data_V7E # _chem_comp.id V7E _chem_comp.name "3',3'-c-di-araAMP" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H24 N10 O12 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(1S,6R,8R,9S,10S,15R,17R,18S)-8,17-bis(6-aminopurin-9-yl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^5-diphosphatricyclo[13.3.0.0^{6,10}]octadecane-9,18-diol" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-04-22 _chem_comp.pdbx_modified_date 2022-04-29 _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 658.412 _chem_comp.one_letter_code ? _chem_comp.three_letter_code V7E _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 7OB3 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # # 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 V7E P P1 P 0 1 N N N 73.101 58.549 31.802 0.716 2.275 0.685 P V7E 1 V7E O1P O1 O 0 1 N N N 73.749 57.429 31.023 0.921 2.508 -0.762 O1P V7E 2 V7E O2P O2 O 0 1 N N N 71.634 58.667 31.461 0.450 3.682 1.423 O2P V7E 3 V7E "O5'" O3 O 0 1 N N N 73.259 58.248 33.373 -0.554 1.309 0.899 "O5'" V7E 4 V7E "C5'" C1 C 0 1 N N N 72.585 59.076 34.313 -1.901 1.735 0.684 "C5'" V7E 5 V7E "C4'" C2 C 0 1 N N R 73.187 58.903 35.696 -2.860 0.736 1.334 "C4'" V7E 6 V7E "O4'" O4 O 0 1 N N N 73.274 57.524 36.085 -4.205 1.214 1.235 "O4'" V7E 7 V7E "C3'" C3 C 0 1 N N S 74.612 59.436 35.802 -2.793 -0.609 0.592 "C3'" V7E 8 V7E "O3'" O5 O 0 1 N N N 74.705 60.832 36.005 -2.033 -1.556 1.346 "O3'" V7E 9 V7E "C2'" C4 C 0 1 N N S 75.175 58.648 36.977 -4.260 -1.067 0.472 "C2'" V7E 10 V7E "O2'" O6 O 0 1 N N N 76.589 58.519 36.901 -4.581 -1.351 -0.891 "O2'" V7E 11 V7E "C1'" C5 C 0 1 N N R 74.455 57.308 36.871 -5.090 0.121 0.980 "C1'" V7E 12 V7E N9 N1 N 0 1 Y N N 75.367 56.339 36.216 -6.073 0.507 -0.035 N9 V7E 13 V7E C8 C6 C 0 1 Y N N 75.440 56.089 34.895 -5.924 1.489 -0.969 C8 V7E 14 V7E N7 N2 N 0 1 Y N N 76.389 55.152 34.638 -6.991 1.562 -1.710 N7 V7E 15 V7E C5 C7 C 0 1 Y N N 76.944 54.797 35.810 -7.890 0.635 -1.300 C5 V7E 16 V7E C6 C8 C 0 1 Y N N 78.002 53.860 36.257 -9.180 0.260 -1.711 C6 V7E 17 V7E N6 N3 N 0 1 N N N 78.678 53.091 35.371 -9.801 0.901 -2.769 N6 V7E 18 V7E N1 N4 N 0 1 Y N N 78.269 53.799 37.580 -9.791 -0.725 -1.060 N1 V7E 19 V7E C2 C9 C 0 1 Y N N 77.611 54.555 38.480 -9.206 -1.342 -0.050 C2 V7E 20 V7E N3 N5 N 0 1 Y N N 76.641 55.421 38.139 -7.999 -1.025 0.369 N3 V7E 21 V7E C4 C10 C 0 1 Y N N 76.269 55.585 36.848 -7.309 -0.056 -0.223 C4 V7E 22 V7E P1 P2 P 0 1 N N N 76.101 61.566 35.675 -0.700 -2.259 0.779 P1 V7E 23 V7E O1P1 O7 O 0 0 N N N 75.987 63.032 36.017 -0.529 -3.581 1.420 O1P1 V7E 24 V7E O2P1 O8 O 0 0 N N N 77.214 60.912 36.460 -0.829 -2.448 -0.815 O2P1 V7E 25 V7E "O5'1" O9 O 0 0 N N N 76.408 61.409 34.106 0.575 -1.333 1.108 "O5'1" V7E 26 V7E "C5'1" C11 C 0 0 N N N 75.571 62.070 33.164 1.920 -1.732 0.835 "C5'1" V7E 27 V7E "C4'1" C12 C 0 0 N N R 75.753 61.468 31.783 2.883 -0.697 1.418 "C4'1" V7E 28 V7E "O4'1" O10 O 0 0 N N N 77.136 61.389 31.406 4.230 -1.173 1.327 "O4'1" V7E 29 V7E "C3'1" C13 C 0 0 N N S 75.232 60.040 31.670 2.800 0.607 0.607 "C3'1" V7E 30 V7E "O3'1" O11 O 0 0 N N N 73.838 59.943 31.461 2.030 1.582 1.309 "O3'1" V7E 31 V7E "C2'1" C14 C 0 0 N N S 76.023 59.497 30.488 4.263 1.074 0.463 "C2'1" V7E 32 V7E "O2'1" O12 O 0 0 N N N 76.160 58.083 30.549 4.576 1.310 -0.912 "O2'1" V7E 33 V7E "C1'1" C15 C 0 0 N N R 77.363 60.219 30.605 5.105 -0.088 1.011 "C1'1" V7E 34 V7E N91 N6 N 0 1 Y N N 78.334 59.307 31.256 6.075 -0.515 -0.001 N91 V7E 35 V7E C81 C16 C 0 1 Y N N 78.601 59.248 32.574 5.918 -1.538 -0.887 C81 V7E 36 V7E N71 N7 N 0 1 Y N N 79.535 58.296 32.832 6.974 -1.640 -1.640 N71 V7E 37 V7E C51 C17 C 0 1 Y N N 79.873 57.726 31.661 7.874 -0.691 -1.286 C51 V7E 38 V7E C61 C18 C 0 1 Y N N 80.797 56.657 31.214 9.156 -0.329 -1.732 C61 V7E 39 V7E N61 N8 N 0 1 N N N 81.573 55.985 32.097 9.764 -1.014 -2.769 N61 V7E 40 V7E N11 N9 N 0 1 Y N N 80.841 56.375 29.893 9.771 0.688 -1.136 N11 V7E 41 V7E C21 C19 C 0 1 Y N N 80.080 57.029 28.995 9.198 1.347 -0.146 C21 V7E 42 V7E N31 N10 N 0 1 Y N N 79.222 58.007 29.336 7.999 1.043 0.305 N31 V7E 43 V7E C41 C20 C 0 1 Y N N 79.076 58.394 30.625 7.305 0.045 -0.233 C41 V7E 44 V7E H1 H1 H 0 1 N N N 71.404 58.007 30.817 -0.327 4.156 1.097 H1 V7E 45 V7E "H5'A" H2 H 0 0 N N N 72.681 60.127 34.005 -2.046 2.719 1.129 "H5'A" V7E 46 V7E "H5'" H3 H 0 1 N N N 71.521 58.799 34.343 -2.100 1.786 -0.386 "H5'" V7E 47 V7E "H4'" H4 H 0 1 N N N 72.560 59.448 36.417 -2.597 0.595 2.382 "H4'" V7E 48 V7E "H3'" H5 H 0 1 N N N 75.161 59.150 34.893 -2.359 -0.474 -0.398 "H3'" V7E 49 V7E "H2'" H6 H 0 1 N N N 74.882 59.141 37.916 -4.435 -1.946 1.093 "H2'" V7E 50 V7E "HO2'" H7 H 0 0 N N N 76.903 58.023 37.648 -5.493 -1.644 -1.027 "HO2'" V7E 51 V7E "H1'" H8 H 0 1 N N N 74.192 56.954 37.879 -5.604 -0.157 1.900 "H1'" V7E 52 V7E H8 H9 H 0 1 N N N 74.829 56.567 