data_4RA # _chem_comp.id 4RA _chem_comp.name ;[(2R,3R,4R,5S,6R)-3-acetamido-6-methyl-5-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-4-oxidanyl-oxan-2-yl] [[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C25 H36 N5 O20 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-05-14 _chem_comp.pdbx_modified_date 2015-07-24 _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 819.496 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 4RA _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 4ZTC _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 4RA O2C O1 O 0 1 N N N 31.082 12.534 0.799 -6.441 -4.331 -1.743 O2C 4RA 1 4RA O3 O2 O 0 1 N N N 22.643 2.467 -7.422 2.669 -2.415 -0.115 O3 4RA 2 4RA C2 C1 C 0 1 Y N N 20.535 2.352 -8.311 4.189 -4.242 -0.307 C2 4RA 3 4RA C3 C2 C 0 1 Y N N 21.379 2.969 -7.433 3.942 -2.883 -0.167 C3 4RA 4 4RA C4 C3 C 0 1 Y N N 20.923 3.963 -6.579 5.031 -2.002 -0.081 C4 4RA 5 4RA C5 C4 C 0 1 Y N N 19.592 4.353 -6.649 6.322 -2.541 -0.140 C5 4RA 6 4RA C6 C5 C 0 1 Y N N 18.775 3.708 -7.586 6.472 -3.905 -0.280 C6 4RA 7 4RA C2C C6 C 0 1 N N N 32.016 11.759 1.152 -6.925 -4.203 -0.636 C2C 4RA 8 4RA N3C N1 N 0 1 N N N 33.216 12.271 1.408 -7.161 -5.295 0.115 N3C 4RA 9 4RA C4C C7 C 0 1 N N N 34.231 11.451 1.806 -7.697 -5.171 1.346 C4C 4RA 10 4RA O4C O3 O 0 1 N N N 35.342 11.949 2.033 -7.911 -6.159 2.026 O4C 4RA 11 4RA C5C C8 C 0 1 N N N 34.041 10.077 1.956 -8.010 -3.882 1.841 C5C 4RA 12 4RA C6C C9 C 0 1 N N N 32.771 9.565 1.694 -7.763 -2.804 1.067 C6C 4RA 13 4RA N1C N2 N 0 1 N N N 31.827 10.421 1.263 -7.213 -2.972 -0.175 N1C 4RA 14 4RA C1B C10 C 0 1 N N R 30.504 9.924 0.951 -6.940 -1.802 -1.013 C1B 4RA 15 4RA C2B C11 C 0 1 N N R 30.522 8.927 -0.210 -8.251 -1.050 -1.330 C2B 4RA 16 4RA "O2'" O4 O 0 1 N N N 30.877 9.417 -1.546 -8.736 -1.412 -2.625 "O2'" 4RA 17 4RA C3B C12 C 0 1 N N S 29.120 8.367 -0.031 -7.846 0.441 -1.301 C3B 4RA 18 4RA O3B O5 O 0 1 N N N 28.104 9.080 -0.757 -8.067 1.045 -2.577 O3B 4RA 19 4RA O4B O6 O 0 1 N N N 29.989 9.210 2.053 -6.131 -0.846 -0.293 O4B 4RA 20 4RA C4B C13 C 0 1 N N R 28.906 8.459 1.484 -6.337 0.413 -0.970 C4B 4RA 21 4RA C5B C14 C 0 1 N N N 28.894 7.074 2.118 -5.972 1.579 -0.049 C5B 4RA 22 4RA O5B O7 O 0 1 N N N 27.723 6.406 1.732 -4.557 1.603 0.151 O5B 4RA 23 4RA PA P1 P 0 1 N N N 27.764 4.817 1.374 -3.820 2.702 1.069 PA 4RA 24 4RA O1A O8 O 0 1 N N N 27.731 4.106 2.654 -4.282 2.518 2.601 O1A 4RA 25 4RA O2A O9 O 0 1 N N N 28.827 4.595 0.391 -4.185 4.058 0.604 O2A 4RA 26 4RA O3A O10 O 0 1 N N N 26.341 4.759 0.747 -2.226 2.508 0.962 O3A 4RA 27 4RA PB P2 P 0 1 N N N 25.551 3.475 0.279 -0.959 3.419 1.358 PB 4RA 28 4RA O2B O11 O 0 1 N N N 26.550 2.506 -0.175 -1.241 4.831 1.015 O2B 4RA 29 4RA O1B O12 O 0 1 N N N 24.512 3.077 1.329 -0.683 3.296 2.940 O1B 4RA 30 4RA "O1'" O13 O 0 1 N N N 24.737 4.102 -0.991 0.338 