data_VE8 # _chem_comp.id VE8 _chem_comp.name "Non-hydrolasable alarmone analogue" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H19 N6 O19 P5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "~{N}-[(2~{S},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxymethyl]oxolan-3-yl]-phosphonooxy-phosphonamidic acid" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-05-11 _chem_comp.pdbx_modified_date 2022-05-27 _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 682.155 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VE8 _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 7OHG _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 VE8 O17 O1 O 0 1 N N N 58.857 51.008 -2.980 -2.761 0.854 -1.905 O17 VE8 1 VE8 P2 P1 P 0 1 N N N 59.911 50.069 -2.539 -2.858 0.835 -0.428 P2 VE8 2 VE8 O9 O2 O 0 1 N N N 59.474 48.606 -2.421 -3.165 2.321 0.109 O9 VE8 3 VE8 O10 O3 O 0 1 N N N 61.178 50.100 -3.509 -4.048 -0.154 0.019 O10 VE8 4 VE8 P3 P2 P 0 1 N N N 61.434 50.420 -5.051 -5.525 -0.453 -0.547 P3 VE8 5 VE8 O16 O4 O 0 1 N N N 61.604 49.169 -5.831 -6.160 0.817 -0.964 O16 VE8 6 VE8 O15 O5 O 0 1 N N N 60.288 51.351 -5.516 -5.425 -1.443 -1.812 O15 VE8 7 VE8 O11 O6 O 0 1 N N N 62.779 51.287 -5.023 -6.412 -1.143 0.606 O11 VE8 8 VE8 P4 P3 P 0 1 N N N 63.630 52.183 -6.046 -7.989 -1.403 0.799 P4 VE8 9 VE8 O14 O7 O 0 1 N N N 62.854 53.385 -6.501 -8.716 -0.021 1.193 O14 VE8 10 VE8 O13 O8 O 0 1 N N N 64.008 51.221 -7.192 -8.562 -1.920 -0.463 O13 VE8 11 VE8 O12 O9 O 0 1 N N N 64.910 52.549 -5.271 -8.215 -2.482 1.973 O12 VE8 12 VE8 O8 O10 O 0 1 N N N 60.474 50.487 -1.093 -1.467 0.316 0.194 O8 VE8 13 VE8 C7 C1 C 0 1 N N N 61.022 51.776 -0.740 -0.207 0.920 -0.104 C7 VE8 14 VE8 C6 C2 C 0 1 N N S 62.504 51.789 -1.025 0.903 0.185 0.650 C6 VE8 15 VE8 C5 C3 C 0 1 N N S 63.401 51.128 0.032 2.258 0.897 0.441 C5 VE8 16 VE8 N1 N1 N 0 1 N N N 63.680 49.694 -0.213 2.565 1.765 1.587 N1 VE8 17 VE8 P P4 P 0 1 N N N 64.146 48.563 0.895 3.373 3.155 1.091 P VE8 18 VE8 O7 O11 O 0 1 N N N 64.798 47.393 0.307 3.665 4.003 2.269 O7 VE8 19 VE8 O6 O12 O 0 1 N N N 65.232 49.235 1.845 4.753 2.746 0.369 O6 VE8 20 VE8 O2 O13 O 0 1 N N N 62.886 48.108 1.835 2.449 3.973 0.057 O2 VE8 21 VE8 P1 P5 P 0 1 N N N 61.366 47.627 1.665 2.631 5.348 -0.760 P1 VE8 22 VE8 O5 O14 O 0 1 N N N 60.387 48.709 2.051 1.188 5.901 -1.210 O5 VE8 23 VE8 O4 O15 O 0 1 N N N 61.257 47.189 0.184 3.295 6.351 0.103 O4 VE8 24 VE8 O3 O16 O 0 1 N N N 61.249 46.377 2.560 3.535 5.081 -2.065 O3 VE8 25 VE8 C4 C4 C 0 1 N N R 64.616 52.081 0.205 3.279 -0.258 0.348 C4 VE8 26 VE8 O1 O17 O 0 1 N N N 65.863 51.414 