data_EMA # _chem_comp.id EMA _chem_comp.name "(ADENIN-9-YL-ETHOXYMETHYL)-HYDROXYPHOSPHINYL-DIPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C8 H14 N5 O10 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "9-(2-PHOSPHONYLMETHOXYETHYL)ADENINE DIPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-08-25 _chem_comp.pdbx_modified_date 2020-06-17 _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 433.146 _chem_comp.one_letter_code ? _chem_comp.three_letter_code EMA _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1PK0 _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 EMA PG PG P 0 1 N N N 2.590 54.884 61.160 1.150 0.235 -5.452 PG EMA 1 EMA O1G O1G O 0 1 N N N 3.064 55.024 59.783 1.407 1.049 -6.816 O1G EMA 2 EMA O2G O2G O 0 1 N N N 1.525 53.922 61.346 0.709 -1.140 -5.774 O2G EMA 3 EMA O3G O3G O 0 1 N N N 2.375 56.180 61.854 2.514 0.175 -4.598 O3G EMA 4 EMA PB PB P 0 1 N N S 5.351 54.455 62.210 -0.193 0.112 -3.247 PB EMA 5 EMA O1B O1B O 0 1 N N N 5.997 54.886 60.928 -0.614 -1.260 -3.603 O1B EMA 6 EMA O2B O2B O 0 1 N N N 5.417 55.362 63.360 1.192 0.054 -2.430 O2B EMA 7 EMA O3B O3B O 0 1 N N N 3.780 54.097 61.908 0.010 0.976 -4.590 O3B EMA 8 EMA PA PA P 0 1 N N S 5.877 51.591 61.788 -1.477 -0.110 -1.015 PA EMA 9 EMA O1A O1A O 0 1 N N N 4.460 51.193 61.729 -1.878 -1.480 -1.405 O1A EMA 10 EMA O2A O2A O 0 1 N N N 6.667 51.632 60.530 -0.070 -0.164 -0.235 O2A EMA 11 EMA O3A O3A O 0 1 N N N 5.865 53.002 62.539 -1.326 0.801 -2.333 O3A EMA 12 EMA "C5'" C5* C 0 1 N N N 6.545 50.562 62.822 -2.749 0.607 0.076 "C5'" EMA 13 EMA "O5'" O5* O 0 1 N N N 7.930 50.406 63.356 -2.884 -0.201 1.246 "O5'" EMA 14 EMA "C4'" C4* C 0 1 N N N 8.987 49.928 62.356 -1.963 0.311 2.211 "C4'" EMA 15 EMA "C1'" C1* C 0 1 N N N 10.332 49.331 63.000 -2.057 -0.514 3.496 "C1'" EMA 16 EMA N9 N9 N 0 1 Y N N 10.678 49.132 64.518 -1.113 0.012 4.485 N9 EMA 17 EMA C8 C8 C 0 1 Y N N 10.451 49.795 65.773 -1.370 0.980 5.409 C8 EMA 18 EMA N7 N7 N 0 1 Y N N 11.009 49.082 66.804 -0.307 1.204 6.126 N7 EMA 19 EMA C5 C5 C 0 1 Y N N 11.618 48.027 66.195 0.694 0.391 5.713 C5 EMA 20 EMA C6 C6 C 0 1 Y N N 12.330 46.880 66.694 2.032 0.198 6.097 C6 EMA 21 EMA N6 N6 N 0 1 N N N 12.541 46.734 67.988 2.584 0.932 7.132 N6 EMA 22 EMA N1 N1 N 0 1 Y N N 12.838 45.979 65.819 2.752 -0.709 5.446 N1 EMA 23 EMA C2 C2 C 0 1 Y N N 12.614 46.137 64.508 2.234 -1.413 4.457 C2 EMA 24 EMA N3 N3 N 0 1 Y N N 11.921 47.137 63.914 0.988 -1.262 4.060 N3 EMA 25 EMA C4 C4 C 0 1 Y N N 11.443 48.081 64.856 0.191 -0.378 4.651 C4 EMA 26 EMA H1G H1G H 0 1 N N N 3.763 55.655 59.660 2.095 0.573 -7.301 H1G EMA 27 EMA H3G H3G H 0 1 N N N 2.067 56.089 62.748 2.766 1.089 -4.409 H3G EMA 28 EMA H2B H2B H 0 1 N N N 5.007 55.088 64.172 1.430 0.967 -2.218 H2B EMA 29 EMA H2A H2A H 0 1 N N N 7.580 51.888 60.568 0.153 0.746 0.000 H2A EMA 30 EMA "H5'1" 1H5* H 0 0 N N N 5.910 50.646 63.735 -2.454 1.616 0.364 "H5'1" EMA 31 EMA "H5'2" 2H5* H 0 0 N N N 6.303 49.558 62.399 -3.702 0.643 -0.451 "H5'2" EMA 32 EMA "H4'1" 1H4* H 0 0 N N N 8.539 49.186 61.653 -0.950 0.252 1.814 "H4'1" EMA 33 EMA "H4'2" 2H4* H 0 0 N N N 9.237 50.749 61.644 -2.208 1.351 2.429 "H4'2" EMA 34 EMA "H1'1" 1H1* H 0 0 N N N 10.474 48.332 62.525 -3.070 -0.454 3.893 "H1'1" EMA 35 EMA "H1'2" 2H1* H 0 0 N N N 11.163 49.943 62.579 -1.812 -1.553 3.278 "H1'2" EMA 36 EMA H8 H8 H 0 1 N N N 9.909 50.743 65.927 -2.316 1.488 5.528 H8 EMA 37 EMA HN61 1HN6 H 0 0 N N N 13.045 45.921 68.341 3.508 0.787 7.390 HN61 EMA 38 EMA HN62 2HN6 H 0 0 N N N 11.641 46.784 68.466 2.049 1.594 7.597 HN62 EMA 39 EMA H2 H2 H 0 1 N N N 13.044 45.363 63.849 2.855 -2.140 3.956 H2 EMA 40 # # 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 EMA PG O1G SING N N 1 EMA PG O2G DOUB N N 2 EMA PG O3G SING N N 3 EMA PG O3B SING N N 4 EMA O1G H1G SING N N 5 EMA O3G H3G SING N N 6 EMA PB O1B DOUB N N 7 EMA PB O2B SING N N 8 EMA PB O3B SING N N 9 EMA PB O3A SING N N 10 EMA O2B H2B SING N N 11 EMA PA O1A DOUB N N 12 EMA PA O2A SING N N 13 EMA PA O3A SING N N 14 EMA PA "C5'" SING N N 15 EMA O2A H2A SING N N 16 EMA "C5'" "O5'" SING N N 17 EMA "C5'" "H5'1" SING N N 18 EMA "C5'" "H5'2" SING N N 19 EMA "O5'" "C4'" SING N N 20 EMA "C4'" "C1'" SING N N 21 EMA "C4'" "H4'1" SING N N 22 EMA "C4'" "H4'2" SING N N 23 EMA "C1'" N9 SING N N 24 EMA "C1'" "H1'1" SING N N 25 EMA "C1'" "H1'2" SING N N 26 EMA N9 C8 SING Y N 27 EMA N9 C4 SING Y N 28 EMA C8 N7 DOUB Y N 29 EMA C8 H8 SING N N 30 EMA N7 C5 SING Y N 31 EMA C5 C6 SING Y N 32 EMA C5 C4 DOUB Y N 33 EMA C6 N6 SING N N 34 EMA C6 N1 DOUB Y N 35 EMA N6 HN61 SING N N 36 EMA N6 HN62 SING N N 37 EMA N1 C2 SING Y N 38 EMA C2 N3 DOUB Y N 39 EMA C2 H2 SING N N 40 EMA N3 C4 SING Y N 41 # # 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 EMA SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(CCOC[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)cnc12" EMA SMILES CACTVS 3.341 "Nc1ncnc2n(CCOC[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)cnc12" EMA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)CCOC[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)N" EMA SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)CCOCP(=O)(O)OP(=O)(O)OP(=O)(O)O)N" EMA InChI InChI 1.03 "InChI=1S/C8H14N5O10P3/c9-7-6-8(11-3-10-7)13(4-12-6)1-2-21-5-24(14,15)22-26(19,20)23-25(16,17)18/h3-4H,1-2,5H2,(H,14,15)(H,19,20)(H2,9,10,11)(H2,16,17,18)" EMA InChIKey InChI 1.03 MELHEUHXJKQZNC-UHFFFAOYSA-N # _pdbx_chem_comp_identifier.comp_id EMA _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 1.5.0 _pdbx_chem_comp_identifier.identifier "2-(6-aminopurin-9-yl)ethoxymethyl-(hydroxy-phosphonooxy-phosphoryl)oxy-phosphinic 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 EMA "Create component" 2003-08-25 RCSB EMA "Modify descriptor" 2011-06-04 RCSB EMA "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id EMA _pdbx_chem_comp_synonyms.name "9-(2-PHOSPHONYLMETHOXYETHYL)ADENINE DIPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##