2.918 0.546 "O1'" 4RA 31 4RA "C1'" C15 C 0 1 N N R 25.424 4.692 -2.113 1.598 3.590 0.600 "C1'" 4RA 32 4RA "C2'" C16 C 0 1 N N R 24.713 5.964 -2.621 2.339 3.393 -0.724 "C2'" 4RA 33 4RA "N2'" N3 N 0 1 N N N 24.378 6.710 -1.373 1.513 3.892 -1.827 "N2'" 4RA 34 4RA "C7'" C17 C 0 1 N N N 25.187 7.645 -0.976 1.543 5.199 -2.153 "C7'" 4RA 35 4RA "C8'" C18 C 0 1 N N N 24.811 8.275 0.331 0.694 5.713 -3.287 "C8'" 4RA 36 4RA "O7'" O14 O 0 1 N N N 26.167 8.036 -1.621 2.255 5.962 -1.535 "O7'" 4RA 37 4RA "C3'" C19 C 0 1 N N S 23.501 5.581 -3.454 2.617 1.900 -0.928 "C3'" 4RA 38 4RA "O3'" O15 O 0 1 N N N 23.041 6.776 -4.061 3.371 1.714 -2.127 "O3'" 4RA 39 4RA "C4'" C20 C 0 1 N N S 23.926 4.594 -4.561 3.414 1.373 0.269 "C4'" 4RA 40 4RA "C5'" C21 C 0 1 N N R 24.556 3.338 -3.974 2.632 1.648 1.555 "C5'" 4RA 41 4RA "C6'" C22 C 0 1 N N N 25.155 2.383 -4.994 3.449 1.178 2.760 "C6'" 4RA 42 4RA "O5'" O16 O 0 1 N N N 25.612 3.655 -3.085 2.380 3.050 1.668 "O5'" 4RA 43 4RA "N4'" N4 N 0 1 N N N 22.837 4.120 -5.370 3.622 -0.070 0.121 "N4'" 4RA 44 4RA C4A C23 C 0 1 N N N 21.768 4.622 -5.616 4.822 -0.548 0.068 C4A 4RA 45 4RA C2A C24 C 0 1 N N N 20.999 1.263 -9.240 3.032 -5.203 -0.401 C2A 4RA 46 4RA N1 N5 N 0 1 Y N N 19.240 2.714 -8.356 5.422 -4.701 -0.363 N1 4RA 47 4RA C5A C25 C 0 1 N N N 18.968 5.407 -5.734 7.530 -1.645 -0.053 C5A 4RA 48 4RA O4P O17 O 0 1 N N N 19.631 6.676 -5.813 8.717 -2.436 -0.138 O4P 4RA 49 4RA P P3 P 0 1 N N N 19.424 7.716 -4.665 10.197 -1.805 -0.078 P 4RA 50 4RA O3P O18 O 0 1 N N N 20.540 7.419 -3.715 10.433 -0.868 -1.367 O3P 4RA 51 4RA O1P O19 O 0 1 N N N 19.700 9.054 -5.411 10.340 -0.995 1.153 O1P 4RA 52 4RA O2P O20 O 0 1 N N N 18.036 7.536 -4.091 11.286 -2.990 -0.070 O2P 4RA 53 4RA H1 H1 H 0 1 N N N 23.168 2.944 -6.790 2.303 -2.369 0.778 H1 4RA 54 4RA H2 H2 H 0 1 N N N 17.746 4.019 -7.691 7.464 -4.329 -0.327 H2 4RA 55 4RA H3 H3 H 0 1 N N N 33.374 13.253 1.309 -6.944 -6.175 -0.231 H3 4RA 56 4RA H4 H4 H 0 1 N N N 34.850 9.432 2.265 -8.440 -3.763 2.824 H4 4RA 57 4RA H5 H5 H 0 1 N N N 32.552 8.516 1.832 -7.995 -1.812 1.427 H5 4RA 58 4RA H6 H6 H 0 1 N N N 29.840 10.761 0.690 -6.441 -2.104 -1.934 H6 4RA 59 4RA H7 H7 H 0 1 N N N 31.230 8.129 0.058 -9.003 -1.256 -0.568 H7 4RA 60 4RA H8 H8 H 0 1 N N N 31.770 9.741 -1.538 -9.524 -0.925 -2.900 H8 4RA 61 4RA H9 H9 H 0 1 N N N 29.119 7.307 -0.325 -8.397 0.972 -0.525 H9 4RA 62 4RA H10 H10 H 0 1 N N N 27.416 8.477 -1.014 -8.991 1.035 -2.862 H10 4RA 63 4RA H11 H11 H 0 1 N N N 27.946 8.957 1.683 -5.747 0.452 -1.885 H11 4RA 64 4RA H12 H12 H 0 1 N N N 29.772 6.505 1.778 -6.291 2.516 -0.505 H12 4RA 65 4RA H13 H13 H 0 1 N N N 28.920 7.170 3.214 -6.473 1.454 0.911 H13 4RA 66 4RA H14 H14 H 0 1 N N N 28.477 3.521 2.711 -4.074 1.649 2.972 H14 4RA 67 4RA H15 H15 H 0 1 N N N 24.649 2.172 1.584 -0.491 2.396 3.236 H15 4RA 68 4RA H16 H16 H 0 1 N N N 