34.144 -5.050 2.114 -1.078 H8 V7E 53 V7E H3 H10 H 0 1 N N N 79.346 52.529 35.859 -9.345 1.619 -3.236 H3 V7E 54 V7E HN6 H11 H 0 1 N N N 78.035 52.499 34.885 -10.692 0.633 -3.043 HN6 V7E 55 V7E H2 H12 H 0 1 N N N 77.875 54.461 39.523 -9.738 -2.138 0.451 H2 V7E 56 V7E H4 H13 H 0 1 N N N 77.628 61.557 37.021 -0.060 -2.866 -1.225 H4 V7E 57 V7E "HC5'" H14 H 0 0 N N N 74.521 61.960 33.472 2.111 -2.704 1.291 "HC5'" V7E 58 V7E HC5A H15 H 0 0 N N N 75.834 63.138 33.132 2.068 -1.800 -0.243 HC5A V7E 59 V7E "HC4'" H16 H 0 0 N N N 75.210 62.092 31.058 2.633 -0.500 2.460 "HC4'" V7E 60 V7E "HC3'" H17 H 0 0 N N N 75.522 59.485 32.575 2.370 0.414 -0.376 "HC3'" V7E 61 V7E "HC2'" H18 H 0 0 N N N 75.530 59.799 29.552 4.432 1.977 1.050 "HC2'" V7E 62 V7E HO2A H19 H 0 0 N N N 75.313 57.690 30.725 5.484 1.607 -1.063 HO2A V7E 63 V7E "HC1'" H20 H 0 0 N N N 77.719 60.496 29.602 5.632 0.232 1.910 "HC1'" V7E 64 V7E HC8 H21 H 0 1 N N N 78.136 59.872 33.323 5.045 -2.171 -0.955 HC8 V7E 65 V7E H5 H22 H 0 1 N N N 82.125 55.309 31.609 9.306 -1.754 -3.197 H5 V7E 66 V7E H1N6 H23 H 0 0 N N N 82.175 56.629 32.569 10.650 -0.754 -3.069 H1N6 V7E 67 V7E HC2 H24 H 0 1 N N N 80.162 56.756 27.953 9.733 2.167 0.311 HC2 V7E 68 # # 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 V7E P O1P DOUB N N 1 V7E P O2P SING N N 2 V7E P "O5'" SING N N 3 V7E P "O3'1" SING N N 4 V7E "O5'" "C5'" SING N N 5 V7E "C5'" "C4'" SING N N 6 V7E "C4'" "O4'" SING N N 7 V7E "C4'" "C3'" SING N N 8 V7E "O4'" "C1'" SING N N 9 V7E "C3'" "O3'" SING N N 10 V7E "C3'" "C2'" SING N N 11 V7E "O3'" P1 SING N N 12 V7E "C2'" "O2'" SING N N 13 V7E "C2'" "C1'" SING N N 14 V7E "C1'" N9 SING N N 15 V7E N9 C8 SING Y N 16 V7E N9 C4 SING Y N 17 V7E C8 N7 DOUB Y N 18 V7E N7 C5 SING Y N 19 V7E C5 C6 DOUB Y N 20 V7E C5 C4 SING Y N 21 V7E C6 N6 SING N N 22 V7E C6 N1 SING Y N 23 V7E N1 C2 DOUB Y N 24 V7E C2 N3 SING Y N 25 V7E N3 C4 DOUB Y N 26 V7E P1 O1P1 DOUB N N 27 V7E P1 O2P1 SING N N 28 V7E P1 "O5'1" SING N N 29 V7E "O5'1" "C5'1" SING N N 30 V7E "C5'1" "C4'1" SING N N 31 V7E "C4'1" "O4'1" SING N N 32 V7E "C4'1" "C3'1" SING N N 33 V7E "O4'1" "C1'1" SING N N 34 V7E "C3'1" "O3'1" SING N N 35 V7E "C3'1" "C2'1" SING N N 36 V7E "C2'1" "O2'1" SING N N 37 V7E "C2'1" "C1'1" SING N N 38 V7E "C1'1" N91 SING N N 39 V7E N91 C81 SING Y N 40 V7E N91 C41 SING Y N 41 V7E C81 N71 DOUB Y N 42 V7E N71 C51 SING Y N 43 V7E C51 C61 DOUB Y N 44 V7E