data_O5W # _chem_comp.id O5W _chem_comp.name "[(3~{S},5~{R})-5-(6-azanyl-1-methyl-purin-9-yl)-2-(phosphonooxymethyl)oxolan-3-yl] [(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H28 N7 O13 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "[(1~{R},3~{R})-1-(6-azanyl-1-methyl-purin-9-yl)-1-oxidanyl-5-phosphonooxy-pentan-3-yl] [(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate" _chem_comp.pdbx_formal_charge -1 _chem_comp.pdbx_initial_date 2020-02-10 _chem_comp.pdbx_modified_date 2021-03-13 _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 648.434 _chem_comp.one_letter_code ? _chem_comp.three_letter_code O5W _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 6Y0Q _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # # 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 O5W C31 C1 C 0 1 N N N -16.868 -9.152 3.575 7.403 -0.918 1.695 C31 O5W 1 O5W C32 C2 C 0 1 N N N -17.951 -9.320 4.602 7.933 -2.105 2.060 C32 O5W 2 O5W C01 C3 C 0 1 N N N -1.186 -4.128 4.709 -7.392 -6.099 0.182 C01 O5W 3 O5W C03 C4 C 0 1 Y N N -2.935 -4.852 6.239 -7.187 -3.788 -0.484 C03 O5W 4 O5W C04 C5 C 0 1 Y N N -4.274 -5.273 6.475 -6.506 -2.560 -0.440 C04 O5W 5 O5W C05 C6 C 0 1 Y N N -5.114 -5.350 5.397 -5.340 -2.475 0.339 C05 O5W 6 O5W C07 C7 C 0 1 Y N N -6.228 -5.945 7.189 -5.751 -0.535 -0.624 C07 O5W 7 O5W C09 C8 C 0 1 N N R -7.470 -5.953 5.012 -3.693 -0.618 0.834 C09 O5W 8 O5W C10 C9 C 0 1 N N N -8.082 -7.407 5.125 -2.451 -0.924 -0.025 C10 O5W 9 O5W C11 C10 C 0 1 N N S -9.595 -7.108 4.873 -1.874 0.471 -0.368 C11 O5W 10 O5W C12 C11 C 0 1 N N R -9.832 -5.941 5.415 -2.492 1.360 0.741 C12 O5W 11 O5W C14 C12 C 0 1 N N N -10.322 -6.053 6.821 -2.567 2.818 0.284 C14 O5W 12 O5W C24 C13 C 0 1 N N N -12.414 -9.300 2.182 3.138 1.174 -1.849 C24 O5W 13 O5W C25 C14 C 0 1 N N R -13.701 -9.310 1.333 4.394 1.452 -1.020 C25 O5W 14 O5W C26 C15 C 0 1 N N S -14.452 -7.901 1.376 5.618 1.637 -1.943 C26 O5W 15 O5W C27 C16 C 0 1 N N N -15.857 -8.271 0.938 6.777 0.972 -1.167 C27 O5W 16 O5W C28 C17 C 0 1 N N R -16.011 -9.567 1.260 6.115 0.464 0.134 C28 O5W 17 O5W C33 C18 C 0 1 N N N -19.187 -10.082 4.260 7.741 -3.231 1.225 C33 O5W 18 O5W C35 C19 C 0 1 N N N -18.265 -10.488 1.911 6.516 -1.902 -0.255 C35 O5W 19 O5W C38 C20 C 0 1 N N N -17.790 -8.710 6.012 8.720 -2.228 3.339 C38 O5W 20 O5W C42 C21 C 0 1 Y N N -3.432 -4.648 3.961 -5.597 -4.681 0.932 C42 O5W 21 O5W N02 N1 N 1 1 Y N N -2.578 -4.560 4.980 -6.698 -4.809 0.213 N02 O5W 22 O5W N06 N2 N 0 1 Y N N -6.302 -5.772 5.868 -4.887 -1.188 0.204 N06 O5W 23 O5W N08 N3 N 0 1 Y N N -4.982 -5.647 7.579 -6.701 -1.342 -1.001 N08 O5W 24 O5W N30 N4 N 0 1 N N N -17.026 -9.726 2.246 6.691 -0.824 0.530 N30 O5W 25 O5W N34 N5 N 0 1 N N N -19.340 -10.658 2.933 7.034 -3.097 0.085 N34 O5W 26 O5W N41 N6 N 0 1 Y N N -4.689 -5.036 4.130 -4.927 -3.551 1.002 N41 O5W 27 O5W N43 N7 N 0 1 N N N -1.997 -4.751 7.344 -8.344 -3.930 -1.230 N43 O5W 28 O5W O13 O1 O 0 1 N N N -8.376 -5.120 5.412 -3.817 0.812 0.912 O13 O5W 29 O5W O15 O2 O 0 1 N N N -9.368 -6.767 7.567 -3.031 3.632 1.363 O15 O5W 30 O5W O17 O3 O 0 1 N N N -10.053 -6.625 10.054 -3.921 5.536 -0.036 O17 O5W 31 O5W O18 O4 O 0 1 N N N -8.829 -8.774 9.318 -4.118 5.754 2.471 O18 O5W 32 O5W O19 O5 O 0 1 N N N -11.229 -8.077 8.762 -1.910 5.891 1.257 O19 O5W 33 O5W O20 O6 O 0 1 N N N -9.774 -6.998 3.393 -0.447 0.468 -0.282 O20 O5W 34 O5W O22 O7 O 0 1 N N N -11.684 -5.648 2.188 -0.010 2.062 -2.190 O22 O5W 35 O5W O23 O8 O 0 1 N N N -11.583 -8.218 1.726 2.000 1.122 -0.987 O23 O5W 36 O5W O29 O9 O 0 1 N N N -14.564 -10.100 1.839 4.719 0.309 -0.199 O29 O5W 37 O5W O36 O10 O 0 1 N N N -18.394 -10.956 0.829 5.880 -1.796 -1.286 O36 O5W 38 O5W O37 O11 O 0 1 N N N -20.040 -10.216 5.071 8.210 -4.312 1.533 O37 O5W 39 O5W O39 O12 O 0 1 N N N -13.892 -7.024 0.522 5.886 3.025 -2.148 O39 O5W 40 O5W O40 O13 O 0 1 N N N -12.304 -6.947 3.877 0.528 -0.275 -2.489 O40 O5W 41 O5W P16 P1 P -1 1 N N N -9.873 -7.560 8.944 -3.231 5.225 1.236 P16 O5W 42 O5W P21 P2 P -1 1 N N N -11.343 -6.935 2.781 0.507 0.846 -1.523 P21 O5W 43 O5W H311 H1 H 0 0 N N N -15.971 -8.605 3.823 7.535 -0.048 2.322 H311 O5W 44 O5W H012 H2 H 0 0 N N N -1.066 -3.930 3.634 -7.001 -6.702 -0.637 H012 O5W 45 O5W H011 H3 H 0 0 N N N -0.970 -3.211 5.277 -7.232 -6.620 1.126 H011 O5W 46 O5W H013 H4 H 0 0 N N N -0.489 -4.922 5.016 -8.459 -5.934 0.035 H013 O5W 47 O5W H071 H5 H 0 0 N N N -7.033 -6.269 7.832 -5.662 0.499 -0.923 H071 O5W 48 O5W H091 H6 H 0 0 N N N -7.186 -5.785 3.963 -3.566 -1.036 1.832 H091 O5W 49 O5W H101 H7 H 0 0 N N N -7.669 -8.081 4.359 -1.727 -1.507 0.545 H101 O5W 50 O5W H102 H8 H 0 0 N N N -7.916 -7.840 6.122 -2.736 -1.452 -0.935 H102 O5W 51 O5W H111 H9 H 0 0 N N N -10.210 -7.923 5.282 -2.202 0.796 -1.355 H111 O5W 52 O5W H1 H11 H 0 1 N N N -10.544 -5.345 4.826 -1.918 1.277 1.664 H1 O5W 53 O5W H141 H12 H 0 0 N N N -10.453 -5.049 7.250 -1.577 3.154 -0.025 H141 O5W 54 O5W H142 H13 H 0 0 N N N -11.283 -6.588 6.838 -3.257 2.901 -0.556 H142 O5W 55 O5W H242 H14 H 0 0 N N N -12.668 -9.153 3.242 3.004 1.969 -2.582 H242 O5W 56 O5W H241 H15 H 0 0 N N N -11.881 -10.255 2.062 3.248 0.219 -2.364 H241 O5W 57 O5W H251 H16 H 0 0 N N N -13.448 -9.543 0.288 4.249 2.337 -0.400 H251 O5W 58 O5W H261 H17 H 0 0 N N N -14.465 -7.534 2.413 5.458 1.133 -2.896 H261 O5W 59 O5W H272 H18 H 0 0 N N N -16.598 -7.654 1.467 7.189 0.138 -1.736 H272 O5W 60 O5W H271 H19 H 0 0 N N N -15.970 -8.130 -0.147 7.554 1.702 -0.940 H271 O5W 61 O5W H281 H20 H 0 0 N N N -16.250 -10.173 0.373 6.238 1.195 0.932 H281 O5W 62 O5W H383 H21 H 0 0 N N N -18.681 -8.939 6.615 8.047 -2.487 4.157 H383 O5W 63 O5W H382 H22 H 0 0 N N N -16.900 -9.137 6.497 9.474 -3.007 3.229 H382 O5W 64 O5W H381 H23 H 0 0 N N N -17.674 -7.619 5.928 9.209 -1.278 3.558 H381 O5W 65 O5W H421 H24 H 0 0 N N N -3.090 -4.396 2.968 -5.234 -5.536 1.483 H421 O5W 66 O5W H341 H25 H 0 0 N N N -20.168 -11.170 2.704 6.898 -3.864 -0.493 H341 O5W 67 O5W H431 H26 H 0 0 N N N -1.056 -4.457 7.176 -8.694 -3.177 -1.730 H431 O5W 68 O5W H432 H27 H 0 0 N N N -2.292 -4.976 8.273 -8.806 -4.783 -1.252 H432 O5W 69 O5W H181 H29 H 0 0 N N N -9.300 -9.599 9.348 -4.279 6.708 2.460 H181 O5W 70 O5W H391 H31 H 0 0 N N N -14.356 -6.197 0.567 6.645 3.199 -2.721 H391 O5W 71 # # 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 O5W C31 C32 DOUB N N 1 O5W C31 N30 SING N N 2 O5W C32 C33 SING N N 3 O5W C32 C38 SING N N 4 O5W C01 N02 SING N N 5 O5W C03 C04 SING Y N 6 O5W C03 N02 DOUB Y N 7 O5W C03 N43 SING N N 8 O5W C04 C05 DOUB Y N 9 O5W C04 N08 SING Y N 10 O5W C05 N06 SING Y N 11 O5W C05 N41 SING Y N 12 O5W C07 N06 SING Y N 13 O5W C07 N08 DOUB Y N 14 O5W C09 C10 SING N N 15 O5W C09 N06 SING N N 16 O5W C09 O13 SING N N 17 O5W C10 C11 SING N N 18 O5W C11 C12 SING N N 19 O5W C11 O20 SING N N 20 O5W C12 C14 SING N N 21 O5W C14 O15 SING N N 22 O5W C24 C25 SING N N 23 O5W C24 O23 SING N N 24 O5W C25 C26 SING N N 25 O5W C25 O29 SING N N 26 O5W C26 C27 SING N N 27 O5W C26 O39 SING N N 28 O5W C27 C28 SING N N 29 O5W C28 N30 SING N N 30 O5W C28 O29 SING N N 31 O5W C33 N34 SING N N 32 O5W C33 O37 DOUB N N 33 O5W C35 N30 SING N N 34 O5W C35 N34 SING N N 35 O5W C35 O36 DOUB N N 36 O5W C42 N02 SING Y N 37 O5W C42 N41 DOUB Y N 38 O5W O15 P16 SING N N 39 O5W O17 P16 DOUB N N 40 O5W O18 P16 SING N N 41 O5W O19 P16 DOUB N N 42 O5W O20 P21 SING N N 43 O5W O22 