data_87E # _chem_comp.id 87E _chem_comp.name "(2S)-2-[[(2R)-2-[(2R,3R,4R,5S,6R)-3-acetamido-2-[[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-6-(hydroxymethyl)-5-oxidanyl-oxan-4-yl]oxypropanoyl]amino]-3-oxidanyl-propanoic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C23 H36 N4 O21 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "Uridine-5'-diphosphate-n-acetylmuramoyl-L-Serine" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-11-26 _chem_comp.pdbx_modified_date 2021-12-24 _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 766.494 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 87E _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 7W1G _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 87E N1 N1 N 0 1 N N N 15.587 11.637 15.442 8.136 1.583 2.983 N1 87E 1 87E C2 C1 C 0 1 N N N 15.759 10.379 15.857 7.325 2.062 2.022 C2 87E 2 87E O2 O1 O 0 1 N N N 17.084 10.014 16.253 6.920 3.206 2.094 O2 87E 3 87E N3 N2 N 0 1 N N N 9.687 6.200 8.719 -3.907 -0.695 -0.956 N3 87E 4 87E C4 C2 C 0 1 N N N 13.279 11.215 15.033 8.222 -0.500 1.822 C4 87E 5 87E O4 O2 O 0 1 N N N 14.211 8.078 18.720 7.538 3.149 -1.521 O4 87E 6 87E C5 C3 C 0 1 N N R 14.878 8.122 16.256 6.072 1.842 -0.050 C5 87E 7 87E C6 C4 C 0 1 N N R 13.762 7.619 17.388 6.807 1.926 -1.411 C6 87E 8 87E P1 P1 P 0 1 N N N 10.356 7.074 14.643 2.062 -1.847 -2.095 P1 87E 9 87E P2 P2 P 0 1 N N N 10.721 7.918 11.881 -0.561 -2.969 -1.292 P2 87E 10 87E C1 C5 C 0 1 N N N 14.376 12.069 15.039 8.598 0.318 2.914 C1 87E 11 87E O1 O3 O 0 1 N N N 14.238 13.190 14.684 9.333 -0.116 3.783 O1 87E 12 87E N2 N3 N 0 1 N N N 14.716 9.505 15.867 6.956 1.293 0.981 N2 87E 13 87E C3 C6 C 0 1 N N N 13.462 9.896 15.450 7.399 0.003 0.877 C3 87E 14 87E O3 O4 O 0 1 N N N 14.709 7.320 15.203 4.974 0.942 -0.315 O3 87E 15 87E N4 N4 N 0 1 N N N 5.072 5.978 5.991 -5.187 3.314 1.049 N4 87E 16 87E O5 O5 O 0 1 N N N 14.875 5.700 17.950 5.296 3.217 -2.839 O5 87E 17 87E O6 O6 O 0 1 N N N 12.016 7.052 14.928 2.840 -0.515 -1.631 O6 87E 18 87E C7 C7 C 0 1 N N S 13.714 6.371 17.262 5.632 1.893 -2.418 C7 87E 19 87E O7 O7 O 0 1 N N N 10.099 8.175 13.400 0.760 -2.056 -1.172 O7 87E 20 87E C8 C8 C 0 1 N N R 13.962 6.100 15.687 4.470 1.269 -1.621 C8 87E 21 87E O8 O8 O 0 1 N N N 9.755 5.785 14.309 1.648 -1.710 -3.509 O8 87E 22 87E C9 C9 C 0 1 N N N 12.773 5.842 14.965 3.980 0.001 -2.322 C9 87E 23 87E O9 O9 O 0 1 N N N 9.661 7.503 15.859 3.038 -3.118 -1.942 O9 87E 24 87E C10 C10 C 0 1 N N R 8.885 6.248 11.012 -3.046 -2.893 -0.312 C10 87E 25 87E O10 O10 O 0 1 N N N 11.791 6.916 11.895 -0.218 -4.472 -0.828 O10 87E 26 87E C11 C11 C 0 1 N N R 6.564 7.013 11.571 -2.790 -3.476 2.000 C11 87E 27 87E O11 O11 O 0 1 N N N 11.373 