data_VJ8 # _chem_comp.id VJ8 _chem_comp.name edaGDP _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H25 N7 O13 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl] ~{N}-[2-(propanoylamino)ethyl]carbamate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-05-18 _chem_comp.pdbx_modified_date 2022-07-29 _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 585.356 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VJ8 _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 7OK3 _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 VJ8 C4 C1 C 0 1 Y N N 46.833 26.900 3.201 -0.031 4.463 0.251 C4 VJ8 1 VJ8 C5 C2 C 0 1 Y N N 46.944 25.885 4.081 0.777 5.498 -0.232 C5 VJ8 2 VJ8 C6 C3 C 0 1 N N N 46.045 24.873 4.015 0.328 6.832 -0.087 C6 VJ8 3 VJ8 C8 C4 C 0 1 Y N N 48.579 27.277 4.481 1.807 3.636 -0.641 C8 VJ8 4 VJ8 N1 N1 N 0 1 N N N 45.029 24.931 3.097 -0.864 7.046 0.513 N1 VJ8 5 VJ8 N2 N2 N 0 1 N N N 43.974 26.063 1.274 -2.815 6.242 1.564 N2 VJ8 6 VJ8 N3 N3 N 0 1 N N N 45.878 26.973 2.249 -1.202 4.751 0.830 N3 VJ8 7 VJ8 C1A C5 C 0 1 N N R 48.174 29.044 2.741 0.187 1.945 0.302 C1A VJ8 8 VJ8 C2 C6 C 0 1 N N N 44.956 25.971 2.170 -1.606 5.995 0.964 C2 VJ8 9 VJ8 C2A C7 C 0 1 N N R 48.393 30.149 3.672 -0.747 1.404 -0.810 C2A VJ8 10 VJ8 C3A C8 C 0 1 N N S 49.299 31.107 2.911 -0.589 -0.128 -0.650 C3A VJ8 11 VJ8 C4A C9 C 0 1 N N R 50.178 30.087 2.119 0.747 -0.293 0.100 C4A VJ8 12 VJ8 C5A C10 C 0 1 N N N 51.513 29.817 2.860 1.708 -1.145 -0.731 C5A VJ8 13 VJ8 CBC C11 C 0 1 N N N 49.160 32.759 1.228 -2.766 -1.101 -0.548 CBC VJ8 14 VJ8 CBF C12 C 0 1 N N N 48.967 34.309 -0.643 -4.994 -2.083 -0.621 CBF VJ8 15 VJ8 CBG C13 C 0 1 N N N 49.500 33.621 -1.913 -6.035 -2.620 0.363 CBG VJ8 16 VJ8 CBI C14 C 0 1 N N N 51.192 31.880 -1.514 -8.264 -3.602 0.289 CBI VJ8 17 VJ8 CBJ C15 C 0 1 N N N 52.708 31.528 -1.469 -9.474 -4.081 -0.470 CBJ VJ8 18 VJ8 CBL C16 C 0 1 N N N 53.007 30.976 -0.097 -10.515 -4.617 0.514 CBL VJ8 19 VJ8 N7 N4 N 0 1 Y N N 48.026 26.122 4.886 1.885 4.928 -0.765 N7 VJ8 20 VJ8 N9 N5 N 0 1 Y N N 47.837 27.771 3.476 0.640 3.301 -0.018 N9 VJ8 21 VJ8 NBE N6 N 0 1 N N N 48.445 33.327 0.287 -3.818 -1.618 0.117 NBE VJ8 22 VJ8 NBH N7 N 0 1 N N N 50.906 33.134 -1.822 -7.212 -3.085 -0.375 NBH VJ8 23 VJ8 O2A O1 O 0 1 N N N 47.061 30.816 3.976 -2.099 1.804 -0.579 O2A VJ8 24 VJ8 O3A O2 O 0 1 N N N 48.497 31.804 1.945 -1.685 -0.673 0.131 O3A VJ8 25 VJ8 O4A O3 O 0 1 N N N 49.439 28.801 2.129 1.297 1.021 0.288 O4A VJ8 26 VJ8 O5A O4 O 0 1 N N N 51.271 29.441 4.215 2.906 -1.376 0.014 O5A VJ8 27 VJ8 O6 O5 O 0 1 N N N 46.075 23.869 4.767 1.000 7.765 -0.493 O6 VJ8 28 VJ8 OAV O6 O 0 1 N N N 53.684 29.130 4.643 5.256 -2.402 0.593 OAV VJ8 29 VJ8 OAX O7 O 0 1 N N N 56.108 29.768 4.458 6.199 -4.727 0.317 OAX VJ8 30 VJ8 OAY O8 O 0 1 N N N 55.070 29.465 6.771 7.768 -2.789 -0.078 OAY VJ8 31 VJ8 OAZ O9 O 0 1 N N N 52.547 31.373 5.307 3.659 -3.576 -0.969 OAZ VJ8 32 VJ8 OBA O10 O 0 1 N N N 55.365 27.472 5.261 6.943 -3.412 2.339 OBA VJ8 33 VJ8 OBB O11 O 0 1 N N N 51.873 29.201 6.550 4.782 -1.483 -1.824 OBB VJ8 34 VJ8 OBD O12 O 0 1 N N N 50.342 33.061 1.454 -2.793 -1.020 -1.760 OBD VJ8 35 VJ8 OBK O13 O 0 1 N N N 50.302 31.060 -1.277 -8.237 -3.682 1.499 OBK VJ8 36 VJ8 PAU P1 P 0 1 N N N 52.350 29.883 5.295 4.140 -2.239 -0.556 PAU VJ8 37 VJ8 PAW P2 P 0 1 N N N 55.173 28.927 5.366 6.534 -3.362 0.783 PAW VJ8 38 VJ8 H1 H1 H 0 1 N N N 49.468 27.731 4.893 2.554 2.933 -0.980 H1 VJ8 39 VJ8 H2 H2 H 0 1 N N N 44.329 24.217 3.092 -1.193 7.951 0.624 H2 VJ8 40 VJ8 H3 H3 H 0 1 N N N 43.920 26.859 0.671 -3.358 5.504 1.883 H3 VJ8 41 VJ8 H4 H4 H 0 1 N N N 43.291 25.336 1.205 -3.126 7.155 1.670 H4 VJ8 42 VJ8 H5 H5 H 0 1 N N N 47.396 29.287 2.002 -0.317 1.928 1.268 H5 VJ8 43 VJ8 H6 H6 H 0 1 N N N 48.878 29.808 4.598 -0.410 1.730 -1.794 H6 VJ8 44 VJ8 H7 H7 H 0 1 N N N 49.894 31.757 3.569 -0.540 -0.610 -1.627 H7 VJ8 45 VJ8 H8 H8 H 0 1 N N N 50.363 30.445 1.096 0.575 -0.765 1.067 H8 VJ8 46 VJ8 H9 H9 H 0 1 N N N 52.051 29.004 2.350 1.237 -2.099 -0.967 H9 VJ8 47 VJ8 H10 H10 H 0 1 N N N 52.127 30.730 2.843 1.951 -0.622 -1.656 H10 VJ8 48 VJ8 H11 H11 H 0 1 N N N 49.786 34.864 -0.161 -4.701 -2.877 -1.309 H11 VJ8 49 VJ8 H12 H12 H 0 1 N N N 48.164 35.008 -0.920 -5.421 -1.253 -1.185 H12 VJ8 50 VJ8 H13 H13 H 0 1 N N N 49.441 34.342 -2.742 -5.609 -3.449 0.927 H13 VJ8 51 VJ8 H14 H14 H 0 1 N N N 48.853 32.758 -2.131 -6.328 -1.826 1.051 H14 VJ8 52 VJ8 H15 H15 H 0 1 N N N 52.941 30.774 -2.236 -9.901 -3.251 -1.034 H15 VJ8 53 VJ8 H16 H16 H 0 1 N N N 53.309 32.432 -1.649 -9.181 -4.874 -1.158 H16 VJ8 54 VJ8 H17 H17 H 0 1 N N N 54.074 30.716 -0.030 -11.391 -4.963 -0.035 H17 VJ8 55 VJ8 H18 H18 H 0 1 N N N 52.766 31.734 0.663 -10.089 -5.447 1.078 H18 VJ8 56 VJ8 H19 H19 H 0 1 N N N 52.399 30.076 0.077 -10.808 -3.824 1.202 H19 VJ8 57 VJ8 H20 H20 H 0 1 N N N 47.483 33.067 0.206 -3.796 -1.682 1.085 H20 VJ8 58 VJ8 H21 H21 H 0 1 N N N 51.654 33.774 -1.999 -7.234 -3.021 -1.343 H21 VJ8 59 VJ8 H22 H22 H 0 1 N N N 47.197 31.536 4.581 -2.232 2.762 -0.580 H22 VJ8 60 VJ8 H23 H23 H 0 1 N N N 55.609 30.243 6.853 8.043 -1.897 0.173 H23 VJ8 61 VJ8 H24 H24 H 0 1 N N N 56.053 27.287 4.633 7.707 -3.973 2.528 H24 VJ8 62 VJ8 H25 H25 H 0 1 N N N 51.750 29.848 7.235 5.119 -0.599 -1.626 H25 VJ8 63 # 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 VJ8 CBG NBH SING N N 1 VJ8 CBG CBF SING N N 2 VJ8 NBH CBI SING N N 3 VJ8 CBI CBJ SING N N 4 VJ8 CBI OBK DOUB N N 5 VJ8 CBJ CBL SING N N 6 VJ8 CBF NBE SING N N 7 VJ8 NBE CBC SING N N 8 VJ8 CBC OBD DOUB N N 9 VJ8 CBC O3A SING