data_J2B # _chem_comp.id J2B _chem_comp.name ;O-[(1R,2R,3R)-5-{[(S)-{[(2R,3R,4R,5R)-2-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-4-hydroxy-5-(hydroxymethyl)tetrahydro furan-3-yl]oxy}(sulfanyl)phosphoryl]oxy}-1-(6-amino-9H-purin-9-yl)-1,2-dihydroxypentan-3-yl] dihydrogen (R)-phosphorothioate ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H28 N10 O12 P2 S2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "cleaved nonhydrolyzable phosphorothioate analog of 2'3' cyclic GMP-AMP" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-08-30 _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 726.574 _chem_comp.one_letter_code ? _chem_comp.three_letter_code J2B _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 6EA8 _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 J2B C02 C1 C 0 1 N N R -8.320 70.866 -72.134 5.677 1.870 -1.706 C02 J2B 1 J2B C03 C2 C 0 1 N N R -8.331 69.719 -71.580 4.954 0.844 -0.805 C03 J2B 2 J2B C08 C3 C 0 1 N N N -5.529 67.916 -74.077 -0.229 1.018 0.183 C08 J2B 3 J2B C09 C4 C 0 1 N N N -5.681 68.536 -75.398 -1.436 0.749 -0.717 C09 J2B 4 J2B C11 C5 C 0 1 N N R -5.378 67.366 -77.444 -5.206 0.602 0.054 C11 J2B 5 J2B C13 C6 C 0 1 Y N N -4.137 66.230 -79.248 -6.756 -1.192 -0.833 C13 J2B 6 J2B C15 C7 C 0 1 Y N N -3.236 66.983 -81.247 -6.981 -3.468 -0.604 C15 J2B 7 J2B C17 C8 C 0 1 Y N N -2.994 64.734 -80.708 -8.503 -2.401 -1.972 C17 J2B 8 J2B C19 C9 C 0 1 Y N N -3.686 64.953 -79.505 -7.867 -1.179 -1.692 C19 J2B 9 J2B C21 C10 C 0 1 Y N N -4.744 64.959 -77.609 -7.171 0.866 -1.507 C21 J2B 10 J2B C22 C11 C 0 1 N N R -6.750 67.028 -76.698 -3.918 0.461 -0.760 C22 J2B 11 J2B C24 C12 C 0 1 N N R -6.922 68.317 -75.864 -2.720 0.852 0.108 C24 J2B 12 J2B C31 C13 C 0 1 N N R -9.525 69.756 -70.553 5.590 -0.510 -1.192 C31 J2B 13 J2B C33 C14 C 0 1 Y N N -10.519 67.738 -71.371 4.787 -2.176 0.521 C33 J2B 14 J2B C35 C15 C 0 1 N N N -11.012 66.680 -73.654 2.784 -3.372 0.944 C35 J2B 15 J2B C38 C16 C 0 1 N N N -11.644 65.482 -71.562 4.550 -3.730 2.400 C38 J2B 16 J2B C40 C17 C 0 1 Y N N -11.078 66.639 -70.739 5.364 -2.786 1.628 C40 J2B 17 J2B C42 C18 C 0 1 Y N N -10.408 68.026 -69.236 6.857 -1.480 0.763 C42 J2B 18 J2B C44 C19 C 0 1 N N R -9.707 71.656 -71.700 6.664 1.015 -2.531 C44 J2B 19 J2B C45 C20 C 0 1 N N N -10.368 72.255 -72.911 7.978 1.770 -2.739 C45 J2B 20 J2B N12 N1 N 0 1 Y N N -4.773 66.205 -78.064 -6.338 0.111 -0.735 N12 J2B 21 J2B N14 N2 N 0 1 Y N N -3.893 67.216 -80.126 -6.352 -2.348 -0.317 N14 J2B 22 J2B N16 N3 N 0 1 Y N N -2.797 65.763 -81.519 -8.030 -3.506 -1.405 N16 J2B 23 J2B N18 N4 N 0 1 N N N -2.497 63.409 -81.048 -9.603 -2.451 -2.811 N18 J2B 24 