data_IB2 # _chem_comp.id IB2 _chem_comp.name "P1-P2-METHYLENE-P3-THIO-DIADENOSINE TRIPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H29 N10 O14 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ADO-P-CH2-P-PS-ADO _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _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 770.500 _chem_comp.one_letter_code ? _chem_comp.three_letter_code IB2 _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 2FHI _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 IB2 PA PA P 0 1 N N S 9.263 12.986 23.227 -0.622 1.325 2.707 PA IB2 1 IB2 O1A O1A O 0 1 N N N 10.376 13.188 22.200 -1.719 2.235 2.309 O1A IB2 2 IB2 O2A O2A O 0 1 N N N 8.027 12.209 22.726 0.688 2.189 3.062 O2A IB2 3 IB2 C3A C3A C 0 1 N N N 8.651 14.692 23.665 -0.247 0.187 1.334 C3A IB2 4 IB2 PB PB P 0 1 N N S 8.321 15.940 22.351 0.261 1.148 -0.129 PB IB2 5 IB2 O1B O1B O 0 1 N N N 7.177 16.769 22.887 1.466 1.942 0.196 O1B IB2 6 IB2 O2B O2B O 0 1 N N N 8.039 15.200 21.076 -0.932 2.137 -0.563 O2B IB2 7 IB2 O3B O3B O 0 1 N N N 9.570 16.814 22.137 0.592 0.143 -1.342 O3B IB2 8 IB2 PG PG P 0 1 N N R 10.059 17.936 21.167 1.032 1.054 -2.594 PG IB2 9 IB2 O1G O1G O 0 1 N N N 9.076 18.418 20.266 2.226 1.850 -2.230 O1G IB2 10 IB2 S2G S2G S 0 1 N N N 11.198 17.465 20.425 -0.556 2.359 -3.111 S2G IB2 11 IB2 O5D O5* O 0 1 N N N 9.882 12.256 24.549 -1.071 0.477 4.000 O5D IB2 12 IB2 C5D C5* C 0 1 N N N 10.249 10.898 24.461 -1.350 1.420 5.037 C5D IB2 13 IB2 C4D C4* C 0 1 N N R 11.446 10.779 25.359 -1.785 0.675 6.300 C4D IB2 14 IB2 O4D O4* O 0 1 N N N 11.085 9.893 26.436 -0.726 -0.190 6.763 O4D IB2 15 IB2 C3D C3* C 0 1 N N S 12.663 10.160 24.643 -2.018 1.668 7.460 C3D IB2 16 IB2 O3D O3* O 0 1 N N N 13.870 10.845 25.008 -3.409 1.968 7.591 O3D IB2 17 IB2 C2D C2* C 0 1 N N R 12.717 8.678 25.063 -1.506 0.915 8.710 C2D IB2 18 IB2 O2D O2* O 0 1 N N N 14.103 8.105 25.051 -2.564 0.729 9.651 O2D IB2 19 IB2 C1D C1* C 0 1 N N R 12.010 8.736 26.446 -1.021 -0.442 8.154 C1D IB2 20 IB2 "O5'" "O5'" O 0 1 N N N 10.513 19.059 22.212 1.380 0.109 -3.850 "O5'" IB2 21 IB2 "C5'" "C5'" C 0 1 N N N 9.522 19.922 22.826 1.761 0.971 -4.924 "C5'" IB2 22 IB2 "C4'" "C4'" C 0 1 N N R 9.641 19.743 24.350 2.106 0.132 -6.155 "C4'" IB2 23 IB2 "O4'" "O4'" O 0 1 N N N 9.851 21.047 24.963 0.953 -0.614 -6.577 "O4'" IB2 24 IB2 "C3'" "C3'" C 0 1 N N S 8.338 19.146 24.944 2.511 1.054 -7.322 "C3'" IB2 25 IB2 "O3'" "O3'" O 0 1 N N N 8.569 18.100 25.912 3.846 0.774 -7.748 "O3'" IB2 26 IB2 "C2'" "C2'" C 0 1 N N