data_A1IEA # _chem_comp.id A1IEA _chem_comp.name ;N3-methyl adenosine-5'-monophosphate ; _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H17 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id A _chem_comp.pdbx_synonyms "[(2R,3S,4R,5R)-5-(6-azanyl-3-methyl-purin-3-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2024-06-13 _chem_comp.pdbx_modified_date 2025-01-17 _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 362.256 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1IEA _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 9FN2 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _chem_comp.pdbx_pcm ? # 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.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 A1IEA C4 C1 C 0 1 Y N N N N N 26.593 25.026 -4.120 3.010 -0.219 0.218 C4 A1IEA 1 A1IEA C5 C2 C 0 1 Y N N N N N 26.162 25.344 -5.381 3.645 -1.316 -0.386 C5 A1IEA 2 A1IEA C6 C3 C 0 1 Y N N N N N 26.781 26.388 -6.066 5.015 -1.510 -0.137 C6 A1IEA 3 A1IEA N1 N1 N 0 1 Y N N N N N 27.773 27.051 -5.492 5.642 -0.648 0.657 N1 A1IEA 4 A1IEA C8 C4 C 0 1 Y N N N N N 24.961 23.711 -4.692 1.566 -1.353 -1.003 C8 A1IEA 5 A1IEA N3 N2 N 1 1 Y N N N N N 27.610 25.744 -3.585 3.721 0.593 0.994 N3 A1IEA 6 A1IEA C2 C5 C 0 1 Y N N N N N 28.165 26.718 -4.270 5.001 0.369 1.204 C2 A1IEA 7 A1IEA N6 N3 N 0 1 N N N N N N 26.313 26.723 -7.415 5.694 -2.573 -0.704 N6 A1IEA 8 A1IEA "C1'" C6 C 0 1 N N R N N N 25.898 23.326 -2.431 0.642 0.675 0.179 "C1'" A1IEA 9 A1IEA C1P C7 C 0 1 N N N N N N 28.128 25.469 -2.275 3.073 1.745 1.626 C1P A1IEA 10 A1IEA "C2'" C8 C 0 1 N N R N N N 24.863 22.231 -2.207 0.533 1.799 -0.875 "C2'" A1IEA 11 A1IEA "C3'" C9 C 0 1 N N S N N N 25.549 21.406 -1.125 -0.984 2.076 -0.973 "C3'" A1IEA 12 A1IEA "C4'" C10 C 0 1 N N R N N N 27.021 21.489 -1.533 -1.612 1.087 0.034 "C4'" A1IEA 13 A1IEA "C5'" C11 C 0 1 N N N N N N 27.513 20.321 -2.335 -2.938 0.548 -0.506 "C5'" A1IEA 14 A1IEA N7 N4 N 0 1 Y N N N N N 25.157 24.521 -5.716 2.709 -1.967 -1.118 N7 A1IEA 15 A1IEA N9 N5 N 0 1 Y N N N N N 25.814 23.993 -3.729 1.700 -0.268 -0.189 N9 A1IEA 16 A1IEA "O2'" O1 O 0 1 N N N N N N 23.614 22.769 -1.831 1.228 2.967 -0.435 "O2'" A1IEA 17 A1IEA "O3'" O2 O 0 1 N N N N N N 25.374 22.038 0.144 -1.272 3.424 -0.597 "O3'" A1IEA 18 A1IEA "O4'" O3 O 0 1 N N N N N N 27.149 22.687 -2.340 -0.646 0.021 0.156 "O4'" A1IEA 19 A1IEA "O5'" O4 O 0 1 N N N N N N 27.217 19.112 -1.663 -3.558 -0.272 0.486 "O5'" A1IEA 20 A1IEA OP3 O5 O 0 1 N Y N N N N 26.303 18.078 -3.739 -5.301 -1.944 1.526 OP3 A1IEA 21 A1IEA OP2 O6 O 0 1 N N N N N N 26.497 16.744 -1.487 -6.131 0.100 0.095 OP2 A1IEA 22 A1IEA P P1 P 0 1 N N N N N N 27.058 17.757 -2.465 -4.973 -1.006 0.259 P A1IEA 23 A1IEA H8 H1 H 0 1 N N N N N N 24.213 22.933 -4.650 0.648 -1.659 -1.482 H8 A1IEA 24 A1IEA H2 H2 H 0 1 N N N N N N 28.975 27.271 -3.818 5.549 1.046 1.843 H2 A1IEA 25 A1IEA H61 H3 H 0 1 N N N N N N 26.851 27.485 -7.775 6.639 -2.697 -0.524 H61 A1IEA 26 A1IEA H62 H4 H 0 1 N N N N N N 26.421 25.928 -8.012 5.225 -3.195 -1.283 H62 A1IEA 27 A1IEA "H1'" H5 H 0 1 N N N N N N 25.796 24.073 -1.630 0.835 1.098 1.165 "H1'" A1IEA 28 A1IEA H1P3 H6 H 0 0 N N N N N N 27.569 24.635 -1.827 2.594 1.430 2.553 H1P3 A1IEA 29 A1IEA H1 H7 H 0 1 N N N N N N 29.192 25.199 -2.351 3.821 2.508 1.844 H1 A1IEA 30 A1IEA H3 H8 H 0 1 N N N N N N 28.021 26.363 -1.643 2.323 2.155 0.950 H3 A1IEA 31 A1IEA "H2'" H9 H 0 1 N N N N N N 24.770 21.626 -3.121 0.924 1.462 -1.835 "H2'" A1IEA 