C51 C41 SING Y N 45 V7E C61 N61 SING N N 46 V7E C61 N11 SING Y N 47 V7E N11 C21 DOUB Y N 48 V7E C21 N31 SING Y N 49 V7E N31 C41 DOUB Y N 50 V7E O2P H1 SING N N 51 V7E "C5'" "H5'A" SING N N 52 V7E "C5'" "H5'" SING N N 53 V7E "C4'" "H4'" SING N N 54 V7E "C3'" "H3'" SING N N 55 V7E "C2'" "H2'" SING N N 56 V7E "O2'" "HO2'" SING N N 57 V7E "C1'" "H1'" SING N N 58 V7E C8 H8 SING N N 59 V7E N6 H3 SING N N 60 V7E N6 HN6 SING N N 61 V7E C2 H2 SING N N 62 V7E O2P1 H4 SING N N 63 V7E "C5'1" "HC5'" SING N N 64 V7E "C5'1" HC5A SING N N 65 V7E "C4'1" "HC4'" SING N N 66 V7E "C3'1" "HC3'" SING N N 67 V7E "C2'1" "HC2'" SING N N 68 V7E "O2'1" HO2A SING N N 69 V7E "C1'1" "HC1'" SING N N 70 V7E C81 HC8 SING N N 71 V7E N61 H5 SING N N 72 V7E N61 H1N6 SING N N 73 V7E C21 HC2 SING N N 74 # # 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 V7E InChI InChI 1.03 "InChI=1S/C20H24N10O12P2/c21-15-9-17(25-3-23-15)29(5-27-9)19-11(31)13-7(39-19)1-37-43(33,34)42-14-8(2-38-44(35,36)41-13)40-20(12(14)32)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-32H,1-2H2,(H,33,34)(H,35,36)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11+,12+,13-,14-,19-,20-/m1/s1" V7E InChIKey InChI 1.03 PDXMFTWFFKBFIN-SVHUXIIHSA-N V7E SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]4CO[P](O)(=O)O[C@H]5[C@H](O)[C@@H](O[C@@H]5CO[P](O)(=O)O[C@H]4[C@@H]3O)n6cnc7c(N)ncnc67" V7E SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH]4CO[P](O)(=O)O[CH]5[CH](O)[CH](O[CH]5CO[P](O)(=O)O[CH]4[CH]3O)n6cnc7c(N)ncnc67" V7E SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[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)n6cnc7c6ncnc7N)O)O)N" V7E SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=O)(OC5C(COP(=O)(O4)O)OC(C5O)n6cnc7c6ncnc7N)O)O)N" # _pdbx_chem_comp_identifier.comp_id V7E _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "(1~{S},6~{R},8~{R},9~{S},10~{S},15~{R},17~{R},18~{S})-8,17-bis(6-aminopurin-9-yl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecane-9,18-diol" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id V7E _pdbx_chem_comp_synonyms.name "(1S,6R,8R,9S,10S,15R,17R,18S)-8,17-bis(6-aminopurin-9-yl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^5-diphosphatricyclo[13.3.0.0^{6,10}]octadecane-9,18-diol" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site V7E "Create component" 2021-04-22 PDBE V7E "Initial release" 2022-05-04 RCSB ##