9.177 11.406 -1.027 -2.980 -2.697 O11 87E 28 87E C12 C12 C 0 1 N N S 6.169 6.529 10.180 -3.765 -2.378 2.435 C12 87E 29 87E O12 O12 O 0 1 N N N 9.454 7.474 10.920 -1.717 -2.367 -0.347 O12 87E 30 87E C13 C13 C 0 1 N N R 7.291 6.763 9.194 -3.708 -1.228 1.425 C13 87E 31 87E O13 O13 O 0 1 N N N 7.732 6.252 12.008 -3.127 -3.916 0.683 O13 87E 32 87E C14 C14 C 0 1 N N R 8.444 5.919 9.587 -4.030 -1.772 0.029 C14 87E 33 87E O14 O14 O 0 1 N N N 6.729 6.377 7.883 -4.668 -0.231 1.782 O14 87E 34 87E C15 C15 C 0 1 N N N 5.410 6.797 12.548 -2.885 -4.655 2.971 C15 87E 35 87E O15 O15 O 0 1 N N N 4.965 7.132 9.722 -3.396 -1.897 3.729 O15 87E 36 87E C16 C16 C 0 1 N N R 7.070 7.161 6.816 -4.208 1.110 1.599 C16 87E 37 87E O16 O16 O 0 1 N N N 4.972 5.453 12.402 -1.895 -5.630 2.634 O16 87E 38 87E C17 C17 C 0 1 N N N 6.406 6.509 5.643 -5.387 2.016 1.350 C17 87E 39 87E O17 O17 O 0 1 N N N 6.960 6.555 4.612 -6.515 1.576 1.421 O17 87E 40 87E C18 C18 C 0 1 N N N 6.209 8.443 6.880 -3.467 1.571 2.856 C18 87E 41 87E O18 O18 O 0 1 N N N 10.239 3.975 8.680 -5.365 -1.676 -2.311 O18 87E 42 87E C19 C19 C 0 1 N N N 10.546 5.088 8.316 -4.620 -0.742 -2.099 C19 87E 43 87E O19 O19 O 0 1 N N N 2.380 6.920 5.424 -7.801 4.796 -1.084 O19 87E 44 87E C20 C20 C 0 1 N N N 11.803 5.397 7.436 -4.493 0.366 -3.113 C20 87E 45 87E O20 O20 O 0 1 N N N 3.149 6.500 3.337 -6.172 3.332 -1.380 O20 87E 46 87E C21 C21 C 0 1 N N S 4.056 5.331 5.181 -6.333 4.194 0.808 C21 87E 47 87E O21 O21 O 0 1 N N N 2.718 3.419 5.525 -4.934 6.061 0.174 O21 87E 48 87E C22 C22 C 0 1 N N N 3.120 6.348 4.581 -6.762 4.076 -0.632 C22 87E 49 87E C23 C23 C 0 1 N N N 3.122 4.615 6.150 -5.936 5.642 1.104 C23 87E 50 87E H1 H1 H 0 1 N N N 16.365 12.265 15.430 8.393 2.152 3.726 H1 87E 51 87E H2 H2 H 0 1 N N N 9.903 7.134 8.434 -3.312 0.052 -0.787 H2 87E 52 87E H3 H3 H 0 1 N N N 12.308 11.564 14.713 8.582 -1.516 1.750 H3 87E 53 87E H4 H4 H 0 1 N N N 13.586 7.800 19.379 8.016 3.249 -2.356 H4 87E 54 87E H5 H5 H 0 1 N N N 15.872 7.982 16.706 5.701 2.823 0.247 H5 87E 55 87E H6 H6 H 0 1 N N N 12.809 8.109 17.139 7.465 1.069 -1.552 H6 87E 56 87E H7 H7 H 0 1 N N N 12.639 9.197 15.446 7.101 -0.607 0.037 H7 87E 57 87E H8 H8 H 0 1 N N N 4.826 6.083 6.954 -4.285 3.666 0.993 H8 87E 58 87E H9 H9 H 0 1 N N N 14.798 5.818 18.890 6.013 3.678 -3.295 H9 87E 59 87E H10 H10 H 0 1 N N N 12.763 5.908 17.564 5.883 1.272 -3.278 H10 87E 60 87E H11 H11 H 0 1 N N N 14.634 5.232 15.612 3.653 1.986 -1.534 H11 87E 61 87E H12 H12 H 0 1 N N N 12.194 5.053 15.467 4.774 -0.746 -2.319 H12 87E 62 87E H13 H13 H 0 1 N N N 13.018 5.522 13.942 3.706 0.236 -3.350 H13 87E 63 87E H14 H14 H 0 1 N N N 9.019 6.848 16.105 3.349 -3.269 -1.039 H14 87E 64 87E H15 H15 H 0 1 N N N 9.621 5.496 