data_U5F # _chem_comp.id U5F _chem_comp.name "5'-O-[(R)-hydroxy{[(S)-hydroxy{[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]uridine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H17 N2 O21 P5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-07-22 _chem_comp.pdbx_modified_date 2019-11-01 _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 644.101 _chem_comp.one_letter_code ? _chem_comp.three_letter_code U5F _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 6PVX _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 U5F "C1'" C1 C 0 1 N N R -12.789 -17.593 11.761 5.955 0.926 -0.905 "C1'" U5F 1 U5F C2 C2 C 0 1 N N N -14.787 -18.909 11.353 6.639 3.079 -0.007 C2 U5F 2 U5F C4 C3 C 0 1 N N N -15.097 -21.058 12.223 7.535 3.321 2.138 C4 U5F 3 U5F "C4'" C4 C 0 1 N N R -10.643 -16.956 12.578 4.711 -0.951 -1.352 "C4'" U5F 4 U5F C5 C5 C 0 1 N N N -13.827 -20.977 12.851 7.405 1.925 2.337 C5 U5F 5 U5F "C5'" C6 C 0 1 N N N -9.675 -17.708 13.490 3.950 -2.114 -0.711 "C5'" U5F 6 U5F C6 C7 C 0 1 N N N -13.091 -19.853 12.688 6.893 1.165 1.346 C6 U5F 7 U5F N1 N1 N 0 1 N N N -13.582 -18.815 11.933 6.510 1.751 0.171 N1 U5F 8 U5F N3 N2 N 0 1 N N N -15.541 -20.020 11.486 7.146 3.860 0.965 N3 U5F 9 U5F O01 O1 O 0 1 N N N -6.504 -23.159 15.332 -3.848 -1.109 2.686 O01 U5F 10 U5F O02 O2 O 0 1 N N N -12.322 -25.510 13.827 -8.503 1.722 -1.614 O02 U5F 11 U5F O03 O3 O 0 1 N N N -7.825 -24.848 13.995 -4.778 -2.302 0.665 O03 U5F 12 U5F O04 O4 O 0 1 N N N -8.733 -22.815 12.715 -1.535 -3.451 1.441 O04 U5F 13 U5F O05 O5 O 0 1 N N N -10.954 -22.155 13.684 -1.908 -3.393 -1.055 O05 U5F 14 U5F O06 O6 O 0 1 N N N -10.262 -25.168 15.395 -6.206 1.957 -0.594 O06 U5F 15 U5F O1A O7 O 0 1 N N N -8.517 -19.038 15.776 1.458 -3.998 -0.622 O1A U5F 16 U5F O1B O8 O 0 1 N N N -9.665 -26.377 17.542 -6.453 1.413 1.967 O1B U5F 17 U5F O1G O9 O 0 1 N N N -12.387 -26.288 16.226 -6.927 3.378 -2.685 O1G U5F 18 U5F O2 O10 O 0 1 N N N -15.197 -17.973 10.695 6.297 3.578 -1.061 O2 U5F 19 U5F O2A O11 O 0 1 N N N -10.486 -20.626 15.893 1.879 -3.019 1.666 O2A U5F 20 U5F O2B O12 O 0 1 N N N -8.460 -27.128 15.453 -7.049 -0.287 0.198 O2B U5F 21 U5F O2G O13 O 0 1 N N N -7.964 -24.797 16.594 -4.598 0.213 0.541 O2G U5F 22 U5F O3A O14 O 0 1 N N N -8.842 -20.579 13.798 0.038 -2.030 0.070 O3A U5F 23 U5F O3B O15 O 0 1 N N N -9.000 -22.785 15.288 -2.463 -1.318 0.461 O3B U5F 24 U5F O3G O16 O 0 1 N N N -10.965 -27.610 14.610 -8.017 3.845 -0.339 O3G U5F 25 U5F O4 O17 O 0 1 N N N -15.787 -22.051 12.343 7.994 4.028 3.017 O4 U5F 26 U5F "O4'" O18 O 0 1 N N N -11.382 -17.921 11.791 4.848 0.138 -0.414 "O4'" U5F 27 U5F "O5'" O19 O 0 1 N N N -10.479 -18.593 14.268 2.583 -1.741 -0.522 "O5'" U5F 28 U5F P01 P1 P 0 1 N N N -7.800 -23.874 15.279 -3.940 -1.154 1.079 P01 U5F 29 U5F P02 P2 P 0 1 N N N -9.352 -22.109 13.857 -1.468 -2.567 0.255 P02 U5F 30 U5F PA P3 P 0 1 N N N -9.550 -19.708 14.955 1.489 -2.725 0.131 PA U5F 31 U5F PB P4 P 0 1 N N N -9.105 -25.890 16.261 -6.097 0.800 0.521 PB U5F 32 U5F PG P5 P 0 1 N N N -11.494 -26.155 15.051 -7.437 2.704 -1.314 PG U5F 33 U5F "C2'" C8 C 0 1 N N R -12.966 -16.862 13.115 6.997 -0.111 -1.380 "C2'" U5F 34 U5F "C3'" C9 C 0 1 N N S -11.662 -16.063 13.301 6.160 -1.374 -1.681 "C3'" U5F 35 U5F "O2'" O20 O 0 1 N N N -14.099 -15.999 13.145 7.655 0.348 -2.563 "O2'" U5F 36 U5F "O3'" O21 O 0 1 N N N -11.743 -14.807 12.623 6.275 -1.734 -3.059 "O3'" U5F 37 U5F H1 H1 H 0 1 N N N -13.095 -16.977 10.902 5.634 1.553 -1.737 H1 U5F 38 U5F H2 H2 H 0 1 N N N -10.052 -16.319 11.904 4.200 -0.615 -2.254 H2 U5F 39 U5F H3 H3 H 0 1 N N N -13.455 -21.797 13.448 7.710 1.475 3.270 H3 U5F 40 U5F H4 H4 H 0 1 N N N -8.949 -18.277 12.891 4.002 -2.985 -1.363 H4 U5F 41 U5F H5 H5 H 0 1 N N N -9.139 -17.004 14.143 4.398 -2.354 0.253 H5 U5F 42 U5F H6 H6 H 0 1 N N N -12.119 -19.772 13.151 6.786 0.098 1.481 H6 U5F 43 U5F H7 H7 H 0 1 N N N -16.433 -20.074 11.036 7.232 4.816 0.820 H7 U5F 44 U5F H8 H8 H 0 1 N N N -5.964 -23.427 14.598 -3.312 -0.380 3.029 H8 U5F 45 U5F H9 H9 H 0 1 N N N -11.174 -22.624 12.888 -1.889 -2.875 -1.872 H9 U5F 46 U5F H10 H10 H 0 1 N N N -9.525 -27.314 17.614 -5.869 2.132 2.243 H10 U5F 47 U5F H11 H11 H 0 1 N N N -13.253 -25.965 16.005 -7.618 3.846 -3.173 H11 U5F 48 U5F H12 H12 H 0 1 N N N -10.194 -20.560 16.794 1.918 -2.227 2.220 H12 U5F 49 U5F H13 H13 H 0 1 N N N -11.246 -27.794 13.721 -7.371 4.524 -0.100 H13 U5F 50 U5F H14 H14 H 0 1 N N N -13.037 -17.614 13.914 7.724 -0.310 -0.593 H14 U5F 51 U5F H15 H15 H 0 1 N N N -11.411 -15.957 14.367 6.471 -2.200 -1.042 H15 U5F 52 U5F H16 H16 H 0 1 N N N -14.156 -15.580 13.996 8.320 -0.265 -2.905 H16 U5F 53 U5F H17 H17 H 0 1 N N N -12.372 -14.248 13.064 7.165 -2.008 -3.321 H17 U5F 54 # # 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 U5F O2 C2 DOUB N N 1 U5F C2 N3 SING N N 2 U5F C2 N1 SING N N 3 U5F N3 C4 SING N N 4 U5F "C1'" "O4'" SING N N 5 U5F "C1'" N1 SING N N 6 U5F "C1'" "C2'" SING N N 7 U5F "O4'" "C4'" SING N N 8 U5F N1 C6 SING N N 9 U5F C4 O4 DOUB N N 10 U5F C4 C5 SING N N 11 U5F "C4'" "C3'" SING N N 12 U5F "C4'" "C5'" SING N N 13 U5F "O3'" "C3'" SING N N 14 U5F C6 C5 DOUB N N 15 U5F O04 P02 DOUB N N 16 U5F "C2'" "O2'" SING N N 17 U5F "C2'" "C3'" SING N N 18 U5F "C5'" "O5'" SING N N 19 U5F O05 P02 SING N N 20 U5F O3A P02 SING N N 21 U5F O3A PA SING N N 22 U5F O02 PG DOUB N N 23 U5F P02 O3B SING N N 24 U5F O03 P01 DOUB N N 25 U5F "O5'" PA SING N N 26 U5F O3G PG SING N N 27 U5F PA O1A DOUB N N 28 U5F PA O2A SING N N 29 U5F PG O06 SING N N 30 U5F PG O1G SING N N 31 U5F P01 O3B SING N N 32 U5F P01 O01 SING N N 33 U5F P01 O2G SING N N 34 U5F O06 PB SING N N 35 U5F O2B PB DOUB N N 36 U5F PB O2G SING N N 37 U5F PB O1B SING N N 38 U5F "C1'" H1 SING N N 39 U5F "C4'" H2 SING N N 40 U5F C5 H3 SING N N 41 U5F "C5'" H4 SING N N 42 U5F "C5'" H5 SING N N 43 U5F C6 H6 SING N N 44 U5F N3 H7 SING N N 45 U5F O01 H8 SING N N 46 U5F O05 H9 SING N N 47 U5F O1B H10 SING N N 48 U5F O1G H11 SING N N 49 U5F O2A H12 SING N N 50 U5F O3G H13 SING N N 51 U5F "C2'" H14 SING N N 52 U5F "C3'" H15 SING N N 53 U5F "O2'" H16 SING N N 54 U5F "O3'" H17 SING N N 55 # # 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 U5F SMILES ACDLabs 12.01 "C1(OC(C(C1O)O)COP(=O)(O)OP(=O)(O)OP(O)(=O)OP(OP(=O)(O)O)(O)=O)N2C(NC(=O)C=C2)=O" U5F InChI InChI 1.03 "InChI=1S/C9H17N2O21P5/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(28-8)3-27-34(19,20)30-36(23,24)32-37(25,26)31-35(21,22)29-33(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H,23,24)(H,25,26)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1" U5F InChIKey InChI 1.03 SPOOSPLWWBIUFN-XVFCMESISA-N U5F SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O" U5F SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O" U5F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O" U5F SMILES "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)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 U5F "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(R)-hydroxy{[(S)-hydroxy{[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]uridine" U5F "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(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] [oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-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 U5F "Create component" 2019-07-22 RCSB U5F "Initial release" 2019-11-06 RCSB ##