N N 10 VJ8 N2 C2 SING N N 11 VJ8 O3A C3A SING N N 12 VJ8 C4A O4A SING N N 13 VJ8 C4A C5A SING N N 14 VJ8 C4A C3A SING N N 15 VJ8 O4A C1A SING N N 16 VJ8 C2 N3 DOUB N N 17 VJ8 C2 N1 SING N N 18 VJ8 N3 C4 SING N N 19 VJ8 C1A N9 SING N N 20 VJ8 C1A C2A SING N N 21 VJ8 C5A O5A SING N N 22 VJ8 C3A C2A SING N N 23 VJ8 N1 C6 SING N N 24 VJ8 C4 N9 SING Y N 25 VJ8 C4 C5 DOUB Y N 26 VJ8 N9 C8 SING Y N 27 VJ8 C2A O2A SING N N 28 VJ8 C6 C5 SING N N 29 VJ8 C6 O6 DOUB N N 30 VJ8 C5 N7 SING Y N 31 VJ8 O5A PAU SING N N 32 VJ8 OAX PAW DOUB N N 33 VJ8 C8 N7 DOUB Y N 34 VJ8 OAV PAU SING N N 35 VJ8 OAV PAW SING N N 36 VJ8 OBA PAW SING N N 37 VJ8 PAU OAZ DOUB N N 38 VJ8 PAU OBB SING N N 39 VJ8 PAW OAY SING N N 40 VJ8 C8 H1 SING N N 41 VJ8 N1 H2 SING N N 42 VJ8 N2 H3 SING N N 43 VJ8 N2 H4 SING N N 44 VJ8 C1A H5 SING N N 45 VJ8 C2A H6 SING N N 46 VJ8 C3A H7 SING N N 47 VJ8 C4A H8 SING N N 48 VJ8 C5A H9 SING N N 49 VJ8 C5A H10 SING N N 50 VJ8 CBF H11 SING N N 51 VJ8 CBF H12 SING N N 52 VJ8 CBG H13 SING N N 53 VJ8 CBG H14 SING N N 54 VJ8 CBJ H15 SING N N 55 VJ8 CBJ H16 SING N N 56 VJ8 CBL H17 SING N N 57 VJ8 CBL H18 SING N N 58 VJ8 CBL H19 SING N N 59 VJ8 NBE H20 SING N N 60 VJ8 NBH H21 SING N N 61 VJ8 O2A H22 SING N N 62 VJ8 OAY H23 SING N N 63 VJ8 OBA H24 SING N N 64 VJ8 OBB H25 SING N N 65 # 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 VJ8 InChI InChI 1.03 "InChI=1S/C16H25N7O13P2/c1-2-8(24)18-3-4-19-16(27)35-11-7(5-33-38(31,32)36-37(28,29)30)34-14(10(11)25)23-6-20-9-12(23)21-15(17)22-13(9)26/h6-7,10-11,14,25H,2-5H2,1H3,(H,18,24)(H,19,27)(H,31,32)(H2,28,29,30)(H3,17,21,22,26)/t7-,10-,11-,14-/m1/s1" VJ8 InChIKey InChI 1.03 ZYFFWDLDVKYDIX-FRJWGUMJSA-N VJ8 SMILES_CANONICAL CACTVS 3.385 "CCC(=O)NCCNC(=O)O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)n2cnc3C(=O)NC(=Nc23)N" VJ8 SMILES CACTVS 3.385 "CCC(=O)NCCNC(=O)O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)n2cnc3C(=O)NC(=Nc23)N" VJ8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCC(=O)NCCNC(=O)O[C@@H]1[C@H](O[C@H]([C@@H]1O)n2cnc3c2N=C(NC3=O)N)COP(=O)(O)OP(=O)(O)O" VJ8 SMILES "OpenEye OEToolkits" 2.0.7 "CCC(=O)NCCNC(=O)OC1C(OC(C1O)n2cnc3c2N=C(NC3=O)N)COP(=O)(O)OP(=O)(O)O" # _pdbx_chem_comp_identifier.comp_id VJ8 _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 "[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl] ~{N}-[2-(propanoylamino)ethyl]carbamate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VJ8 "Create component" 2021-05-18 PDBE VJ8 "Initial release" 2022-08-03 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id VJ8 _pdbx_chem_comp_synonyms.name "[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl] ~{N}-[2-(propanoylamino)ethyl]carbamate" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type IUPAC #