11.332 -3.297 -3.313 -1.286 H15 87E 65 87E H16 H16 H 0 1 N N N 12.603 7.315 11.606 0.095 -4.541 0.084 H16 87E 66 87E H17 H17 H 0 1 N N N 6.805 8.085 11.527 -1.774 -3.083 2.004 H17 87E 67 87E H18 H18 H 0 1 N N N 6.012 5.442 10.246 -4.777 -2.782 2.471 H18 87E 68 87E H19 H19 H 0 1 N N N 7.576 7.826 9.193 -2.710 -0.791 1.425 H19 87E 69 87E H20 H20 H 0 1 N N N 8.180 4.854 9.517 -5.047 -2.163 0.016 H20 87E 70 87E H21 H21 H 0 1 N N N 5.753 6.970 13.579 -2.715 -4.302 3.988 H21 87E 71 87E H22 H22 H 0 1 N N N 4.586 7.488 12.315 -3.875 -5.104 2.903 H22 87E 72 87E H23 H23 H 0 1 N N N 4.272 6.975 10.353 -3.406 -2.576 4.418 H23 87E 73 87E H24 H24 H 0 1 N N N 8.142 7.362 6.673 -3.533 1.149 0.745 H24 87E 74 87E H25 H25 H 0 1 N N N 4.252 5.288 12.999 -1.897 -6.407 3.209 H25 87E 75 87E H26 H26 H 0 1 N N N 6.555 9.077 7.710 -2.667 0.868 3.084 H26 87E 76 87E H27 H27 H 0 1 N N N 6.303 8.995 5.933 -3.044 2.561 2.686 H27 87E 77 87E H28 H28 H 0 1 N N N 5.156 8.170 7.042 -4.164 1.613 3.694 H28 87E 78 87E H29 H29 H 0 1 N N N 1.801 7.527 4.978 -8.039 4.687 -2.015 H29 87E 79 87E H30 H30 H 0 1 N N N 12.336 4.460 7.216 -5.141 0.155 -3.964 H30 87E 80 87E H31 H31 H 0 1 N N N 11.484 5.867 6.494 -4.788 1.311 -2.657 H31 87E 81 87E H32 H32 H 0 1 N N N 12.472 6.081 7.979 -3.459 0.432 -3.451 H32 87E 82 87E H33 H33 H 0 1 N N N 4.472 4.648 4.426 -7.158 3.904 1.458 H33 87E 83 87E H34 H34 H 0 1 N N N 2.132 2.942 6.101 -4.634 6.971 0.303 H34 87E 84 87E H35 H35 H 0 1 N N N 3.651 4.391 7.088 -6.811 6.285 1.010 H35 87E 85 87E H36 H36 H 0 1 N N N 2.245 5.244 6.364 -5.542 5.710 2.118 H36 87E 86 # # 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 87E O20 C22 DOUB N N 1 87E C22 C21 SING N N 2 87E C22 O19 SING N N 3 87E O17 C17 DOUB N N 4 87E C21 N4 SING N N 5 87E C21 C23 SING N N 6 87E O21 C23 SING N N 7 87E C17 N4 SING N N 8 87E C17 C16 SING N N 9 87E C16 C18 SING N N 10 87E C16 O14 SING N N 11 87E C20 C19 SING N N 12 87E O14 C13 SING N N 13 87E C19 O18 DOUB N N 14 87E C19 N3 SING N N 15 87E N3 C14 SING N N 16 87E C13 C14 SING N N 17 87E C13 C12 SING N N 18 87E C14 C10 SING N N 19 87E O15 C12 SING N N 20 87E C12 C11 SING N N 21 87E O12 C10 SING N N 22 87E O12 P2 SING N N 23 87E C10 O13 SING N N 24 87E O11 P2 DOUB N N 25 87E C11 O13 SING N N 26 87E C11 C15 SING N N 27 87E P2 O10 SING N N 28 87E P2 O7 SING N N 29 87E O16 C15 SING N N 30 87E O7 P1 SING N N 31 87E O8 P1 DOUB N N 32 87E P1 O6 SING N N 33 87E P1 O9 SING N N 34 87E O1 C1 DOUB N N 35 87E O6 C9 SING N N 36 87E C9 C8 SING N N 37 87E C4 C1 SING N N 38 87E C4 C3 DOUB N N 39 87E C1 N1 SING N N 40 87E O3 C8 SING N N 41 87E O3 C5 SING N N 42 87E N1 C2 SING N N 43 87E C3 N2 SING N N 44 87E C8 C7 SING N N 45 87E C2 N2 SING N N 46 87E C2 