data_9B7 # _chem_comp.id 9B7 _chem_comp.name "3',3'-cdIMP" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H22 N8 O14 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-3,5,10,12-tetrahydroxy-2,9-bis(6-oxo-3,6-dihydro-9H-purin-9-yl)octahydro-2H,5H, 7H,12H-5lambda~5~,12lambda~5~-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-5,12-dione ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-04-17 _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 660.381 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 9B7 _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 5VDR _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 9B7 C11 C1 C 0 1 N N R -29.423 -1.227 25.311 -4.991 0.117 0.761 C11 9B7 1 9B7 C13 C2 C 0 1 N N R -29.238 -0.266 27.348 -2.704 0.586 0.856 C13 9B7 2 9B7 C14 C3 C 0 1 N N N -28.928 1.040 28.030 -1.760 1.535 0.116 C14 9B7 3 9B7 O17 O1 O 0 1 N N N -28.545 4.276 25.941 0.849 2.030 -1.044 O17 9B7 4 9B7 C19 C4 C 0 1 N N S -27.832 -1.029 26.878 -2.807 -0.747 0.098 C19 9B7 5 9B7 O22 O2 O 0 1 N N N -25.056 0.179 27.728 0.557 -1.506 0.752 O22 9B7 6 9B7 C23 C5 C 0 1 N N N -25.235 1.228 28.675 1.921 -1.904 0.601 C23 9B7 7 9B7 C24 C6 C 0 1 N N R -24.959 2.555 27.997 2.827 -0.858 1.255 C24 9B7 8 9B7 C25 C7 C 0 1 N N S -25.945 2.898 27.235 2.750 0.463 0.473 C25 9B7 9 9B7 C27 C8 C 0 1 N N R -25.285 3.947 26.356 4.206 0.969 0.410 C27 9B7 10 9B7 C29 C9 C 0 1 N N R -23.959 3.234 25.983 5.049 -0.187 0.973 C29 9B7 11 9B7 C31 C10 C 0 1 Y N N -24.463 2.961 23.521 7.303 0.022 -0.136 C31 9B7 12 9B7 C35 C11 C 0 1 N N N -24.934 2.140 21.177 9.295 -0.224 -1.537 C35 9B7 13 9B7 C37 C12 C 0 1 Y N N -24.620 1.889 22.656 7.944 -0.654 -1.171 C37 9B7 14 9B7 C39 C13 C 0 1 Y N N -24.191 1.124 24.631 5.994 -1.558 -0.923 C39 9B7 15 9B7 O01 O3 O 0 1 N N N -27.688 -0.361 19.822 -10.111 1.161 -2.114 O01 9B7 16 9B7 C02 C14 C 0 1 N N N -28.064 -1.112 20.655 -9.458 0.543 -1.289 C02 9B7 17 9B7 N03 N1 N 0 1 N N N -28.228 -2.506 20.346 -10.017 -0.444 -0.563 N03 9B7 18 9B7 C04 C15 C 0 1 N N N -28.691 -3.422 21.375 -9.328 -1.111 0.322 C04 9B7 19 9B7 N05 N2 N 0 1 N N N -28.988 -2.921 22.723 -8.029 -0.869 0.571 N05 9B7 20 9B7 C06 C16 C 0 1 Y N N -28.815 -1.475 23.040 -7.358 0.111 -0.107 C06 9B7 21 9B7 C07 C17 C 0 1 Y N N -28.375 -0.599 22.064 -8.043 0.851 -1.067 C07 9B7 22 9B7 N08 N3 N 0 1 Y N N -28.319 0.613 22.632 -7.169 1.739 -1.592 N08 9B7 23 9B7 C09 C18 C 0 1 Y N N -28.702 