data_BMR # _chem_comp.id BMR _chem_comp.name "((2R,3S,5R)-3-hydroxy-5-(3-methoxynaphthalen-2-yl)methyl-tetrahydrogen-triphosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H21 O13 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms dNaM-Triphosphate _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-10-02 _chem_comp.pdbx_modified_date 2021-03-01 _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 514.251 _chem_comp.one_letter_code ? _chem_comp.three_letter_code BMR _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 4C8k _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 BMR C1 C1 C 0 1 Y N N 20.627 -20.061 -3.923 4.330 0.080 0.442 C1 BMR 1 BMR C2 C2 C 0 1 Y N N 20.337 -18.727 -4.220 3.765 -0.877 -0.341 C2 BMR 2 BMR C3 C3 C 0 1 Y N N 19.380 -18.035 -3.487 4.470 -2.063 -0.610 C3 BMR 3 BMR C4 C4 C 0 1 Y N N 18.701 -18.671 -2.453 5.763 -2.245 -0.060 C4 BMR 4 BMR C5 C5 C 0 1 Y N N 18.984 -20.000 -2.156 6.318 -1.237 0.745 C5 BMR 5 BMR C6 C6 C 0 1 Y N N 19.945 -20.690 -2.892 5.606 -0.097 0.986 C6 BMR 6 BMR PA PA P 0 1 N N N 20.247 -17.084 -8.306 -1.972 1.390 -1.061 PA BMR 7 BMR PB PB P 0 1 N N N 18.231 -17.369 -10.268 -4.614 0.366 -0.192 PB BMR 8 BMR PC PC P 0 1 N N N 18.018 -14.844 -11.491 -6.278 -1.763 1.026 PC BMR 9 BMR "C1'" "C1'" C 0 1 N N R 21.648 -20.816 -4.700 3.573 1.353 0.723 "C1'" BMR 10 BMR O1A O1A O 0 1 N N N 21.138 -16.884 -9.512 -1.650 0.462 -2.337 O1A BMR 11 BMR O1B O1B O 0 1 N N N 16.934 -18.133 -10.409 -4.963 -0.091 -1.556 O1B BMR 12 BMR O1C O1C O 0 1 N N N 17.575 -13.491 -10.988 -7.522 -1.041 0.678 O1C BMR 13 BMR "C2'" "C2'" C 0 1 N N N 20.980 -21.899 -5.537 3.986 2.465 -0.276 "C2'" BMR 14 BMR C20 C20 C 0 1 Y N N 17.743 -17.975 -1.722 6.466 -3.432 -0.330 C20 BMR 15 BMR C21 C21 C 0 1 Y N N 17.470 -16.646 -2.028 5.897 -4.389 -1.113 C21 BMR 16 BMR C22 C22 C 0 1 Y N N 18.153 -16.010 -3.062 4.625 -4.209 -1.655 C22 BMR 17 BMR C23 C23 C 0 1 Y N N 19.107 -16.707 -3.793 3.915 -3.073 -1.415 C23 BMR 18 BMR O2A O2A O 0 1 N N N 19.999 -15.933 -7.363 -2.543 2.676 -1.518 O2A BMR 19 BMR O2B O2B O 0 1 N N N 19.332 -17.575 -11.284 -5.413 1.724 0.139 O2B BMR 20 BMR O2C O2C O 0 1 N N N 19.487 -14.918 -11.844 -6.092 -3.019 0.037 O2C BMR 21 BMR "C3'" "C3'" C 0 1 N N S 20.871 -21.277 -6.913 2.741 3.385 -0.269 "C3'" BMR 22 BMR "O3'" "O3'" O 0 1 N N N 20.902 -22.269 -7.941 2.944 4.493 0.610 "O3'" BMR 23 BMR O37 O37 O 0 1 N N N 20.221 -21.997 -2.588 6.144 0.878 1.765 O37 BMR 24 BMR C38 C38 C 0 1 N N N 20.890 -22.316 -1.368 7.451 0.639 2.293 C38 BMR 25 BMR O3A O3A O 0 1 N N N 18.826 -17.672 -8.800 -3.030 0.641 -0.106 O3A BMR 26 BMR O3B O3B O 0 1 N N N 17.887 -15.794 -10.193 -5.021 -0.769 0.875 O3B BMR 27 BMR O3C O3C O 0 1 N N N 17.093 -15.474 -12.509 -6.369 -2.286 2.546 O3C BMR 28 BMR "C4'" "C4'" C 0 1 N N R 22.071 -20.349 -6.977 1.607 2.483 0.253 "C4'" BMR 29 BMR "O4'" "O4'" O 0 1 N N N 22.331 -19.955 -5.623 2.164 1.174 0.464 "O4'" BMR 30 BMR "C5'" "C5'" C 0 1 N N N 21.859 -19.155 -7.905 0.482 2.409 -0.782 "C5'" BMR 31 BMR "O5'" "O5'" O 0 1 N N N 20.805 -18.317 -7.428 -0.613 1.666 -0.243 "O5'" BMR 32 BMR H2 H2 H 0 1 N N N 20.860 -18.230 -5.024 2.779 -0.726 -0.755 H2 BMR 33 BMR H5 H5 H 0 1 N N N 18.458 -20.497 -1.354 7.303 -1.363 1.171 H5 BMR 34 BMR "H2'" "H2'" H 0 1 N N N 21.598 -22.809 -5.566 4.867 2.999 0.080 "H2'" BMR 35 BMR "H5'" "H5'" H 0 1 N N N 22.789 -18.570 -7.956 0.151 3.417 -1.031 "H5'" BMR 36 BMR "H1'" "H1'" H 0 1 N N N 22.365 -21.284 -4.010 3.739 1.679 1.749 "H1'" BMR 37 BMR "H2'A" "H2'A" H 0 0 N N N 19.985 -22.144 -5.138 4.158 2.051 -1.269 "H2'A" BMR 38 BMR H20 H20 H 0 1 N N N 17.213 -18.466 -0.919 7.452 -3.585 0.083 H20 BMR 39 BMR H21 H21 H 0 1 N N N 16.726 -16.105 -1.462 6.439 -5.299 -1.319 H21 BMR 40 BMR H22 H22 H 0 1 N N N 17.941 -14.977 -3.295 4.197 -4.983 -2.274 H22 BMR 41 BMR H23 H23 H 0 1 N N N 19.636 -16.218 -4.598 2.931 -2.948 -1.841 H23 BMR 42 BMR "H3'" "H3'" H 0 1 N N N 19.947 -20.684 -6.974 2.520 3.735 -1.277 "H3'" BMR 43 BMR "HO3'" "HO3'" H 0 0 N N N 20.832 -21.848 -8.790 3.684 5.063 0.361 "HO3'" BMR 44 BMR H38 H38 H 0 1 N N N 21.024 -23.405 -1.297 8.154 0.498 1.472 H38 BMR 45 BMR "H4'" "H4'" H 0 1 N N N 22.928 -20.925 -7.356 1.222 2.877 1.194 "H4'" BMR 46 BMR "H5'A" "H5'A" H 0 0 N N N 21.601 -19.521 -8.909 0.849 1.914 -1.682 "H5'A" BMR 47 BMR H38A H38A H 0 0 N N N 21.873 -21.823 -1.350 7.761 1.493 2.894 H38A BMR 48 BMR H38B H38B H 0 0 N N N 20.288 -21.965 -0.517 7.434 -0.256 2.914 H38B BMR 49 BMR H1A H1A H 0 1 N N N 21.455 -15.989 -9.527 -1.272 -0.399 -2.112 H1A BMR 50 BMR H2B H2B H 0 1 N N N 19.049 -18.207 -11.934 -5.233 2.082 1.019 H2B BMR 51 BMR H2C H2C H 0 1 N N N 19.894 -14.075 -11.684 -5.295 -3.539 0.208 H2C BMR 52 BMR H3C H3C H 0 1 N N N 16.358 -14.894 -12.671 -7.106 -2.890 2.711 H3C BMR 53 # # 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 BMR C1 C2 DOUB Y N 1 BMR C1 C6 SING Y N 2 BMR C1 "C1'" SING N N 3 BMR C2 C3 SING Y N 4 BMR C2 H2 SING N N 5 BMR C3 C4 DOUB Y N 6 BMR C3 C23 SING Y N 7 BMR C4 C5 SING Y N 8 BMR