data_6AD # _chem_comp.id 6AD _chem_comp.name "2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate)" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H17 N5 O10 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2-methylthio-adenosine-5'-diphosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-03-31 _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 473.293 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 6AD _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 4PXZ _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 6AD O2B O2B O 0 1 N N N 16.181 1.025 59.445 -6.634 2.036 -2.191 O2B 6AD 1 6AD PB PB P 0 1 N N N 16.569 0.984 57.870 -6.253 1.557 -0.702 PB 6AD 2 6AD O3B O3B O 0 1 N N N 18.003 0.277 57.772 -5.854 2.838 0.188 O3B 6AD 3 6AD O1B O1B O 0 1 N N N 16.571 2.339 57.263 -7.416 0.875 -0.091 O1B 6AD 4 6AD O3A O3A O 0 1 N N N 15.481 -0.035 57.297 -5.008 0.539 -0.767 O3A 6AD 5 6AD PA PA P 0 1 N N N 15.599 -0.994 55.991 -4.418 -0.573 0.237 PA 6AD 6 6AD O2A O2A O 0 1 N N N 15.940 -2.388 56.356 -5.290 -1.921 0.116 O2A 6AD 7 6AD O1A O1A O 0 1 N N N 16.343 -0.306 54.904 -4.483 -0.067 1.627 O1A 6AD 8 6AD "O5'" "O5'" O 0 1 N N N 14.034 -1.053 55.675 -2.887 -0.887 -0.149 "O5'" 6AD 9 6AD "C5'" "C5'" C 0 1 N N N 13.267 0.075 55.188 -2.053 -1.755 0.621 "C5'" 6AD 10 6AD "C4'" "C4'" C 0 1 N N R 11.889 -0.406 54.659 -0.666 -1.831 -0.021 "C4'" 6AD 11 6AD "O4'" "O4'" O 0 1 N N N 12.011 -1.113 53.382 0.028 -0.574 0.131 "O4'" 6AD 12 6AD "C3'" "C3'" C 0 1 N N S 11.197 -1.374 55.631 0.214 -2.861 0.721 "C3'" 6AD 13 6AD "O3'" "O3'" O 0 1 N N N 9.769 -1.226 55.606 0.219 -4.109 0.026 "O3'" 6AD 14 6AD "C2'" "C2'" C 0 1 N N R 11.582 -2.723 55.107 1.623 -2.227 0.710 "C2'" 6AD 15 6AD "O2'" "O2'" O 0 1 N N N 10.634 -3.727 55.422 2.543 -3.063 0.006 "O2'" 6AD 16 6AD "C1'" "C1'" C 0 1 N N R 11.687 -2.525 53.603 1.427 -0.889 -0.038 "C1'" 6AD 17 6AD N9 N9 N 0 1 Y N N 12.703 -3.449 53.002 2.261 0.156 0.561 N9 6AD 18 6AD C8 C8 C 0 1 Y N N 13.886 -3.813 53.502 1.889 1.018 1.551 C8 6AD 19 6AD N7 N7 N 0 1 Y N N 14.434 -4.713 52.697 2.876 1.814 1.841 N7 6AD 20 6AD C5 C5 C 0 1 Y N N 13.612 -4.895 51.659 3.942 1.516 1.058 C5 6AD 21 6AD C4 C4 C 0 1 Y N N 12.518 -4.136 51.880 3.561 0.445 0.231 C4 6AD 22 6AD N3 N3 N 0 1 Y N N 11.505 -4.135 50.996 4.437 -0.043 -0.641 N3 6AD 23 6AD C2 C2 C 0 1 Y N N 11.566 -4.903 49.892 5.654 0.471 -0.732 C2 6AD 24 6AD S1 S1 S 0 1 N N N 10.191 -4.864 48.788 6.780 -0.210 -1.904 S1 6AD 25 6AD C11 C11 C 0 1 N N N 10.293 -6.409 47.909 8.223 0.839 -1.600 C11 6AD 26 6AD N1 N1 N 0 1 Y N N 12.677 -5.636 49.644 6.055 1.483 0.028 N1 6AD 27 6AD C6 C6 C 0 1 Y N N 13.688 -5.642 50.532 5.246 2.024 0.932 C6 6AD 28 6AD N6 N6 N 0 1 N N N 14.761 -6.416 50.348 5.672 3.079 1.720 N6 6AD 29 6AD H1 H1 H 0 1 N N N 16.020 1.923 59.709 -7.378 2.652 -2.228 H1 6AD 30 6AD H2 H2 H 0 1 N N N 18.614 0.859 57.335 -5.098 3.334 -0.154 H2 6AD 31 6AD H3 H3 H 0 1 N N N 16.650 -2.695 55.805 -5.293 -2.309 -0.769 H3 6AD 32 6AD H4 H4 H 0 1 N N N 13.819 0.565 54.373 -1.963 -1.367 1.635 H4 6AD 33 6AD H5 H5 H 0 1 N N N 13.112 0.791 56.008 -2.495 -2.751 0.650 H5 6AD 34 6AD H6 H6 H 0 1 N N N 11.244 0.475 54.528 -0.751 -2.095 -1.076 H6 6AD 35 6AD H7 H7 H 0 1 N N N 11.595 -1.230 56.646 -0.136 -2.996 1.744 H7 6AD 36 6AD H8 H8 H 0 1 N N N 9.376 -1.838 56.217 0.757 -4.793 0.449 H8 6AD 37 6AD H9 H9 H 0 1 N N N 12.572 -2.995 55.501 1.971 -2.050 1.728 H9 6AD 38 6AD H10 H10 H 0 1 N N N 10.586 -3.833 56.365 2.658 -3.939 0.400 H10 6AD 39 6AD H11 H11 H 0 1 N N N 10.706 -2.743 53.156 1.665 -1.007 -1.095 H11 6AD 40 6AD H12 H12 H 0 1 N N N 14.325 -3.436 54.414 0.918 1.036 2.024 H12 6AD 41 6AD H13 H13 H 0 1 N N N 9.465 -6.476 47.188 9.035 0.540 -2.264 H13 6AD 42 6AD H14 H14 H 0 1 N N N 11.252 -6.463 47.373 7.962 1.880 -1.790 H14 6AD 43 6AD H15 H15 H 0 1 N N N 10.225 -7.242 48.624 8.541 0.727 -0.564 H15 6AD 44 6AD H16 H16 H 0 1 N N N 14.658 -6.933 49.498 6.570 3.430 1.615 H16 6AD 45 6AD H17 H17 H 0 1 N N N 15.579 -5.844 50.293 5.073 3.467 2.377 H17 6AD 46 # # 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 6AD C11 S1 SING N N 1 6AD S1 C2 SING N N 2 6AD N1 C2 DOUB Y N 3 6AD N1 C6 SING Y N 4 6AD C2 N3 SING Y N 5 6AD N6 C6 SING N N 6 6AD C6 C5 DOUB Y N 7 6AD N3 C4 DOUB Y N 8 6AD C5 C4 SING Y N 9 6AD C5 N7 SING Y N 10 6AD C4 N9 SING Y N 11 6AD N7 C8 DOUB Y N 12 6AD N9 C8 SING Y N 13 6AD N9 "C1'" SING N N 14 6AD "O4'" "C1'" SING N N 15 6AD "O4'" "C4'" SING N N 16 6AD "C1'" "C2'" SING N N 17 6AD "C4'" "C5'" SING N N 18 6AD "C4'" "C3'" SING N N 19 6AD O1A PA DOUB N N 20 6AD "C2'" "O2'" SING N N 21 6AD "C2'" "C3'" SING N N 22 6AD "C5'" "O5'" SING N N 23 6AD "O3'" "C3'" SING N N 24 6AD "O5'" PA SING N N 25 6AD PA O2A SING N N 26 6AD PA O3A SING N N 27 6AD O1B PB DOUB N N 28 6AD O3A PB SING N N 29 6AD O3B PB SING N N 30 6AD PB O2B SING N N 31 6AD O2B H1 SING N N 32 6AD O3B H2 SING N N 33 6AD O2A H3 SING N N 34 6AD "C5'" H4 SING N N 35 6AD "C5'" H5 SING N N 36 6AD "C4'" H6 SING N N 37 6AD "C3'" H7 SING N N 38 6AD "O3'" H8 SING N N 39 6AD "C2'" H9 SING N N 40 6AD "O2'" H10 SING N N 41 6AD "C1'" H11 SING N N 42 6AD C8 H12 SING N N 43 6AD C11 H13 SING N N 44 6AD C11 H14 SING N N 45 6AD C11 H15 SING N N 46 6AD N6 H16 SING N N 47 6AD N6 H17 SING N N 48 # # 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 6AD SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(nc(SC)nc12)N)C(O)C3O" 6AD InChI InChI 1.03 "InChI=1S/C11H17N5O10P2S/c1-29-11-14-8(12)5-9(15-11)16(3-13-5)10-7(18)6(17)4(25-10)2-24-28(22,23)26-27(19,20)21/h3-4,6-7,10,17-18H,2H2,1H3,(H,22,23)(H2,12,14,15)(H2,19,20,21)/t4-,6-,7-,10-/m1/s1" 6AD InChIKey InChI 1.03 WLMZTKAZJUWXCB-KQYNXXCUSA-N 6AD SMILES_CANONICAL CACTVS 3.385 "CSc1nc(N)c2ncn([C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O)c2n1" 6AD SMILES CACTVS 3.385 "CSc1nc(N)c2ncn([CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O)c2n1" 6AD SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CSc1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)O)O)O)N" 6AD SMILES "OpenEye OEToolkits" 1.7.6 "CSc1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)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 6AD "SYSTEMATIC NAME" ACDLabs 12.01 "2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate)" 6AD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4R,5R)-5-(6-azanyl-2-methylsulfanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl 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 6AD "Create component" 2014-03-31 PDBJ 6AD "Initial release" 2014-04-30 RCSB 6AD "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 6AD _pdbx_chem_comp_synonyms.name "2-methylthio-adenosine-5'-diphosphate" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##