0.506 23.895 -6.008 1.584 -1.023 C09 9B7 24 9B7 N10 N4 N 0 1 Y N N -29.006 -0.756 24.155 -6.085 0.591 -0.091 N10 9B7 25 9B7 O12 O4 O 0 1 N N N -29.872 -0.066 26.249 -4.016 1.151 0.915 O12 9B7 26 9B7 O15 O5 O 0 1 N N N -29.356 2.082 27.192 -0.665 1.878 0.969 O15 9B7 27 9B7 P16 P1 P 0 1 N N N -28.572 3.545 27.262 0.791 2.281 0.414 P16 9B7 28 9B7 O18 O6 O 0 1 N N N -29.431 4.401 28.159 1.058 3.843 0.699 O18 9B7 29 9B7 O20 O7 O 0 1 N N N -27.156 -1.628 28.018 -2.059 -1.762 0.771 O20 9B7 30 9B7 P21 P2 P 0 1 N N N -25.522 -1.359 28.173 -0.683 -2.366 0.192 P21 9B7 31 9B7 O26 O8 O 0 1 N N N -27.093 3.486 28.017 1.919 1.403 1.153 O26 9B7 32 9B7 O28 O9 O 0 1 N N N -25.033 5.074 27.071 4.361 2.137 1.218 O28 9B7 33 9B7 N30 N5 N 0 1 Y N N -24.195 2.445 24.733 6.082 -0.561 0.004 N30 9B7 34 9B7 N32 N6 N 0 1 N N N -24.600 4.358 23.017 7.962 1.044 0.490 N32 9B7 35 9B7 C33 C19 C 0 1 N N N -24.902 4.602 21.599 9.203 1.396 0.110 C33 9B7 36 9B7 N34 N7 N 0 1 N N N -25.067 3.485 20.688 9.845 0.801 -0.857 N34 9B7 37 9B7 O36 O10 O 0 1 N N N -25.068 1.226 20.438 9.906 -0.779 -2.436 O36 9B7 38 9B7 N38 N8 N 0 1 Y N N -24.445 0.772 23.375 7.096 -1.610 -1.615 N38 9B7 39 9B7 O40 O11 O 0 1 N N N -23.700 2.451 26.969 4.188 -1.301 1.214 O40 9B7 40 9B7 O41 O12 O 0 1 N N N -24.952 -1.813 29.495 -0.530 -3.898 0.663 O41 9B7 41 9B7 O42 O13 O 0 1 N N N -24.885 -2.264 27.149 -0.700 -2.303 -1.286 O42 9B7 42 9B7 C43 C20 C 0 1 N N R -28.237 -1.922 26.074 -4.309 -1.092 0.105 C43 9B7 43 9B7 O44 O14 O 0 1 N N N -28.739 -3.111 26.836 -4.544 -2.273 0.873 O44 9B7 44 9B7 H1 H1 H 0 1 N N N -30.250 -1.945 25.206 -5.384 -0.167 1.737 H1 9B7 45 9B7 H2 H2 H 0 1 N N N -29.768 -0.934 28.043 -2.333 0.404 1.865 H2 9B7 46 9B7 H3 H3 H 0 1 N N N -27.845 1.122 28.204 -1.383 1.044 -0.781 H3 9B7 47 9B7 H4 H4 H 0 1 N N N -29.459 1.093 28.992 -2.300 2.439 -0.164 H4 9B7 48 9B7 H5 H5 H 0 1 N N N -27.186 -0.275 26.405 -2.451 -0.631 -0.924 H5 9B7 49 9B7 H6 H6 H 0 1 N N N -26.269 1.214 29.051 2.074 -2.870 1.083 H6 9B7 50 9B7 H7 H7 H 0 1 N N N -24.538 1.090 29.514 2.163 -1.984 -0.458 H7 9B7 51 9B7 H8 H8 H 0 1 N N N -24.718 3.313 28.757 2.522 -0.693 2.288 H8 9B7 52 9B7 H9 H9 H 0 1 N N N -26.311 2.072 26.607 2.374 0.283 -0.534 H9 9B7 53 9B7 H10 H10 H 0 1 N N N -25.885 4.131 25.453 4.490 1.180 -0.621 H10 9B7 54 9B7 H11 H11 H 0 1 N N N -23.179 3.989 25.808 5.519 0.123 1.906 H11 9B7 55 9B7 H12 H12 H 0 1 N N N -24.009 0.438 25.445 