O2 DOUB N N 47 87E N2 C5 SING N N 48 87E C5 C6 SING N N 49 87E C7 C6 SING N N 50 87E C7 O5 SING N N 51 87E C6 O4 SING N N 52 87E N1 H1 SING N N 53 87E N3 H2 SING N N 54 87E C4 H3 SING N N 55 87E O4 H4 SING N N 56 87E C5 H5 SING N N 57 87E C6 H6 SING N N 58 87E C3 H7 SING N N 59 87E N4 H8 SING N N 60 87E O5 H9 SING N N 61 87E C7 H10 SING N N 62 87E C8 H11 SING N N 63 87E C9 H12 SING N N 64 87E C9 H13 SING N N 65 87E O9 H14 SING N N 66 87E C10 H15 SING N N 67 87E O10 H16 SING N N 68 87E C11 H17 SING N N 69 87E C12 H18 SING N N 70 87E C13 H19 SING N N 71 87E C14 H20 SING N N 72 87E C15 H21 SING N N 73 87E C15 H22 SING N N 74 87E O15 H23 SING N N 75 87E C16 H24 SING N N 76 87E O16 H25 SING N N 77 87E C18 H26 SING N N 78 87E C18 H27 SING N N 79 87E C18 H28 SING N N 80 87E O19 H29 SING N N 81 87E C20 H30 SING N N 82 87E C20 H31 SING N N 83 87E C20 H32 SING N N 84 87E C21 H33 SING N N 85 87E O21 H34 SING N N 86 87E C23 H35 SING N N 87 87E C23 H36 SING N N 88 # # 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 87E InChI InChI 1.03 "InChI=1S/C23H36N4O21P2/c1-8(19(35)25-10(5-28)21(36)37)44-18-14(24-9(2)30)22(46-11(6-29)16(18)33)47-50(41,42)48-49(39,40)43-7-12-15(32)17(34)20(45-12)27-4-3-13(31)26-23(27)38/h3-4,8,10-12,14-18,20,22,28-29,32-34H,5-7H2,1-2H3,(H,24,30)(H,25,35)(H,36,37)(H,39,40)(H,41,42)(H,26,31,38)/t8-,10+,11-,12-,14-,15-,16-,17-,18-,20-,22-/m1/s1" 87E InChIKey InChI 1.03 IACRIBHKJKCIBJ-KWWGHZHGSA-N 87E SMILES_CANONICAL CACTVS 3.385 "C[C@@H](O[C@H]1[C@H](O)[C@@H](CO)O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@@H]1NC(C)=O)C(=O)N[C@@H](CO)C(O)=O" 87E SMILES CACTVS 3.385 "C[CH](O[CH]1[CH](O)[CH](CO)O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH]1NC(C)=O)C(=O)N[CH](CO)C(O)=O" 87E SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@H](C(=O)N[C@@H](CO)C(=O)O)O[C@@H]1[C@H]([C@H](O[C@@H]([C@H]1O)CO)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C" 87E SMILES "OpenEye OEToolkits" 2.0.7 "CC(C(=O)NC(CO)C(=O)O)OC1C(C(OC(C1O)CO)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C" # _pdbx_chem_comp_identifier.comp_id 87E _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "(2~{S})-2-[[(2~{R})-2-[(2~{R},3~{R},4~{R},5~{S},6~{R})-3-acetamido-2-[[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-6-(hydroxymethyl)-5-oxidanyl-oxan-4-yl]oxypropanoyl]amino]-3-oxidanyl-propanoic acid" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 87E _pdbx_chem_comp_synonyms.name "Uridine-5'-diphosphate-n-acetylmuramoyl-L-Serine" _pdbx_chem_comp_synonyms.provenance AUTHOR _pdbx_chem_comp_synonyms.type ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 87E "Create component" 2021-11-26 PDBJ 87E "Initial release" 2021-12-29 RCSB ##