26.418 5.009 -1.765 1.435 4.654 0.771 H16 4RA 69 4RA H17 H17 H 0 1 N N N 25.412 6.551 -3.234 3.282 3.940 -0.699 H17 4RA 70 4RA H18 H18 H 0 1 N N N 23.550 6.495 -0.855 0.944 3.282 -2.321 H18 4RA 71 4RA H19 H19 H 0 1 N N N 25.523 9.079 0.569 -0.357 5.520 -3.070 H19 4RA 72 4RA H20 H20 H 0 1 N N N 23.796 8.693 0.258 0.850 6.785 -3.402 H20 4RA 73 4RA H21 H21 H 0 1 N N N 24.838 7.515 1.125 0.973 5.204 -4.210 H21 4RA 74 4RA H22 H22 H 0 1 N N N 22.730 5.122 -2.817 1.673 1.361 -1.003 H22 4RA 75 4RA H23 H23 H 0 1 N N N 22.776 7.392 -3.388 3.583 0.790 -2.319 H23 4RA 76 4RA H24 H24 H 0 1 N N N 24.671 5.092 -5.199 4.379 1.878 0.314 H24 4RA 77 4RA H25 H25 H 0 1 N N N 23.773 2.795 -3.425 1.684 1.110 1.526 H25 4RA 78 4RA H26 H26 H 0 1 N N N 25.583 1.512 -4.475 4.396 1.717 2.789 H26 4RA 79 4RA H27 H27 H 0 1 N N N 24.370 2.047 -5.687 2.891 1.374 3.676 H27 4RA 80 4RA H28 H28 H 0 1 N N N 25.946 2.898 -5.558 3.641 0.109 2.674 H28 4RA 81 4RA H29 H29 H 0 1 N N N 21.455 5.535 -5.131 5.672 0.116 0.133 H29 4RA 82 4RA H30 H30 H 0 1 N N N 20.152 0.913 -9.848 2.750 -5.330 -1.446 H30 4RA 83 4RA H31 H31 H 0 1 N N N 21.786 1.655 -9.900 3.325 -6.167 0.016 H31 4RA 84 4RA H32 H32 H 0 1 N N N 21.399 0.424 -8.651 2.185 -4.808 0.159 H32 4RA 85 4RA H33 H33 H 0 1 N N N 17.915 5.542 -6.021 7.511 -0.929 -0.874 H33 4RA 86 4RA H34 H34 H 0 1 N N N 19.021 5.047 -4.696 7.517 -1.109 0.896 H34 4RA 87 4RA H35 H35 H 0 1 N N N 21.190 8.111 -3.763 10.355 -1.334 -2.211 H35 4RA 88 4RA H36 H36 H 0 1 N N N 17.512 8.305 -4.281 12.202 -2.683 -0.035 H36 4RA 89 # 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 4RA C2A C2 SING N N 1 4RA N1 C2 DOUB Y N 2 4RA N1 C6 SING Y N 3 4RA C2 C3 SING Y N 4 4RA C6 C5 DOUB Y N 5 4RA C3 O3 SING N N 6 4RA C3 C4 DOUB Y N 7 4RA C5 C4 SING Y N 8 4RA C5 C5A SING N N 9 4RA C4 C4A SING N N 10 4RA O4P C5A SING N N 11 4RA O4P P SING N N 12 4RA C4A "N4'" DOUB N N 13 4RA O1P P DOUB N N 14 4RA "N4'" "C4'" SING N N 15 4RA "C6'" "C5'" SING N N 16 4RA P O2P SING N N 17 4RA P O3P SING N N 18 4RA "C4'" "C5'" SING N N 19 4RA "C4'" "C3'" SING N N 20 4RA "O3'" "C3'" SING N N 21 4RA "C5'" "O5'" SING N N 22 4RA "C3'" "C2'" SING N N 23 4RA "O5'" "C1'" SING N N 24 4RA "C2'" "C1'" SING N N 25 4RA "C2'" "N2'" SING N N 26 4RA "C1'" "O1'" SING N N 27 4RA "O7'" "C7'" DOUB N N 28 4RA "O2'" C2B SING N N 29 4RA "N2'" "C7'" SING N N 30 4RA "O1'" PB SING N N 31 4RA "C7'" "C8'" SING N N 32 4RA O3B C3B SING N N 33 4RA C2B C3B SING N N 34 4RA C2B C1B SING N N 35 4RA O2B PB DOUB N N 36 4RA C3B C4B SING N N 37 4RA PB O3A SING N N 38 4RA PB O1B SING N N 39 4RA O2A PA DOUB N N 40 4RA O3A PA SING N N 41 4RA O2C C2C DOUB N N 42 4RA C1B N1C SING N N 43 4RA C1B O4B SING N N 44 4RA C2C N1C SING N N 45 4RA C2C N3C SING N N 46 4RA N1C C6C SING N N 47 4RA PA O5B SING N N 48 4RA PA O1A SING N N 49 4RA N3C C4C SING N N 50 4RA C4B O4B