C4 C20 SING Y N 9 BMR C5 C6 DOUB Y N 10 BMR C5 H5 SING N N 11 BMR C6 O37 SING N N 12 BMR PA O1A SING N N 13 BMR PA O2A DOUB N N 14 BMR PA O3A SING N N 15 BMR PA "O5'" SING N N 16 BMR PB O1B DOUB N N 17 BMR PB O2B SING N N 18 BMR PB O3A SING N N 19 BMR PB O3B SING N N 20 BMR PC O1C DOUB N N 21 BMR PC O2C SING N N 22 BMR PC O3B SING N N 23 BMR PC O3C SING N N 24 BMR "C1'" "C2'" SING N N 25 BMR "C1'" "O4'" SING N N 26 BMR "C1'" "H1'" SING N N 27 BMR "C2'" "C3'" SING N N 28 BMR "C2'" "H2'" SING N N 29 BMR "C2'" "H2'A" SING N N 30 BMR C20 C21 DOUB Y N 31 BMR C20 H20 SING N N 32 BMR C21 C22 SING Y N 33 BMR C21 H21 SING N N 34 BMR C22 C23 DOUB Y N 35 BMR C22 H22 SING N N 36 BMR C23 H23 SING N N 37 BMR "C3'" "O3'" SING N N 38 BMR "C3'" "C4'" SING N N 39 BMR "C3'" "H3'" SING N N 40 BMR "O3'" "HO3'" SING N N 41 BMR O37 C38 SING N N 42 BMR C38 H38 SING N N 43 BMR C38 H38A SING N N 44 BMR C38 H38B SING N N 45 BMR "C4'" "O4'" SING N N 46 BMR "C4'" "C5'" SING N N 47 BMR "C4'" "H4'" SING N N 48 BMR "C5'" "O5'" SING N N 49 BMR "C5'" "H5'" SING N N 50 BMR "C5'" "H5'A" SING N N 51 BMR O1A H1A SING N N 52 BMR O2B H2B SING N N 53 BMR O2C H2C SING N N 54 BMR O3C H3C 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 BMR InChI InChI 1.03 "InChI=1S/C16H21O13P3/c1-25-14-7-11-5-3-2-4-10(11)6-12(14)15-8-13(17)16(27-15)9-26-31(21,22)29-32(23,24)28-30(18,19)20/h2-7,13,15-17H,8-9H2,1H3,(H,21,22)(H,23,24)(H2,18,19,20)/p-4/t13-,15+,16+/m0/s1" BMR InChIKey InChI 1.03 OYLYLYUMXXAEFZ-NUEKZKHPSA-J BMR SMILES_CANONICAL CACTVS 3.385 "COc1cc2ccccc2cc1[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3" BMR SMILES CACTVS 3.385 "COc1cc2ccccc2cc1[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3" BMR SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "COc1cc2ccccc2cc1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O" BMR SMILES "OpenEye OEToolkits" 1.7.6 "COc1cc2ccccc2cc1C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id BMR _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 1.7.6 _pdbx_chem_comp_identifier.identifier "[[(2R,3S,5R)-5-(3-methoxynaphthalen-2-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono 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 BMR "Create component" 2013-10-02 EBI BMR "Other modification" 2013-10-14 EBI BMR "Initial release" 2013-12-11 RCSB BMR "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id BMR _pdbx_chem_comp_synonyms.name dNaM-Triphosphate _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##