32 A1IEA "H3'" H10 H 0 1 N N N N N N 25.194 20.365 -1.133 -1.344 1.877 -1.982 "H3'" A1IEA 33 A1IEA "H4'" H11 H 0 1 N N N N N N 27.634 21.585 -0.625 -1.765 1.573 0.998 "H4'" A1IEA 34 A1IEA "H5''" H12 H 0 0 N N N N N N 28.601 20.405 -2.471 -3.596 1.381 -0.752 "H5''" A1IEA 35 A1IEA "H5'" H13 H 0 1 N N N N N N 27.020 20.321 -3.318 -2.752 -0.044 -1.402 "H5'" A1IEA 36 A1IEA "HO2'" H14 H 0 0 N N N N N N 22.992 22.064 -1.699 1.192 3.705 -1.060 "HO2'" A1IEA 37 A1IEA "HO3'" H15 H 0 0 N Y N N N N 25.802 21.522 0.817 -0.852 4.088 -1.160 "HO3'" A1IEA 38 A1IEA HOP3 H16 H 0 0 N Y N N N N 26.877 17.959 -4.486 -6.141 -2.418 1.457 HOP3 A1IEA 39 A1IEA HOP2 H17 H 0 0 N N N N N N 27.165 16.102 -1.278 -6.232 0.681 0.862 HOP2 A1IEA 40 A1IEA OP1 O1P O 0 1 N N N N N N 28.576 17.319 -2.749 -4.907 -1.836 -0.965 OP1 A1IEA 41 # 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 A1IEA N6 C6 SING N N 1 A1IEA C6 N1 DOUB Y N 2 A1IEA C6 C5 SING Y N 3 A1IEA N7 C5 SING Y N 4 A1IEA N7 C8 DOUB Y N 5 A1IEA N1 C2 SING Y N 6 A1IEA C5 C4 DOUB Y N 7 A1IEA C8 N9 SING Y N 8 A1IEA C2 N3 DOUB Y N 9 A1IEA C4 N9 SING Y N 10 A1IEA C4 N3 SING Y N 11 A1IEA OP3 P SING N N 12 A1IEA N9 "C1'" SING N N 13 A1IEA N3 C1P SING N N 14 A1IEA P "O5'" SING N N 15 A1IEA P OP2 SING N N 16 A1IEA "C1'" "O4'" SING N N 17 A1IEA "C1'" "C2'" SING N N 18 A1IEA "O4'" "C4'" SING N N 19 A1IEA "C5'" "O5'" SING N N 20 A1IEA "C5'" "C4'" SING N N 21 A1IEA "C2'" "O2'" SING N N 22 A1IEA "C2'" "C3'" SING N N 23 A1IEA "C4'" "C3'" SING N N 24 A1IEA "C3'" "O3'" SING N N 25 A1IEA C8 H8 SING N N 26 A1IEA C2 H2 SING N N 27 A1IEA N6 H61 SING N N 28 A1IEA N6 H62 SING N N 29 A1IEA "C1'" "H1'" SING N N 30 A1IEA C1P H1P3 SING N N 31 A1IEA C1P H1 SING N N 32 A1IEA C1P H3 SING N N 33 A1IEA "C2'" "H2'" SING N N 34 A1IEA "C3'" "H3'" SING N N 35 A1IEA "C4'" "H4'" SING N N 36 A1IEA "C5'" "H5''" SING N N 37 A1IEA "C5'" "H5'" SING N N 38 A1IEA "O2'" "HO2'" SING N N 39 A1IEA "O3'" "HO3'" SING N N 40 A1IEA OP3 HOP3 SING N N 41 A1IEA OP2 HOP2 SING N N 42 A1IEA P OP1 DOUB N N 43 # 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 A1IEA InChI InChI 1.06 "InChI=1S/C11H16N5O7P/c1-15-3-14-9(12)6-10(15)16(4-13-6)11-8(18)7(17)5(23-11)2-22-24(19,20)21/h3-5,7-8,11-12,17-18H,2H2,1H3,(H2,19,20,21)/p+1/t5-,7-,8-,11-/m1/s1" A1IEA InChIKey InChI 1.06 XPHLDSANNGAVEC-IOSLPCCCSA-O A1IEA SMILES_CANONICAL CACTVS 3.385 "C[n+]1cnc(N)c2ncn([C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O)c12" A1IEA SMILES CACTVS 3.385 "C[n+]1cnc(N)c2ncn([CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O)c12" A1IEA SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[n+]1cnc(c2c1n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N" A1IEA SMILES "OpenEye OEToolkits" 2.0.7 "C[n+]1cnc(c2c1n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N" # _pdbx_chem_comp_identifier.comp_id A1IEA _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 "[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-3-methyl-purin-3-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen 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 A1IEA "Create component" 2024-06-13 PDBE A1IEA "Modify name" 2024-08-30 PDBE A1IEA "Initial release" 2025-01-22 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id A1IEA _pdbx_chem_comp_synonyms.name "[(2R,3S,4R,5R)-5-(6-azanyl-3-methyl-purin-3-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" _pdbx_chem_comp_synonyms.provenance AUTHOR _pdbx_chem_comp_synonyms.type ? #