R 7.610 20.318 25.544 1.499 0.707 -8.444 "C2'" IB2 27 IB2 "O2'" "O2'" O 0 1 N N N 6.768 19.973 26.678 2.147 0.657 -9.717 "O2'" IB2 28 IB2 "C1'" "C1'" C 0 1 N N R 8.742 21.285 25.880 1.010 -0.700 -8.017 "C1'" IB2 29 IB2 N9 N9 N 0 1 Y N N 8.273 22.716 25.789 -0.317 -0.978 -8.571 N9 IB2 30 IB2 C8 C8 C 0 1 Y N N 7.901 23.367 24.656 -1.512 -0.623 -8.019 C8 IB2 31 IB2 N7 N7 N 0 1 Y N N 7.546 24.636 24.927 -2.489 -1.029 -8.775 N7 IB2 32 IB2 C5 C5 C 0 1 Y N N 7.681 24.806 26.235 -1.986 -1.669 -9.858 C5 IB2 33 IB2 C6 C6 C 0 1 Y N N 7.474 25.883 27.091 -2.546 -2.299 -10.982 C6 IB2 34 IB2 N6 N6 N 0 1 N N N 7.052 27.076 26.632 -3.918 -2.354 -11.153 N6 IB2 35 IB2 N1 N1 N 0 1 Y N N 7.733 25.680 28.496 -1.726 -2.841 -11.878 N1 IB2 36 IB2 C2 C2 C 0 1 Y N N 8.183 24.462 29.023 -0.416 -2.792 -11.723 C2 IB2 37 IB2 N3 N3 N 0 1 Y N N 8.380 23.440 28.166 0.152 -2.213 -10.687 N3 IB2 38 IB2 C4 C4 C 0 1 Y N N 8.143 23.563 26.756 -0.586 -1.639 -9.743 C4 IB2 39 IB2 N9A AN9 N 0 1 Y N N 11.294 7.452 26.725 0.184 -0.881 8.860 N9A IB2 40 IB2 C8A AC8 C 0 1 Y N N 11.871 6.231 26.842 1.470 -0.574 8.527 C8A IB2 41 IB2 N7A AN7 N 0 1 Y N N 10.934 5.304 27.083 2.292 -1.130 9.369 N7A IB2 42 IB2 C5A AC5 C 0 1 Y N N 9.753 5.933 27.120 1.588 -1.823 10.296 C5A IB2 43 IB2 C6A AC6 C 0 1 Y N N 8.426 5.510 27.326 1.927 -2.608 11.411 C6A IB2 44 IB2 N6A AN6 N 0 1 N N N 8.119 4.235 27.540 3.251 -2.794 11.770 N6A IB2 45 IB2 N1A AN1 N 0 1 Y N N 7.402 6.493 27.297 0.947 -3.164 12.115 N1A IB2 46 IB2 C2A AC2 C 0 1 Y N N 7.682 7.862 27.070 -0.318 -2.993 11.780 C2A IB2 47 IB2 N3A AN3 N 0 1 Y N N 8.986 8.246 26.867 -0.682 -2.271 10.741 N3A IB2 48 IB2 C4A AC4 C 0 1 Y N N 10.044 7.302 26.889 0.227 -1.676 9.977 C4A IB2 49 IB2 HOA2 2HOA H 0 0 N N N 7.334 12.083 23.364 1.377 1.560 3.316 HOA2 IB2 50 IB2 H3A1 1H3A H 0 0 N N N 7.728 14.583 24.280 0.560 -0.482 1.627 H3A1 IB2 51 IB2 H3A2 2H3A H 0 0 N N N 9.361 15.138 24.398 -1.135 -0.397 1.094 H3A2 IB2 52 IB2 HOB2 2HOB H 0 0 N N N 7.868 15.843 20.398 -1.696 1.581 -0.766 HOB2 IB2 53 IB2 HSG2 2HSG H 0 0 N N N 11.495 18.147 19.834 -1.513 1.459 -3.399 HSG2 IB2 54 IB2 "H5'1" 1H5* H 0 0 N N N 9.425 10.186 24.701 -2.150 2.087 4.715 "H5'1" IB2 55 IB2 "H5'2" 2H5* H 0 0 N N N 10.421 10.538 23.419 -0.454 2.002 5.249 "H5'2" IB2 56 IB2 H4D H4* H 0 1 N N N 11.728 11.801 25.702 -2.690 0.098 6.107 H4D IB2 57 IB2 H3D H3* H 0 1 N N N 12.566 10.252 23.536 -1.445 2.582 7.301 H3D IB2 58 IB2 "HO3'" *HO3 H 0 0 N N N 14.619 10.463 24.566 -3.493 2.590 8.326 "HO3'" IB2 59 IB2 H2D H2* H 0 1 N N N 