J2B N20 N5 N 0 1 Y N N -4.078 64.197 -78.463 -8.067 0.107 -2.068 N20 J2B 25 J2B N32 N6 N 0 1 Y N N -10.113 68.576 -70.404 5.739 -1.360 -0.008 N32 J2B 26 J2B N34 N7 N 0 1 N N N -10.473 67.787 -72.856 3.491 -2.485 0.196 N34 J2B 27 J2B N36 N8 N 0 1 N N N -10.960 66.739 -75.105 1.492 -3.653 0.586 N36 J2B 28 J2B N37 N9 N 0 1 N N N -11.597 65.530 -72.994 3.292 -3.970 1.999 N37 J2B 29 J2B N41 N10 N 0 1 Y N N -10.991 66.854 -69.421 6.632 -2.323 1.730 N41 J2B 30 J2B O01 O1 O 0 1 N N N -7.149 71.627 -71.687 4.744 2.526 -2.566 O01 J2B 31 J2B O04 O2 O 0 1 N N N -7.030 69.462 -70.875 3.552 0.836 -1.080 O04 J2B 32 J2B O07 O3 O 0 1 N N N -5.595 68.916 -73.097 0.971 0.923 -0.589 O07 J2B 33 J2B O10 O4 O 0 1 N N N -4.632 67.830 -76.481 -5.414 1.977 0.382 O10 J2B 34 J2B O23 O5 O 0 1 N N N -7.725 66.828 -77.566 -3.772 -0.893 -1.191 O23 J2B 35 J2B O25 O6 O 0 1 N N N -7.320 69.473 -76.690 -2.884 2.194 0.570 O25 J2B 36 J2B O28 O7 O 0 1 N N N -8.806 69.277 -78.768 -1.470 2.185 2.661 O28 J2B 37 J2B O29 O8 O 0 1 N N N -9.727 68.553 -76.599 -2.935 4.203 2.266 O29 J2B 38 J2B O30 O9 O 0 1 N N N -4.741 68.348 -70.762 2.625 0.238 1.190 O30 J2B 39 J2B O39 O10 O 0 1 N N N -12.121 64.541 -71.020 5.010 -4.292 3.382 O39 J2B 40 J2B O43 O11 O 0 1 N N N -10.490 70.773 -71.160 6.885 -0.168 -1.732 O43 J2B 41 J2B O46 O12 O 0 1 N N N -10.207 71.371 -73.984 8.832 1.013 -3.600 O46 J2B 42 J2B P05 P1 P 0 1 N N S -5.957 68.421 -71.568 2.436 1.148 0.038 P05 J2B 43 J2B P26 P2 P 0 1 N N N -8.854 69.576 -77.288 -2.783 2.606 2.123 P26 J2B 44 J2B S06 S1 S 0 1 N N N -6.840 66.496 -71.701 2.627 3.158 0.685 S06 J2B 45 J2B S27 S2 S 0 1 N N N -9.659 71.517 -76.978 -4.332 1.649 3.210 S27 J2B 46 J2B H1 H1 H 0 1 N N N -8.315 70.801 -73.232 6.217 2.597 -1.099 H1 J2B 47 J2B H2 H2 H 0 1 N N N -8.519 68.905 -72.295 5.136 1.064 0.247 H2 J2B 48 J2B H3 H3 H 0 1 N N N -6.337 67.187 -73.916 -0.308 2.019 0.608 H3 J2B 49 J2B H4 H4 H 0 1 N N N -4.557 67.405 -74.018 -0.203 0.283 0.986 H4 J2B 50 J2B H5 H5 H 0 1 N N N -5.508 69.619 -75.315 -1.462 1.485 -1.521 H5 J2B 51 J2B H6 H6 H 0 1 N N N -4.948 68.100 -76.093 -1.357 -0.251 -1.143 H6 J2B 52 J2B H7 H7 H 0 1 N N N -5.589 68.129 -78.208 -5.122 0.018 0.970 H7 J2B 53 J2B H8 H8 H 0 1 N N N -3.056 67.788 -81.944 -6.627 -4.390 -0.167 H8 J2B 54 J2B H9 H9 H 0 1 N N N -5.193 64.620 -76.687 -7.097 1.936 -1.635 H9 J2B 55 J2B H10 H10 H 0 1 N N N -6.589 66.172 -76.026 -3.965 1.116 -1.630 H10 J2B 56 J2B H11 H11 H 0 1 N N N -7.654 68.144 -75.061 -2.657 0.179 0.964 H11 J2B 57 J2B H12 H12 H 0 1 N N N -9.147 70.150 -69.598 4.983 -1.012 -1.945 H12 J2B 58 J2B H13 H13 H 0 1 N N N -10.202 68.470 -68.273 7.786 -0.955 0.598 H13 