P21 DOUB N N 44 O5W O23 P21 SING N N 45 O5W O40 P21 DOUB N N 46 O5W C31 H311 SING N N 47 O5W C01 H012 SING N N 48 O5W C01 H011 SING N N 49 O5W C01 H013 SING N N 50 O5W C07 H071 SING N N 51 O5W C09 H091 SING N N 52 O5W C10 H101 SING N N 53 O5W C10 H102 SING N N 54 O5W C11 H111 SING N N 55 O5W C12 H1 SING N N 56 O5W C14 H141 SING N N 57 O5W C14 H142 SING N N 58 O5W C24 H242 SING N N 59 O5W C24 H241 SING N N 60 O5W C25 H251 SING N N 61 O5W C26 H261 SING N N 62 O5W C27 H272 SING N N 63 O5W C27 H271 SING N N 64 O5W C28 H281 SING N N 65 O5W C38 H383 SING N N 66 O5W C38 H382 SING N N 67 O5W C38 H381 SING N N 68 O5W C42 H421 SING N N 69 O5W N34 H341 SING N N 70 O5W N43 H431 SING N N 71 O5W N43 H432 SING N N 72 O5W O18 H181 SING N N 73 O5W O39 H391 SING N N 74 O5W C12 O13 SING N N 75 # # 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 O5W InChI InChI 1.03 "InChI=1S/C21H27N7O13P2/c1-10-5-27(21(31)25-20(10)30)15-3-11(29)13(39-15)6-38-43(35,36)41-12-4-16(40-14(12)7-37-42(32,33)34)28-9-23-17-18(22)26(2)8-24-19(17)28/h5,8-9,11-16,22,29H,3-4,6-7H2,1-2H3,(H2,25,30,31,32,33,34)/q-2/p+1/t11-,12-,13+,14+,15+,16+/m0/s1" O5W InChIKey InChI 1.03 AESRSXSUEFZXFW-KPRKPIBOSA-O O5W SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P-](=O)(=O)O[C@H]3C[C@@H](O[C@@H]3CO[P-](O)(=O)=O)n4cnc5c(N)[n+](C)cnc45)O2)C(=O)NC1=O" O5W SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P-](=O)(=O)O[CH]3C[CH](O[CH]3CO[P-](O)(=O)=O)n4cnc5c(N)[n+](C)cnc45)O2)C(=O)NC1=O" O5W SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P-](=O)(=O)O[C@H]3C[C@@H](O[C@@H]3CO[P-](=O)(=O)O)n4cnc5c4nc[n+](c5N)C)O" O5W SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)CO[P-](=O)(=O)OC3CC(OC3CO[P-](=O)(=O)O)n4cnc5c4nc[n+](c5N)C)O" # _pdbx_chem_comp_identifier.comp_id O5W _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 "1-[(2~{R},4~{S},5~{R})-5-[[[(2~{R},3~{S},5~{R})-5-(6-azanyl-1-methyl-purin-1-ium-9-yl)-2-[[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxymethyl]oxolan-3-yl]oxy-bis(oxidanylidene)-$l^{6}-phosphanyl]oxymethyl]-4-oxidanyl-oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site O5W "Create component" 2020-02-10 PDBE O5W "Initial release" 2020-09-09 RCSB O5W "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id O5W _pdbx_chem_comp_synonyms.name "[(1~{R},3~{R})-1-(6-azanyl-1-methyl-purin-9-yl)-1-oxidanyl-5-phosphonooxy-pentan-3-yl] [(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##