0.023 4.242 -0.162 1.400 O1 VE8 27 VE8 O18 O18 O 0 1 N N N 62.968 53.152 -1.084 1.093 -1.137 0.101 O18 VE8 28 VE8 C3 C5 C 0 1 N N R 64.363 53.137 -0.875 2.421 -1.532 0.511 C3 VE8 29 VE8 N N2 N 0 1 Y N N 64.799 54.500 -0.517 2.925 -2.601 -0.355 N VE8 30 VE8 C8 C6 C 0 1 Y N N 65.665 55.288 -1.226 2.520 -2.865 -1.631 C8 VE8 31 VE8 N2 N3 N 0 1 Y N N 65.857 56.467 -0.685 3.178 -3.884 -2.101 N2 VE8 32 VE8 C1 C7 C 0 1 Y N N 65.071 56.453 0.454 4.042 -4.333 -1.158 C1 VE8 33 VE8 C2 C8 C 0 1 Y N N 64.412 55.249 0.570 3.893 -3.514 -0.033 C2 VE8 34 VE8 N3 N4 N 0 1 N N N 63.566 54.857 1.538 4.641 -3.737 1.054 N3 VE8 35 VE8 C9 C9 C 0 1 N N N 63.389 55.787 2.475 5.519 -4.715 1.085 C9 VE8 36 VE8 N4 N5 N 0 1 N N N 62.559 55.548 3.488 6.263 -4.905 2.222 N4 VE8 37 VE8 N5 N6 N 0 1 N N N 64.005 57.011 2.452 5.711 -5.544 0.021 N5 VE8 38 VE8 C C10 C 0 1 N N N 64.870 57.443 1.468 4.988 -5.384 -1.110 C VE8 39 VE8 O O19 O 0 1 N N N 65.366 58.565 1.524 5.154 -6.120 -2.067 O VE8 40 VE8 H1 H1 H 0 1 N N N 58.558 48.529 -2.659 -3.242 2.384 1.071 H1 VE8 41 VE8 H2 H2 H 0 1 N N N 59.848 50.963 -6.263 -5.018 -2.297 -1.612 H2 VE8 42 VE8 H3 H3 H 0 1 N N N 62.727 53.343 -7.442 -8.389 0.375 2.012 H3 VE8 43 VE8 H4 H4 H 0 1 N N N 65.655 52.107 -5.662 -9.144 -2.687 2.144 H4 VE8 44 VE8 H5 H5 H 0 1 N N N 60.528 52.559 -1.333 -0.020 0.859 -1.176 H5 VE8 45 VE8 H6 H6 H 0 1 N N N 60.853 51.965 0.330 -0.224 1.966 0.203 H6 VE8 46 VE8 H7 H7 H 0 1 N N N 62.683 51.295 -1.991 0.665 0.126 1.712 H7 VE8 47 VE8 H8 H8 H 0 1 N N N 62.843 51.181 0.978 2.248 1.474 -0.484 H8 VE8 48 VE8 H9 H9 H 0 1 N N N 62.836 49.333 -0.609 1.728 1.997 2.100 H9 VE8 49 VE8 H10 H10 H 0 1 N N N 66.037 48.732 1.812 4.637 2.189 -0.413 H10 VE8 50 VE8 H11 H11 H 0 1 N N N 59.858 48.941 1.297 1.221 6.729 -1.709 H11 VE8 51 VE8 H12 H12 H 0 1 N N N 61.135 45.607 2.016 3.160 4.433 -2.677 H12 VE8 52 VE8 H13 H13 H 0 1 N N N 64.565 52.553 1.197 3.774 -0.253 -0.623 H13 VE8 53 VE8 H14 H14 H 0 1 N N N 65.981 50.770 0.711 4.908 -0.863 1.389 H14 VE8 54 VE8 H15 H15 H 0 1 N N N 64.879 52.823 -1.795 2.416 -1.857 1.551 H15 VE8 55 VE8 H16 H16 H 0 1 N N N 66.143 54.970 -2.141 1.765 -2.311 -2.170 H16 VE8 56 VE8 H17 H17 H 0 1 N N N 62.074 54.675 3.542 6.137 -4.323 2.987 H17 VE8 57 VE8 H18 H18 H 0 1 N N N 62.421 56.241 4.195 6.915 -5.623 2.260 H18 VE8 58 VE8 H19 H19 H 0 1 N N N 63.813 57.639 3.206 6.368 -6.256 0.076 H19 VE8 59 # # 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 VE8 O13 P4 DOUB N N 1 VE8 O14 P4 SING N N 2 VE8 P4 O12 SING N N 3 VE8 P4 O11 SING N N 4 VE8 O16 P3 DOUB N N 5 VE8 O15 P3 SING N N 6 VE8 P3 O11 SING N N 7 