SING N N 51 4RA C4B C5B SING N N 52 4RA C6C C5C DOUB N N 53 4RA O5B C5B SING N N 54 4RA C4C C5C SING N N 55 4RA C4C O4C DOUB N N 56 4RA O3 H1 SING N N 57 4RA C6 H2 SING N N 58 4RA N3C H3 SING N N 59 4RA C5C H4 SING N N 60 4RA C6C H5 SING N N 61 4RA C1B H6 SING N N 62 4RA C2B H7 SING N N 63 4RA "O2'" H8 SING N N 64 4RA C3B H9 SING N N 65 4RA O3B H10 SING N N 66 4RA C4B H11 SING N N 67 4RA C5B H12 SING N N 68 4RA C5B H13 SING N N 69 4RA O1A H14 SING N N 70 4RA O1B H15 SING N N 71 4RA "C1'" H16 SING N N 72 4RA "C2'" H17 SING N N 73 4RA "N2'" H18 SING N N 74 4RA "C8'" H19 SING N N 75 4RA "C8'" H20 SING N N 76 4RA "C8'" H21 SING N N 77 4RA "C3'" H22 SING N N 78 4RA "O3'" H23 SING N N 79 4RA "C4'" H24 SING N N 80 4RA "C5'" H25 SING N N 81 4RA "C6'" H26 SING N N 82 4RA "C6'" H27 SING N N 83 4RA "C6'" H28 SING N N 84 4RA C4A H29 SING N N 85 4RA C2A H30 SING N N 86 4RA C2A H31 SING N N 87 4RA C2A H32 SING N N 88 4RA C5A H33 SING N N 89 4RA C5A H34 SING N N 90 4RA O3P H35 SING N N 91 4RA O2P H36 SING N N 92 # 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 4RA SMILES ACDLabs 12.01 "O=C1N(C=CC(N1)=O)C2OC(C(C2O)O)COP(O)(=O)OP(O)(=O)OC3C(NC(C)=O)C(O)C(C(O3)C)\N=C\c4c(O)c(C)ncc4COP(O)(O)=O" 4RA InChI InChI 1.03 ;InChI=1S/C25H36N5O20P3/c1-10-19(33)14(13(6-26-10)8-45-51(38,39)40)7-27-17-11(2)47-24(18(21(17)35)28-12(3)31)49-53(43,44)50-52(41,42)46-9-15-20(34)22(36)23(48-15)30-5-4-16(32)29-25(30)37/h4-7,11,15,17-18,20-24,33-36H,8-9H2,1-3H3,(H,28,31)(H,41,42)(H,43,44)(H,29,32,37)(H2,38,39,40)/b27-7+/t11-,15-,17-,18-,20-,21+,22-,23-,24-/m1/s1 ; 4RA InChIKey InChI 1.03 BKHPSAUTHKIVAK-OTBUILFPSA-N 4RA 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@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](NC(C)=O)[C@@H](O)[C@@H]1N=Cc4c(O)c(C)ncc4CO[P](O)(O)=O" 4RA SMILES CACTVS 3.385 "C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](NC(C)=O)[CH](O)[CH]1N=Cc4c(O)c(C)ncc4CO[P](O)(O)=O" 4RA SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)NC(=O)C)OP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)N4C=CC(=O)NC4=O)O)O)C)O" 4RA SMILES "OpenEye OEToolkits" 1.9.2 "Cc1c(c(c(cn1)COP(=O)(O)O)C=NC2C(OC(C(C2O)NC(=O)C)OP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)N4C=CC(=O)NC4=O)O)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 4RA "SYSTEMATIC NAME" ACDLabs 12.01 ;(2R,3R,4R,5S,6R)-3-(acetylamino)-4-hydroxy-5-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name) ; 4RA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 ;[(2R,3R,4R,5S,6R)-3-acetamido-6-methyl-5-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-4-oxidanyl-oxan-2-yl] [[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(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 4RA "Create component" 2015-05-14 RCSB 4RA "Modify name" 2015-06-03 RCSB 4RA "Initial release" 2015-07-29 RCSB #