5.141 -2.207 -1.061 H12 9B7 56 9B7 H13 H13 H 0 1 N N N -28.817 -4.470 21.148 -9.823 -1.893 0.878 H13 9B7 57 9B7 H14 H14 H 0 1 N N N -29.307 -3.552 23.430 -7.563 -1.394 1.240 H14 9B7 58 9B7 H15 H15 H 0 1 N N N -28.758 1.320 24.602 -5.122 2.160 -1.247 H15 9B7 59 9B7 H16 H16 H 0 1 N N N -29.730 5.164 27.678 0.417 4.434 0.281 H16 9B7 60 9B7 H17 H17 H 0 1 N N N -25.853 5.499 27.292 5.258 2.500 1.216 H17 9B7 61 9B7 H18 H18 H 0 1 N N N -24.486 5.129 23.644 7.530 1.520 1.216 H18 9B7 62 9B7 H19 H19 H 0 1 N N N -25.001 5.614 21.235 9.691 2.209 0.628 H19 9B7 63 9B7 H20 H20 H 0 1 N N N -24.352 -2.535 29.350 0.279 -4.326 0.350 H20 9B7 64 9B7 H21 H21 H 0 1 N N N -27.478 -2.238 25.343 -4.672 -1.224 -0.914 H21 9B7 65 9B7 H22 H22 H 0 1 N N N -28.015 -3.523 27.293 -5.477 -2.513 0.950 H22 9B7 66 # # 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 9B7 O01 C02 DOUB N N 1 9B7 N03 C02 SING N N 2 9B7 N03 C04 DOUB N N 3 9B7 O36 C35 DOUB N N 4 9B7 C02 C07 SING N N 5 9B7 N34 C35 SING N N 6 9B7 N34 C33 DOUB N N 7 9B7 C35 C37 SING N N 8 9B7 C04 N05 SING N N 9 9B7 C33 N32 SING N N 10 9B7 C07 N08 SING Y N 11 9B7 C07 C06 DOUB Y N 12 9B7 N08 C09 DOUB Y N 13 9B7 C37 N38 SING Y N 14 9B7 C37 C31 DOUB Y N 15 9B7 N05 C06 SING N N 16 9B7 N32 C31 SING N N 17 9B7 C06 N10 SING Y N 18 9B7 N38 C39 DOUB Y N 19 9B7 C31 N30 SING Y N 20 9B7 C09 N10 SING Y N 21 9B7 N10 C11 SING N N 22 9B7 C39 N30 SING Y N 23 9B7 N30 C29 SING N N 24 9B7 C11 C43 SING N N 25 9B7 C11 O12 SING N N 26 9B7 O17 P16 DOUB N N 27 9B7 C29 C27 SING N N 28 9B7 C29 O40 SING N N 29 9B7 C43 O44 SING N N 30 9B7 C43 C19 SING N N 31 9B7 O12 C13 SING N N 32 9B7 C27 O28 SING N N 33 9B7 C27 C25 SING N N 34 9B7 C19 C13 SING N N 35 9B7 C19 O20 SING N N 36 9B7 O40 C24 SING N N 37 9B7 O42 P21 DOUB N N 38 9B7 O15 P16 SING N N 39 9B7 O15 C14 SING N N 40 9B7 C25 C24 SING N N 41 9B7 C25 O26 SING N N 42 9B7 P16 O26 SING N N 43 9B7 P16 O18 SING N N 44 9B7 C13 C14 SING N N 45 9B7 O22 P21 SING N N 46 9B7 O22 C23 SING N N 47 9B7 C24 C23 SING N N 48 9B7 O20 P21 SING N N 49 9B7 P21 O41 SING N N 50 9B7 C11 H1 SING N N 51 9B7 C13 H2 SING N N 52 9B7 C14 H3 SING N N 53 9B7 C14 H4 SING N N 54 9B7 C19 H5 SING N N 55 9B7 C23 H6 SING N N 56 9B7 C23 H7 SING N N 57 9B7 C24 H8 SING N N 58 9B7 C25 H9 SING N N 59 9B7 C27 H10 SING N N 60 9B7 C29 H11 SING N N 61 9B7 C39 H12 SING N N 62 9B7 C04 H13 SING N N 63 9B7 N05 H14 SING N N 64 9B7 C09 H15 SING N N 65 9B7 O18 H16 