VE8 P3 O10 SING N N 8 VE8 O10 P2 SING N N 9 VE8 O17 P2 DOUB N N 10 VE8 P2 O9 SING N N 11 VE8 P2 O8 SING N N 12 VE8 C8 N2 DOUB Y N 13 VE8 C8 N SING Y N 14 VE8 O8 C7 SING N N 15 VE8 O18 C6 SING N N 16 VE8 O18 C3 SING N N 17 VE8 C6 C7 SING N N 18 VE8 C6 C5 SING N N 19 VE8 C3 N SING N N 20 VE8 C3 C4 SING N N 21 VE8 N2 C1 SING Y N 22 VE8 N C2 SING Y N 23 VE8 N1 C5 SING N N 24 VE8 N1 P SING N N 25 VE8 O1 C4 SING N N 26 VE8 C5 C4 SING N N 27 VE8 O4 P1 DOUB N N 28 VE8 O7 P DOUB N N 29 VE8 C1 C2 DOUB Y N 30 VE8 C1 C SING N N 31 VE8 C2 N3 SING N N 32 VE8 P O2 SING N N 33 VE8 P O6 SING N N 34 VE8 C O DOUB N N 35 VE8 C N5 SING N N 36 VE8 N3 C9 DOUB N N 37 VE8 P1 O2 SING N N 38 VE8 P1 O5 SING N N 39 VE8 P1 O3 SING N N 40 VE8 N5 C9 SING N N 41 VE8 C9 N4 SING N N 42 VE8 O9 H1 SING N N 43 VE8 O15 H2 SING N N 44 VE8 O14 H3 SING N N 45 VE8 O12 H4 SING N N 46 VE8 C7 H5 SING N N 47 VE8 C7 H6 SING N N 48 VE8 C6 H7 SING N N 49 VE8 C5 H8 SING N N 50 VE8 N1 H9 SING N N 51 VE8 O6 H10 SING N N 52 VE8 O5 H11 SING N N 53 VE8 O3 H12 SING N N 54 VE8 C4 H13 SING N N 55 VE8 O1 H14 SING N N 56 VE8 C3 H15 SING N N 57 VE8 C8 H16 SING N N 58 VE8 N4 H17 SING N N 59 VE8 N4 H18 SING N N 60 VE8 N5 H19 SING N N 61 # # 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 VE8 InChI InChI 1.03 "InChI=1S/C10H19N6O19P5/c11-10-13-7-5(8(18)14-10)12-2-16(7)9-6(17)4(15-36(19,20)33-37(21,22)23)3(32-9)1-31-39(27,28)35-40(29,30)34-38(24,25)26/h2-4,6,9,17H,1H2,(H,27,28)(H,29,30)(H2,15,19,20)(H2,21,22,23)(H2,24,25,26)(H3,11,13,14,18)/t3-,4-,6-,9-/m1/s1" VE8 InChIKey InChI 1.03 IZNYESBVRGWINY-DXTOWSMRSA-N VE8 SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](N[P](O)(=O)O[P](O)(O)=O)[C@H]3O" VE8 SMILES CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](N[P](O)(=O)O[P](O)(O)=O)[CH]3O" VE8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)NP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N" VE8 SMILES "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)NP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N" # _pdbx_chem_comp_identifier.comp_id VE8 _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 "~{N}-[(2~{S},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxymethyl]oxolan-3-yl]-phosphonooxy-phosphonamidic acid" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id VE8 _pdbx_chem_comp_synonyms.name "~{N}-[(2~{S},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxymethyl]oxolan-3-yl]-phosphonooxy-phosphonamidic acid" _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 VE8 "Create component" 2021-05-11 PDBE VE8 "Initial release" 2022-06-01 RCSB ##