J2B 59 J2B H14 H14 H 0 1 N N N -9.428 72.458 -71.001 6.224 0.748 -3.492 H14 J2B 60 J2B H15 H15 H 0 1 N N N -11.439 72.407 -72.713 7.772 2.739 -3.192 H15 J2B 61 J2B H16 H16 H 0 1 N N N -9.899 73.220 -73.151 8.470 1.916 -1.777 H16 J2B 62 J2B H17 H17 H 0 1 N N N -2.027 63.445 -81.930 -9.943 -1.636 -3.213 H17 J2B 63 J2B H18 H18 H 0 1 N N N -1.858 63.102 -80.343 -10.033 -3.300 -2.997 H18 J2B 64 J2B H19 H19 H 0 1 N N N -10.072 68.580 -73.314 3.075 -2.066 -0.574 H19 J2B 65 J2B H20 H20 H 0 1 N N N -11.328 65.985 -75.650 1.099 -3.222 -0.189 H20 J2B 66 J2B H21 H21 H 0 1 N N N -10.556 67.533 -75.559 0.971 -4.283 1.107 H21 J2B 67 J2B H22 H22 H 0 1 N N N -7.147 72.481 -72.104 5.144 3.182 -3.153 H22 J2B 68 J2B H23 H23 H 0 1 N N N -3.779 68.065 -76.826 -5.498 2.557 -0.387 H23 J2B 69 J2B H24 H24 H 0 1 N N N -8.020 67.663 -77.909 -3.724 -1.533 -0.468 H24 J2B 70 J2B H25 H25 H 0 1 N N N -10.062 67.938 -77.241 -2.884 4.523 3.177 H25 J2B 71 J2B H26 H26 H 0 1 N N N -10.619 71.734 -74.759 9.685 1.432 -3.776 H26 J2B 72 J2B H27 H27 H 0 1 N N N -6.017 65.772 -71.001 2.435 3.859 -0.446 H27 J2B 73 J2B H28 H28 H 0 1 N N N -9.890 71.911 -78.195 -5.445 2.229 2.725 H28 J2B 74 # # 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 J2B C02 C03 SING N N 1 J2B C02 C44 SING N N 2 J2B C02 O01 SING N N 3 J2B C03 C31 SING N N 4 J2B C03 O04 SING N N 5 J2B C08 C09 SING N N 6 J2B C08 O07 SING N N 7 J2B C09 C24 SING N N 8 J2B C11 C22 SING N N 9 J2B C11 N12 SING N N 10 J2B C11 O10 SING N N 11 J2B C13 C19 DOUB Y N 12 J2B C13 N12 SING Y N 13 J2B C13 N14 SING Y N 14 J2B C15 N14 DOUB Y N 15 J2B C15 N16 SING Y N 16 J2B C17 C19 SING Y N 17 J2B C17 N16 DOUB Y N 18 J2B C17 N18 SING N N 19 J2B C19 N20 SING Y N 20 J2B C21 N12 SING Y N 21 J2B C21 N20 DOUB Y N 22 J2B C22 C24 SING N N 23 J2B C22 O23 SING N N 24 J2B C24 O25 SING N N 25 J2B C31 N32 SING N N 26 J2B C31 O43 SING N N 27 J2B C33 C40 DOUB Y N 28 J2B C33 N32 SING Y N 29 J2B C33 N34 SING N N 30 J2B C35 N34 SING N N 31 J2B C35 N36 SING N N 32 J2B C35 N37 DOUB N N 33 J2B C38 C40 SING N N 34 J2B C38 N37 SING N N 35 J2B C38 O39 DOUB N N 36 J2B C40 N41 SING Y N 37 J2B C42 N32 SING Y N 38 J2B C42 N41 DOUB Y N 39 J2B C44 C45 SING N N 40 J2B C44 O43 SING N N 41 J2B C45 O46 SING N N 42 J2B O04 P05 SING N N 43 J2B O07 P05 SING N N 44 J2B O25 P26 SING N N 45 J2B O28 P26 DOUB N N 46 J2B O29 P26 SING N N 47 J2B O30 P05 DOUB N N 48 J2B P05 S06 SING N N 49 J2B P26 S27 SING N N 50 J2B C02 H1 SING N N 51 J2B C03 H2 SING N N 52 J2B C08 H3 SING N N 53 J2B C08 H4 SING N N 54 J2B C09 H5 SING N N 55 J2B C09 H6 SING N N 56 J2B C11 H7 SING N N 57 J2B C15 H8 SING N N 58 J2B C21 H9 SING N N 59 J2B C22 