data_7MD # _chem_comp.id 7MD _chem_comp.name "5'-O-[(R)-(3-aminopropoxy)(L-alpha-aspartylamino)phosphoryl]adenosine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H27 N8 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2011-09-11 _chem_comp.pdbx_modified_date 2024-10-07 _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 518.418 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 7MD _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 3TLC _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # 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_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_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 7MD C C C 0 1 N N N Y N Y 12.484 -3.922 47.653 -2.528 1.077 0.261 C 7MD 1 7MD N N N 0 1 N N N Y Y N 10.681 -2.888 46.418 -1.785 3.361 -0.109 N 7MD 2 7MD O O O 0 1 N N N Y N Y 13.402 -4.715 47.483 -2.055 0.817 -0.825 O 7MD 3 7MD P P P 0 1 N N R N N N 13.950 -2.349 49.239 -2.747 -1.481 0.615 P 7MD 4 7MD N1 N1 N 0 1 Y N N N N N 13.967 7.557 50.139 7.326 1.176 -1.707 N1 7MD 5 7MD C2 C2 C 0 1 Y N N N N N 13.160 7.020 51.070 7.054 -0.116 -1.722 C2 7MD 6 7MD N3 N3 N 0 1 Y N N N N N 13.129 5.692 51.273 5.929 -0.607 -1.247 N3 7MD 7 7MD C4 C4 C 0 1 Y N N N N N 13.916 4.865 50.533 5.006 0.195 -0.726 C4 7MD 8 7MD C5 C5 C 0 1 Y N N N N N 14.756 5.396 49.566 5.247 1.579 -0.687 C5 7MD 9 7MD C6 C6 C 0 1 Y N N N N N 14.770 6.774 49.377 6.464 2.055 -1.206 C6 7MD 10 7MD N6 N6 N 0 1 N N N N N N 15.578 7.330 48.442 6.757 3.407 -1.195 N6 7MD 11 7MD N7 N7 N 0 1 Y N N N N N 15.412 4.367 48.991 4.164 2.157 -0.115 N7 7MD 12 7MD C8 C8 C 0 1 Y N N N N N 14.989 3.228 49.585 3.295 1.238 0.192 C8 7MD 13 7MD N8 N8 N 0 1 N N N N N N 12.576 -2.831 48.417 -2.915 0.082 1.083 N8 7MD 14 7MD N9 N9 N 0 1 Y N N N N N 14.080 3.537 50.521 3.768 0.011 -0.165 N9 7MD 15 7MD CA CA C 0 1 N N S Y N N 11.133 -4.134 47.013 -2.676 2.513 0.694 CA 7MD 16 7MD CB CB C 0 1 N N N N N N 11.173 -5.232 45.944 -4.125 2.960 0.490 CB 7MD 17 7MD CG CG C 0 1 N N N N N N 9.844 -5.441 45.236 -4.303 4.353 1.035 CG 7MD 18 7MD "C1'" "C1'" C 0 1 N N R N N N 13.360 2.592 51.410 3.080 -1.270 0.017 "C1'" 7MD 19 7MD O1P O1P O 0 1 N N N N N N 14.539 -3.463 50.205 -3.242 -2.373 1.687 O1P 7MD 20 7MD "C2'" "C2'" C 0 1 N N R N N N 12.046 2.133 50.807 3.476 -1.906 1.368 "C2'" 7MD 21 7MD "O2'" "O2'" O 0 1 N N N N N N 10.999 3.063 51.105 4.493 -2.891 1.179 "O2'" 7MD 22 7MD "C3'" "C3'" C 0 1 N N S N N N 11.818 0.782 51.460 2.171 -2.563 1.870 "C3'" 7MD 23 7MD "O3'" "O3'" O 0 1 N N N N N N 10.905 0.893 52.554 2.342 -3.976 2.006 "O3'" 7MD 24 7MD O31 O31 O 0 1 N N N N N N 15.094 -1.846 48.226 -3.598 -1.733 -0.729 O31 7MD 25 7MD C32 C32 C 0 1 N N N N N N 14.817 -0.888 47.205 -5.026 -1.746 -0.754 C32 7MD 26 7MD C33 C33 C 0 1 N N N N N N 16.122 -0.248 46.747 -5.509 -2.011 -2.182 C33 7MD 27 7MD C34 C34 C 0 1 N N N N N N 15.957 1.259 46.590 -7.038 -2.025 -2.209 C34 7MD 28 7MD N35 N35 N 0 1 N N N N N N 16.188 1.632 45.208 -7.501 -2.280 -3.580 N35 7MD 29 7MD "C4'" "C4'" C 0 1 N N R N N N 13.177 0.365 52.008 1.141 -2.248 0.762 "C4'" 7MD 30 7MD "O4'" "O4'" O 0 1 N N N N N N 14.101 1.391 51.633 1.653 -1.066 0.108 "O4'" 7MD 31 7MD "C5'" "C5'" C 0 1 N N N N N N 13.630 -0.997 51.495 -0.232 -1.967 1.375 "C5'" 7MD 32 7MD "O5'" "O5'" O 0 1 N N N N N N 13.583 -1.022 50.070 -1.193 -1.793 0.332 "O5'" 7MD 33 7MD OD1 OD1 O 0 1 N N N N N N 8.867 -4.697 45.488 -5.501 4.954 0.965 OD1 7MD 34 7MD OD2 OD2 O 0 1 N N N N N N 9.772 -6.373 44.402 -3.367 4.930 1.536 OD2 7MD 35 7MD H HN H 0 1 N N N Y Y N 9.786 -3.026 45.993 -0.817 3.128 0.058 HN 7MD 36 7MD H2 HNA H 0 1 N N N Y Y N 10.609 -2.187 47.127 -2.009 3.294 -1.090 HNA 7MD 37 7MD H21 H2 H 0 1 N N N N N N 12.528 7.664 51.663 7.783 -0.795 -2.139 H2 7MD 38 7MD HN6 HN6 H 0 1 N N N N N N 15.459 8.323 48.446 7.600 3.724 -1.556 HN6 7MD 39 7MD HN6A HN6A H 0 0 N N N N N N 16.531 7.108 48.650 6.119 4.039 -0.826 HN6A 7MD 40 7MD H8 H8 H 0 1 N N N N N N 15.328 2.231 49.344 2.339 1.422 0.661 H8 7MD 41 7MD HN8 HN8 H 0 1 N N N N N N 11.761 -2.258 48.504 -3.293 0.290 1.952 HN8 7MD 42 7MD HA HA H 0 1 N N N Y N N 10.433 -4.458 47.797 -2.413 2.604 1.747 HA 7MD 43 7MD HB HB H 0 1 N N N N N N 11.921 -4.948 45.190 -4.361 2.953 -0.575 HB 7MD 44 7MD HBA HBA H 0 1 N N N N N N 11.452 -6.177 46.434 -4.793 2.276 1.014 HBA 7MD 45 7MD "H1'" "H1'" H 0 1 N N N N N N 13.207 3.154 52.343 3.315 -1.946 -0.805 "H1'" 7MD 46 7MD "H2'" "H2'" H 0 1 N N N N N N 12.062 2.067 49.709 3.812 -1.139 2.067 "H2'" 7MD 47 7MD "HO2'" "HO2'" H 0 0 N N N N N N 10.186 2.759 50.720 4.779 -3.322 1.996 "HO2'" 7MD 48 7MD "H3'" "H3'" H 0 1 N N N N N N 11.400 0.063 50.740 1.860 -2.122 2.817 "H3'" 7MD 49 7MD "HO3'" "HO3'" H 0 0 N N N N N N 10.776 0.038 52.948 3.021 -4.229 2.646 "HO3'" 7MD 50 7MD H32 H32 H 0 1 N N N N N N 14.334 -1.388 46.353 -5.395 -2.531 -0.094 H32 7MD 51 7MD H32A H32A H 0 0 N N N N N N 14.146 -0.112 47.602 -5.404 -0.781 -0.417 H32A 7MD 52 7MD H33 H33 H 0 1 N N N N N N 16.902 -0.448 47.496 -5.140 -1.226 -2.842 H33 7MD 53 7MD H33A H33A H 0 0 N N N N N N 16.414 -0.680 45.778 -5.130 -2.976 -2.519 H33A 7MD 54 7MD H34 H34 H 0 1 N N N N N N 14.936 1.548 46.881 -7.406 -2.810 -1.549 H34 7MD 55 7MD H34A H34A H 0 0 N N N N N N 16.683 1.776 47.235 -7.416 -1.060 -1.872 H34A 7MD 56 7MD HN35 HN35 H 0 0 N N N N N N 16.079 2.621 45.107 -7.111 -3.138 -3.939 HN35 7MD 57 7MD HN3A HN3A H 0 0 N N N N N N 17.116 1.370 44.943 -8.509 -2.294 -3.625 HN3A 7MD 58 7MD "H4'" "H4'" H 0 1 N N N N N N 13.119 0.254 53.101 1.079 -3.075 0.055 "H4'" 7MD 59 7MD "H5'" "H5'" H 0 1 N N N N N N 14.661 -1.186 51.828 -0.527 -2.807 2.005 "H5'" 7MD 60 7MD "H5'A" "H5'A" H 0 0 N N N N N N 12.964 -1.776 51.894 -0.182 -1.061 1.979 "H5'A" 7MD 61 7MD HOD1 HOD1 H 0 0 N N N N N N 8.122 -4.962 44.961 -5.567 5.847 1.328 HOD1 7MD 62 # 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 7MD CA C SING N N 1 7MD O C DOUB N N 2 7MD C N8 SING N N 3 7MD N CA SING N N 4 7MD N H SING N N 5 7MD N H2 SING N N 6 7MD O31 P SING N N 7 7MD N8 P SING N N 8 7MD P "O5'" SING N N 9 7MD P O1P DOUB N N 10 7MD C6 N1 DOUB Y N 11 7MD N1 C2 SING Y N 12 7MD C2 N3 DOUB Y N 13 7MD C2 H21 SING N N 14 7MD C4 N3 SING Y N 15 7MD C5 C4 DOUB Y N 16 7MD N9 C4 SING Y N 17 7MD N7 C5 SING Y N 18 7MD C6 C5 SING Y N 19 7MD N6 C6 SING N N 20 7MD N6 HN6 SING N N 21 