data_B8N # _chem_comp.id B8N _chem_comp.name "(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C14 H22 N3 O11 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-09-25 _chem_comp.pdbx_modified_date 2018-01-19 _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 439.312 _chem_comp.one_letter_code ? _chem_comp.three_letter_code B8N _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 6EK0 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 B8N "O5'" O1 O 0 1 N N N 339.284 283.978 290.376 3.798 0.686 0.600 "O5'" B8N 1 B8N "C5'" C1 C 0 1 N N N 340.047 285.164 290.233 3.284 0.109 -0.602 "C5'" B8N 2 B8N "C4'" C2 C 0 1 N N R 339.638 286.199 291.244 2.751 -1.295 -0.307 "C4'" B8N 3 B8N "O4'" O2 O 0 1 N N N 338.423 285.769 291.895 1.597 -1.229 0.558 "O4'" B8N 4 B8N "C3'" C3 C 0 1 N N S 340.611 286.416 292.386 2.198 -1.951 -1.598 "C3'" B8N 5 B8N "O3'" O3 O 0 1 N N N 341.665 287.294 292.032 3.240 -2.607 -2.323 "O3'" B8N 6 B8N "C2'" C4 C 0 1 N N R 339.717 286.961 293.491 1.188 -2.978 -1.032 "C2'" B8N 7 B8N "O2'" O4 O 0 1 N N N 339.492 288.347 293.304 1.779 -4.278 -0.967 "O2'" B8N 8 B8N "C1'" C5 C 0 1 N N S 338.402 286.226 293.226 0.870 -2.456 0.382 "C1'" B8N 9 B8N C5 C6 C 0 1 N N N 338.193 285.074 294.133 -0.609 -2.199 0.513 C5 B8N 10 B8N C6 C7 C 0 1 N N N 338.428 283.783 293.692 -1.353 -2.912 1.386 C6 B8N 11 B8N N1 N1 N 0 1 N N N 338.238 282.737 294.495 -2.695 -2.666 1.492 N1 B8N 12 B8N C2 C8 C 0 1 N N N 337.780 282.899 295.808 -3.280 -1.720 0.735 C2 B8N 13 B8N N3 N2 N 0 1 N N N 337.508 284.163 296.324 -2.562 -0.994 -0.142 N3 B8N 14 B8N C4 C9 C 0 1 N N N 337.700 285.283 295.512 -1.237 -1.202 -0.272 C4 B8N 15 B8N C34 C10 C 0 1 N N N 335.151 286.748 298.555 -3.745 3.779 -0.389 C34 B8N 16 B8N CN1 C11 C 0 1 N N N 338.501 281.386 294.005 -3.502 -3.441 2.438 CN1 B8N 17 B8N N34 N3 N 0 1 N N N 336.195 285.123 300.076 -5.307 2.105 -1.205 N34 B8N 18 B8N O2 O5 O 0 1 N N N 337.613 281.903 296.528 -4.474 -1.518 0.846 O2 B8N 19 B8N O4 O6 O 0 1 N N N 337.474 286.429 295.942 -0.586 -0.542 -1.062 O4 B8N 20 B8N OP1 O7 O 0 1 N N N 338.710 281.633 289.724 5.532 2.264 -0.335 OP1 B8N 21 B8N OP2 O8 O 0 1 N N N 341.004 282.221 290.805 3.306 3.254 0.328 OP2 B8N 22 B8N P P1 P 0 1 N N N 339.864 282.581 289.896 4.440 2.161 0.660 P B8N 23 B8N C31 C12 C 0 1 N N N 337.051 284.293 297.700 -3.224 0.030 -0.955 CN31 B8N 24 B8N C32 C13 C 0 1 N N N 335.544 284.458 297.793 -3.192 1.368 -0.213 CN32 B8N 25 B8N C33 C14 C 0 1 N N R 335.194 285.320 298.995 -3.883 2.437 -1.062 CN33 B8N 26 B8N O36 O9 O 0 1 N N N 336.282 287.425 298.397 -2.602 4.473 -0.504 O341 B8N 27 B8N O35 O10 O 0 1 N N N 334.088 287.302 298.329 -4.663 4.229 0.254 O342 B8N 28 B8N H1 H1 H 0 1 N N N 341.111 284.925 290.375 2.476 0.731 -0.987 H1 B8N 29 B8N H2 H2 H 0 1 N N N 339.894 285.570 289.222 4.080 0.047 -1.345 H2 B8N 30 B8N H3 H3 H 0 1 N N N 339.470 287.157 290.731 3.529 -1.914 0.138 H3 B8N 31 B8N H4 H4 H 0 1 N N N 341.014 285.442 292.702 1.694 -1.214 -2.224 H4 B8N 32 B8N H5 H5 H 0 1 N N N 342.250 287.402 292.773 2.943 -3.033 -3.139 H5 B8N 33 B8N H6 H6 H 0 1 N N N 340.117 286.719 294.487 0.285 -3.001 -1.642 H6 B8N 34 B8N H7 H7 H 0 1 N N N 338.933 288.674 293.999 2.051 -4.629 -1.826 H7 B8N 35 B8N H8 H8 H 0 1 N N N 337.576 286.940 293.363 1.189 -3.185 1.127 H8 B8N 36 B8N H9 H9 H 0 1 N N N 338.771 283.621 292.681 -0.891 -3.674 1.996 H9 B8N 37 B8N H10 H10 H 0 1 N N N 338.289 280.658 294.802 -3.516 -2.934 3.403 H10 B8N 38 B8N H11 H11 H 0 1 N N N 337.856 281.178 293.139 -4.520 -3.529 2.059 H11 B8N 39 B8N H12 H12 H 0 1 N N N 339.556 281.304 293.705 -3.070 -4.434 2.556 H12 B8N 40 B8N H13 H13 H 0 1 N N N 335.955 285.694 300.861 -5.427 1.241 -1.711 H13 B8N 41 B8N H14 H14 H 0 1 N N N 336.202 284.162 300.353 -5.760 2.064 -0.305 H14 B8N 42 B8N H17 H17 H 0 1 N N N 340.844 281.368 291.192 2.559 3.244 0.941 H17 B8N 43 B8N H18 H18 H 0 1 N N N 337.343 283.390 298.257 -2.703 0.130 -1.907 H18 B8N 44 B8N H19 H19 H 0 1 N N N 337.532 285.174 298.151 -4.258 -0.262 -1.135 H19 B8N 45 B8N H20 H20 H 0 1 N N N 335.172 284.940 296.877 -3.713 1.267 0.739 H20 B8N 46 B8N H21 H21 H 0 1 N N N 335.074 283.469 297.903 -2.158 1.659 -0.033 H21 B8N 47 B8N H22 H22 H 0 1 N N N 334.200 285.027 299.364 -3.418 2.476 -2.047 H22 B8N 48 B8N H23 H23 H 0 1 N N N 336.085 288.309 298.109 -2.561 5.328 -0.054 H23 B8N 49 B8N OP3 OP3 O 0 1 N Y N 340.447 282.892 288.437 5.030 2.429 2.133 OP3 B8N 50 B8N H15 H15 H 0 1 N N N 339.944 282.416 287.786 5.434 3.301 2.242 H15 B8N 51 # 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 B8N OP1 P DOUB N N 1 B8N P "O5'" SING N N 2 B8N P OP2 SING N N 3 B8N "C5'" "O5'" SING N N 4 B8N "C5'" "C4'" SING N N 5 B8N "C4'" "O4'" SING N N 6 B8N "C4'" "C3'" SING N N 7 B8N "O4'" "C1'" SING N N 8 B8N "O3'" "C3'" SING N N 9 B8N "C3'" "C2'" SING N N 10 B8N "C1'" "C2'" SING N N 11 B8N "C1'" C5 SING N N 12 B8N "O2'" "C2'" SING N N 13 B8N C6 C5 DOUB N N 14 B8N C6 N1 SING N N 15 B8N CN1 N1 SING N N 16 B8N C5 C4 SING N N 17 B8N N1 C2 SING N N 18 B8N C4 O4 DOUB N N 19 B8N C4 N3 SING N N 20 B8N C2 N3 SING N N 21 B8N C2 O2 DOUB N N 22 B8N N3 C31 SING N N 23 B8N C31 C32 SING N N 24 B8N C32 C33 SING N N 25 B8N O35 C34 DOUB N N 26 B8N O36 C34 SING N N 27 B8N C34 C33 SING N N 28 B8N C33 N34 SING N N 29 B8N "C5'" H1 SING N N 30 B8N "C5'" H2 SING N N 31 B8N "C4'" H3 SING N N 32 B8N "C3'" H4 SING N N 33 B8N "O3'" H5 SING N N 34 B8N "C2'" H6 SING N N 35 B8N "O2'" H7 SING N N 36 B8N "C1'" H8 SING N N 37 B8N C6 H9 SING N N 38 B8N CN1 H10 SING N N 39 B8N CN1 H11 SING N N 40 B8N CN1 H12 SING N N 41 B8N N34 H13 SING N N 42 B8N N34 H14 SING N N 43 B8N OP2 H17 SING N N 44 B8N C31 H18 SING N N 45 B8N C31 H19 SING N N 46 B8N C32 H20 SING N N 47 B8N C32 H21 SING N N 48 B8N C33 H22 SING N N 49 B8N O36 H23 SING N N 50 B8N P OP3 SING N N 51 B8N OP3 H15 SING N N 52 # 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 B8N InChI InChI 1.03 "InChI=1S/C14H22N3O11P/c1-16-4-6(12(20)17(14(16)23)3-2-7(15)13(21)22)11-10(19)9(18)8(28-11)5-27-29(24,25)26/h4,7-11,18-19H,2-3,5,15H2,1H3,(H,21,22)(H2,24,25,26)/t7-,8-,9-,10-,11+/m1/s1" B8N InChIKey InChI 1.03 BVRIEBGMUPJSJF-ILAIQSSSSA-N B8N SMILES_CANONICAL CACTVS 3.385 "CN1C=C([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=O)N(CC[C@@H](N)C(O)=O)C1=O" B8N SMILES CACTVS 3.385 "CN1C=C([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)N(CC[CH](N)C(O)=O)C1=O" B8N SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CN1C=C(C(=O)N(C1=O)CC[C@H](C(=O)O)N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" B8N SMILES "OpenEye OEToolkits" 2.0.6 "CN1C=C(C(=O)N(C1=O)CCC(C(=O)O)N)C2C(C(C(O2)COP(=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 B8N "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site B8N "Create component" 2017-09-25 EBI B8N "Initial release" 2018-01-24 RCSB #