H10 SING N N 60 J2B C24 H11 SING N N 61 J2B C31 H12 SING N N 62 J2B C42 H13 SING N N 63 J2B C44 H14 SING N N 64 J2B C45 H15 SING N N 65 J2B C45 H16 SING N N 66 J2B N18 H17 SING N N 67 J2B N18 H18 SING N N 68 J2B N34 H19 SING N N 69 J2B N36 H20 SING N N 70 J2B N36 H21 SING N N 71 J2B O01 H22 SING N N 72 J2B O10 H23 SING N N 73 J2B O23 H24 SING N N 74 J2B O29 H25 SING N N 75 J2B O46 H26 SING N N 76 J2B S06 H27 SING N N 77 J2B S27 H28 SING N N 78 # # 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 J2B SMILES ACDLabs 12.01 "C3(C(C(n2c1c(C(N=C(N1)N)=O)nc2)OC3CO)OP(OCCC(C(C(n5c4c(c(ncn4)N)nc5)O)O)OP(=O)(O)S)(=O)S)O" J2B InChI InChI 1.03 "InChI=1S/C20H28N10O12P2S2/c21-14-9-15(24-4-23-14)29(5-25-9)18(35)12(33)7(41-43(36,37)45)1-2-39-44(38,46)42-13-11(32)8(3-31)40-19(13)30-6-26-10-16(30)27-20(22)28-17(10)34/h4-8,11-13,18-19,31-33,35H,1-3H2,(H,38,46)(H2,21,23,24)(H2,36,37,45)(H3,22,27,28,34)/t7-,8-,11-,12-,13-,18-,19-,44+/m1/s1" J2B InChIKey InChI 1.03 WDMUGQSSXDUMIY-MHPWAGLLSA-N J2B SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)c2ncn([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O[P@](S)(=O)OCC[C@@H](O[P](O)(S)=O)[C@@H](O)[C@@H](O)n4cnc5c(N)ncnc45)c2N1" J2B SMILES CACTVS 3.385 "NC1=NC(=O)c2ncn([CH]3O[CH](CO)[CH](O)[CH]3O[P](S)(=O)OCC[CH](O[P](O)(S)=O)[CH](O)[CH](O)n4cnc5c(N)ncnc45)c2N1" J2B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)[C@@H]([C@@H]([C@@H](CCO[P@@](=O)(O[C@@H]3[C@@H]([C@H](O[C@H]3n4cnc5c4NC(=NC5=O)N)CO)O)S)OP(=O)(O)S)O)O)N" J2B SMILES "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)C(C(C(CCOP(=O)(OC3C(C(OC3n4cnc5c4NC(=NC5=O)N)CO)O)S)OP(=O)(O)S)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 J2B "SYSTEMATIC NAME" ACDLabs 12.01 "O-[(1R,2R,3R)-5-{[(S)-{[(2R,3R,4R,5R)-2-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-3-yl]oxy}(sulfanyl)phosphoryl]oxy}-1-(6-amino-9H-purin-9-yl)-1,2-dihydroxypentan-3-yl] dihydrogen (R)-phosphorothioate (non-preferred name)" J2B "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(1~{R},2~{R},3~{R})-1-(6-aminopurin-9-yl)-5-[[(2~{R},3~{R},4~{R},5~{R})-2-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]oxy-sulfanyl-phosphoryl]oxy-1,2-bis(oxidanyl)pentan-3-yl]oxy-sulfanyl-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 J2B "Create component" 2018-08-30 RCSB J2B "Modify synonyms" 2018-08-31 RCSB J2B "Modify synonyms" 2018-09-04 RCSB J2B "Initial release" 2019-02-06 RCSB J2B "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id J2B _pdbx_chem_comp_synonyms.name "cleaved nonhydrolyzable phosphorothioate analog of 2'3' cyclic GMP-AMP" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##