 -1.663 H15 87Z 53 87Z H16 H16 H 0 1 N N N 25.203 -6.281 33.763 0.560 -1.489 2.272 H16 87Z 54 87Z H17 H17 H 0 1 N N N 27.175 -8.125 29.954 3.054 -2.378 0.531 H17 87Z 55 87Z H18 H18 H 0 1 N N N 25.862 -7.461 28.925 2.628 -3.390 -0.869 H18 87Z 56 87Z H19 H19 H 0 1 N N N 25.640 -10.167 30.402 3.098 -1.404 -2.370 H19 87Z 57 87Z H20 H20 H 0 1 N N N 26.603 -9.434 27.600 5.275 -2.525 -0.517 H20 87Z 58 87Z H21 H21 H 0 1 N N N 28.134 -10.306 29.173 5.917 -3.480 -2.609 H21 87Z 59 87Z H22 H22 H 0 1 N N N 25.353 -12.123 28.409 6.756 -0.866 -1.275 H22 87Z 60 87Z H23 H23 H 0 1 N N N 25.557 -11.433 26.764 5.998 -0.807 -2.897 H23 87Z 61 87Z H24 H24 H 0 1 N N N 23.212 -11.141 28.257 4.681 0.953 -2.233 H24 87Z 62 87Z H25 H25 H 0 1 N N N 22.570 -10.473 23.736 6.863 0.916 2.592 H25 87Z 63 87Z H26 H26 H 0 1 N N N 24.504 -7.849 27.272 5.771 2.848 -1.646 H26 87Z 64 87Z H27 H27 H 0 1 N N N 24.468 -5.882 25.997 6.293 5.263 0.220 H27 87Z 65 87Z H28 H28 H 0 1 N N N 24.821 -6.199 24.264 8.004 4.832 0.453 H28 87Z 66 87Z H29 H29 H 0 1 N N N 23.156 -5.760 24.776 7.261 4.686 -1.158 H29 87Z 67 # # 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 87Z O4 C4 DOUB N N 1 87Z C4 N3 SING N N 2 87Z C4 C5 SING N N 3 87Z N3 C2 SING N N 4 87Z C5M C5 SING N N 5 87Z C5 C6 DOUB N N 6 87Z C2 O2 DOUB N N 7 87Z C2 N1 SING N N 8 87Z C6 N1 SING N N 9 87Z N1 "C1'" SING N N 10 87Z "C2'" "C1'" SING N N 11 87Z "C2'" "C3'" SING N N 12 87Z "C1'" "O4'" SING N N 13 87Z "C3'" "O3'" SING N N 14 87Z "C3'" "C4'" SING N N 15 87Z "O4'" "C4'" SING N N 16 87Z "C4'" "C5'" SING N N 17 87Z "C5'" "O5'" SING N N 18 87Z "O5'" PA SING N N 19 87Z C3M C3 SING N N 20 87Z O2Q C2Q SING N N 21 87Z O2A PA DOUB N N 22 87Z PA O3A SING N N 23 87Z PA O1A SING N N 24 87Z O3A PB SING N N 25 87Z O2B PB DOUB N N 26 87Z C3 O3 DOUB N N 27 87Z C3 N3Q SING N N 28 87Z C2Q C1Q SING N N 29 87Z C2Q C3Q SING N N 30 87Z N3Q C3Q SING N N 31 87Z PB O3B SING N N 32 87Z PB O1B SING N N 33 87Z O3B C1Q SING N N 34 87Z C1Q O5Q SING N N 35 87Z C3Q C4Q SING N N 36 87Z O5Q C5Q SING N N 37 87Z C4Q O4Q SING N N 38 87Z C4Q C5Q SING N N 39 87Z C5Q C6Q SING N N 40 87Z C3M H1 SING N N 41 87Z C3M H2 SING N N 42 87Z C3M H3 SING N N 43 87Z N3Q H4 SING N N 44 87Z C3Q H5 SING N N 45 87Z C4Q H6 SING N N 46 87Z O4Q H7 SING N N 47 87Z C2Q H8 SING N N 48 87Z O2Q H9 SING N N 49 87Z C1Q H10 SING N N 50 87Z C5Q H11 SING N N 51 87Z C6Q H12 SING N N 52 87Z C6Q H13 SING N N 53 87Z C6Q H14 SING N N 54 87Z O1B H15 SING N N 55 87Z O1A H16 SING N N 56 87Z "C5'" H17 SING N N 57 87Z "C5'" H18 SING N N 58 87Z "C4'" H19 SING N N 59 87Z "C3'" H20 SING N N 60 87Z "O3'" H21 SING N N 61 87Z "C2'" H22 SING N N 62 87Z "C2'" H23 SING N N 63 87Z "C1'" H24 SING N N 64 87Z N3 H25 SING N N 65 87Z C6 H26 SING N N 66 87Z C5M H27 SING N N 67 87Z C5M H28 SING N N 68 87Z C5M H29 SING N N 69 # # 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 87Z SMILES ACDLabs 12.01 "CC1=CN(C(=O)NC1=O)C1CC(O)C(O1)COP(=O)(O)OP(=O)(O)OC1OC(C)C(O)C(NC(C)=O)C1O" 87Z InChI InChI 1.03 "InChI=1S/C18H29N3O15P2/c1-7-5-21(18(27)20-16(7)26)12-4-10(23)11(34-12)6-32-37(28,29)36-38(30,31)35-17-15(25)13(19-9(3)22)14(24)8(2)33-17/h5,8,10-15,17,23-25H,4,6H2,1-3H3,(H,19,22)(H,28,29)(H,30,31)(H,20,26,27)/t8-,10+,11-,12-,13+,14+,15-,17-/m1/s1" 87Z InChIKey InChI 1.03 CWQDRZJUANNJKC-HYPDDMKDSA-N 87Z SMILES_CANONICAL CACTVS 3.385 "C[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@@H](NC(C)=O)[C@H]1O" 87Z SMILES CACTVS 3.385 "C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH](NC(C)=O)[CH]1O" 87Z SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H]1[C@@H]([C@@H]([C@H]([C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)NC(=O)C)O" 87Z SMILES "OpenEye OEToolkits" 2.0.7 "CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)NC(=O)C)O" # # 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 87Z "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,3R,4S,5R,6R)-4-acetamido-3,5-dihydroxy-6-methyloxan-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)oxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)" 87Z "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{R},4~{S},5~{R},6~{R})-4-acetamido-6-methyl-3,5-bis(oxidanyl)oxan-2-yl] [[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 87Z "Create component" 2021-09-09 RCSB 87Z "Initial release" 2021-09-22 RCSB ##