12.217 7.968 24.362 -0.678 1.455 9.169 H2D IB2 60 IB2 "HO2'" *HO2 H 0 0 N N N 14.136 7.191 25.309 -2.863 1.610 9.914 "HO2'" IB2 61 IB2 H1D H1* H 0 1 N N N 12.756 8.867 27.263 -1.807 -1.192 8.246 H1D IB2 62 IB2 H51X "1H5'" H 0 0 N N N 9.610 20.985 22.503 0.935 1.642 -5.161 H51X IB2 63 IB2 H52X "2H5'" H 0 0 N N N 8.489 19.741 22.444 2.631 1.557 -4.628 H52X IB2 64 IB2 "H4'" "H4'" H 0 1 N N N 10.492 19.052 24.555 2.924 -0.550 -5.921 "H4'" IB2 65 IB2 "H3'" "H3'" H 0 1 N N N 7.741 18.638 24.150 2.416 2.100 -7.031 "H3'" IB2 66 IB2 HO3X "'HO3" H 0 0 N N N 7.771 17.734 26.275 4.019 1.338 -8.515 HO3X IB2 67 IB2 "H2'" "H2'" H 0 1 N N N 6.860 20.761 24.847 0.673 1.418 -8.458 "H2'" IB2 68 IB2 HO2X "'HO2" H 0 0 N N N 6.308 20.713 27.056 2.426 1.559 -9.924 HO2X IB2 69 IB2 "H1'" "H1'" H 0 1 N N N 9.079 21.110 26.928 1.722 -1.464 -8.328 "H1'" IB2 70 IB2 H8 H8 H 0 1 N N N 7.888 22.922 23.646 -1.629 -0.084 -7.090 H8 IB2 71 IB2 HN61 1HN6 H 0 0 N N N 6.900 27.865 27.259 -4.292 -2.793 -11.933 HN61 IB2 72 IB2 HN62 2HN6 H 0 0 N N N 6.191 26.923 26.106 -4.505 -1.955 -10.492 HN62 IB2 73 IB2 H2 H2 H 0 1 N N N 8.379 24.309 30.097 0.212 -3.245 -12.475 H2 IB2 74 IB2 H8A AH8 H 0 1 N N N 12.950 6.021 26.753 1.763 0.039 7.689 H8A IB2 75 IB2 HNA1 1HNA H 0 0 N N N 7.157 3.928 27.689 3.472 -3.335 12.544 HNA1 IB2 76 IB2 HNA2 2HNA H 0 0 N N N 8.675 3.909 28.330 3.957 -2.386 11.245 HNA2 IB2 77 IB2 H2A AH2 H 0 1 N N N 6.887 8.626 27.051 -1.083 -3.463 12.380 H2A IB2 78 # # 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 IB2 PA O1A DOUB N N 1 IB2 PA O2A SING N N 2 IB2 PA C3A SING N N 3 IB2 PA O5D SING N N 4 IB2 O2A HOA2 SING N N 5 IB2 C3A PB SING N N 6 IB2 C3A H3A1 SING N N 7 IB2 C3A H3A2 SING N N 8 IB2 PB O1B DOUB N N 9 IB2 PB O2B SING N N 10 IB2 PB O3B SING N N 11 IB2 O2B HOB2 SING N N 12 IB2 O3B PG SING N N 13 IB2 PG O1G DOUB N N 14 IB2 PG S2G SING N N 15 IB2 PG "O5'" SING N N 16 IB2 S2G HSG2 SING N N 17 IB2 O5D C5D SING N N 18 IB2 C5D C4D SING N N 19 IB2 C5D "H5'1" SING N N 20 IB2 C5D "H5'2" SING N N 21 IB2 C4D O4D SING N N 22 IB2 C4D C3D SING N N 23 IB2 C4D H4D SING N N 24 IB2 O4D C1D SING N N 25 IB2 C3D O3D SING N N 26 IB2 C3D C2D SING N N 27 IB2 C3D H3D SING N N 28 IB2 O3D "HO3'" SING N N 29 IB2 C2D O2D SING N N 30 IB2 C2D C1D SING N N 31 IB2 C2D H2D SING N N 32 IB2 O2D "HO2'" SING N N 33 IB2 C1D N9A SING N N 34 IB2 C1D H1D SING N N 35 IB2 "O5'" "C5'" SING N N 36 IB2 "C5'" "C4'" SING N N 37 IB2 "C5'" H51X SING N N 38 IB2 "C5'" H52X SING N N 39 IB2 "C4'" "O4'" SING N N 40 IB2 "C4'" "C3'" SING N N 41 IB2 "C4'" "H4'" SING N N 42 IB2 "O4'" "C1'" SING N N 43 IB2 "C3'" "O3'" SING N N 44 IB2 "C3'" "C2'" SING N N 45 IB2 "C3'" "H3'" SING N N 46 IB2 "O3'" HO3X SING N N 47 IB2 "C2'" "O2'" SING N N 48 IB2 "C2'" "C1'" SING N N 49 IB2 "C2'" "H2'" SING N N 50 IB2 "O2'" HO2X SING N N 51 IB2 "C1'" N9 SING N N 52 IB2 "C1'" "H1'" SING N N 53 IB2 N9 C8 SING Y N 54 IB2 N9 C4 SING Y N 55 IB2 C8 N7 DOUB Y N 56 IB2 C8 H8 SING N N 57 IB2 N7 C5 SING Y N 58 IB2 C5 C6 SING Y N 59 IB2 C5 C4 DOUB Y N 60 IB2 C6 N6 SING N N 61 IB2 C6 N1 DOUB Y N 62 IB2 N6 HN61 SING N N 63 IB2 N6 HN62 SING N N 64 IB2 N1 C2 SING Y N 65 IB2 C2 N3 DOUB Y N 66 IB2 C2 H2 SING N N 67 IB2 N3 C4 SING Y N 68 IB2 N9A C8A SING Y N 69 IB2 N9A C4A SING Y N 70 IB2 C8A N7A DOUB Y N 71 IB2 C8A H8A SING N N 72 IB2 N7A C5A SING Y N 73 IB2 C5A C6A SING Y N 74 IB2 C5A C4A DOUB Y N 75 IB2 C6A N6A SING N N 76 IB2 C6A N1A DOUB Y N 77 IB2 N6A HNA1 SING N N 78 IB2 N6A HNA2 SING N N 79 IB2 N1A C2A SING Y N 80 IB2 C2A N3A DOUB Y N 81 IB2 C2A H2A SING N N 82 IB2 N3A C4A SING Y N 83 # # 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 IB2 SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)C[P@@](O)(=O)O[P@@](S)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)[C@@H](O)[C@H]3O" IB2 SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](S)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)[CH](O)[CH]3O" IB2 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(C[P@](=O)(O)O[P@@](=O)(OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)S)O)O)O)N" IB2 SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)S)O)O)O)N" IB2 InChI InChI 1.03 "InChI=1S/C21H29N10O14P3S/c22-16-10-18(26-3-24-16)30(5-28-10)20-14(34)12(32)8(43-20)1-41-46(36,37)7-47(38,39)45-48(40,49)42-2-9-13(33)15(35)21(44-9)31-6-29-11-17(23)25-4-27-19(11)31/h3-6,8-9,12-15,20-21,32-35H,1-2,7H2,(H,36,37)(H,38,39)(H,40,49)(H2,22,24,26)(H2,23,25,27)/t8-,9-,12-,13-,14-,15-,20-,21-,48-/m1/s1" IB2 InChIKey InChI 1.03 UJCWOSLCGXVJOD-LCHUORCTSA-N # _pdbx_chem_comp_identifier.comp_id IB2 _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 "[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-sulfanyl-phosphoryl]oxy-hydroxy-phosphoryl]methyl]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 IB2 "Create component" 1999-07-08 RCSB IB2 "Modify descriptor" 2011-06-04 RCSB IB2 "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id IB2 _pdbx_chem_comp_synonyms.name ADO-P-CH2-P-PS-ADO _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##