SING N N 66 9B7 O28 H17 SING N N 67 9B7 N32 H18 SING N N 68 9B7 C33 H19 SING N N 69 9B7 O41 H20 SING N N 70 9B7 C43 H21 SING N N 71 9B7 O44 H22 SING N N 72 # # 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 9B7 SMILES ACDLabs 12.01 "C5(C(C1C(COP(=O)(OC2C(COP(O1)(O)=O)OC(C2O)n4c3c(C(N=CN3)=O)nc4)O)O5)O)n7c6NC=NC(=O)c6nc7" 9B7 InChI InChI 1.03 "InChI=1S/C20H22N8O14P2/c29-11-13-7(39-19(11)27-5-25-9-15(27)21-3-23-17(9)31)1-37-43(33,34)42-14-8(2-38-44(35,36)41-13)40-20(12(14)30)28-6-26-10-16(28)22-4-24-18(10)32/h3-8,11-14,19-20,29-30H,1-2H2,(H,33,34)(H,35,36)(H,21,23,31)(H,22,24,32)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1" 9B7 InChIKey InChI 1.03 VFTRASQVWRBMKD-XPWFQUROSA-N 9B7 SMILES_CANONICAL CACTVS 3.385 "O[C@@H]1[C@@H]2O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O[P](O)(=O)OC[C@H]2O[C@H]1n4cnc5C(=O)N=CNc45)n6cnc7C(=O)N=CNc67" 9B7 SMILES CACTVS 3.385 "O[CH]1[CH]2O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O[P](O)(=O)OC[CH]2O[CH]1n4cnc5C(=O)N=CNc45)n6cnc7C(=O)N=CNc67" 9B7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc2c(n1[C@H]3[C@@H]([C@H]4[C@H](O3)COP(=O)(O[C@@H]5[C@@H](COP(=O)(O4)O)O[C@H]([C@@H]5O)n6cnc7c6NC=NC7=O)O)O)NC=NC2=O" 9B7 SMILES "OpenEye OEToolkits" 2.0.6 "c1nc2c(n1C3C(C4C(O3)COP(=O)(OC5C(COP(=O)(O4)O)OC(C5O)n6cnc7c6NC=NC7=O)O)O)NC=NC2=O" # # 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 9B7 "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-3,5,10,12-tetrahydroxy-2,9-bis(6-oxo-3,6-dihydro-9H-purin-9-yl)octahydro-2H,5H,7H,12H-5lambda~5~,12lambda~5~-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-5,12-dione" 9B7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "9-[(1~{S},6~{R},8~{R},9~{R},10~{S},15~{R},17~{R},18~{R})-3,9,12,18-tetrakis(oxidanyl)-3,12-bis(oxidanylidene)-17-(6-oxidanylidene-3~{H}-purin-9-yl)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-8-yl]-3~{H}-purin-6-one" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 9B7 "Create component" 2017-04-17 RCSB 9B7 "Initial release" 2017-09-27 RCSB 9B7 "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 9B7 _pdbx_chem_comp_synonyms.name "(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-3,5,10,12-tetrahydroxy-2,9-bis(6-oxo-3,6-dihydro-9H-purin-9-yl)octahydro-2H,5H,7H,12H-5lambda~5~,12lambda~5~-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-5,12-dione" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##