7MD N6 HN6A SING N N 22 7MD N7 C8 DOUB Y N 23 7MD C8 N9 SING Y N 24 7MD C8 H8 SING N N 25 7MD N8 HN8 SING N N 26 7MD N9 "C1'" SING N N 27 7MD CB CA SING N N 28 7MD CA HA SING N N 29 7MD CG CB SING N N 30 7MD CB HB SING N N 31 7MD CB HBA SING N N 32 7MD OD2 CG DOUB N N 33 7MD CG OD1 SING N N 34 7MD "C2'" "C1'" SING N N 35 7MD "C1'" "O4'" SING N N 36 7MD "C1'" "H1'" SING N N 37 7MD "C2'" "O2'" SING N N 38 7MD "C2'" "C3'" SING N N 39 7MD "C2'" "H2'" SING N N 40 7MD "O2'" "HO2'" SING N N 41 7MD "C3'" "C4'" SING N N 42 7MD "C3'" "O3'" SING N N 43 7MD "C3'" "H3'" SING N N 44 7MD "O3'" "HO3'" SING N N 45 7MD C32 O31 SING N N 46 7MD C33 C32 SING N N 47 7MD C32 H32 SING N N 48 7MD C32 H32A SING N N 49 7MD C34 C33 SING N N 50 7MD C33 H33 SING N N 51 7MD C33 H33A SING N N 52 7MD N35 C34 SING N N 53 7MD C34 H34 SING N N 54 7MD C34 H34A SING N N 55 7MD N35 HN35 SING N N 56 7MD N35 HN3A SING N N 57 7MD "C5'" "C4'" SING N N 58 7MD "O4'" "C4'" SING N N 59 7MD "C4'" "H4'" SING N N 60 7MD "O5'" "C5'" SING N N 61 7MD "C5'" "H5'" SING N N 62 7MD "C5'" "H5'A" SING N N 63 7MD OD1 HOD1 SING N N 64 # 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 7MD SMILES ACDLabs 12.01 "O=C(O)CC(N)C(=O)NP(=O)(OCCCN)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O" 7MD InChI InChI 1.03 "InChI=1S/C17H27N8O9P/c18-2-1-3-32-35(31,24-16(30)8(19)4-10(26)27)33-5-9-12(28)13(29)17(34-9)25-7-23-11-14(20)21-6-22-15(11)25/h6-9,12-13,17,28-29H,1-5,18-19H2,(H,26,27)(H2,20,21,22)(H,24,30,31)/t8-,9+,12+,13+,17+,35+/m0/s1" 7MD InChIKey InChI 1.03 CBRVFFLBHDTTIM-FGNORGMNSA-N 7MD SMILES_CANONICAL CACTVS 3.370 "NCCCO[P@](=O)(NC(=O)[C@@H](N)CC(O)=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23" 7MD SMILES CACTVS 3.370 "NCCCO[P](=O)(NC(=O)[CH](N)CC(O)=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23" 7MD SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(NC(=O)[C@H](CC(=O)O)N)OCCCN)O)O)N" 7MD SMILES "OpenEye OEToolkits" 1.7.2 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(NC(=O)C(CC(=O)O)N)OCCCN)O)O)N" # 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 7MD "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(R)-(3-aminopropoxy)(L-alpha-aspartylamino)phosphoryl]adenosine" 7MD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "(3S)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-(3-azanylpropoxy)phosphoryl]amino]-3-azanyl-4-oxidanylidene-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 7MD "Create component" 2011-09-11 RCSB 7MD "Modify backbone" 2023-11-03 PDBE 7MD "Modify PCM" 2024-09-27 PDBE 7MD "Modify PCM" 2024-10-07 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id 7MD _pdbx_chem_comp_pcm.modified_residue_id ASP _pdbx_chem_comp_pcm.type ;(3-Aminopropyl)(5'-adenosyl)phosphono amidation ; _pdbx_chem_comp_pcm.category "Named protein modification" _pdbx_chem_comp_pcm.position "Amino-acid backbone" _pdbx_chem_comp_pcm.polypeptide_position C-terminal _pdbx_chem_comp_pcm.comp_id_linking_atom ? _pdbx_chem_comp_pcm.modified_residue_id_linking_atom ? _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession PTM-0335 _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #