data_VLO # _chem_comp.id VLO _chem_comp.name "[[(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H27 N9 O21 P4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-08-30 _chem_comp.pdbx_modified_date 2023-10-20 _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 853.371 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VLO _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 8EAE _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 VLO N1 N1 N 0 1 N N N 3.500 -26.884 -21.289 3.715 -0.706 -2.904 N1 VLO 1 VLO C1 C1 C 0 1 N N N 2.198 -26.877 -20.965 2.575 -0.057 -3.305 C1 VLO 2 VLO N2 N2 N 0 1 N N N 1.590 -28.017 -20.621 1.629 0.176 -2.422 N2 VLO 3 VLO C2 C2 C 0 1 Y N N 0.279 -27.830 -20.327 0.500 0.807 -2.768 C2 VLO 4 VLO C3 C3 C 0 1 Y N N -0.439 -26.651 -20.345 0.318 1.227 -4.091 C3 VLO 5 VLO N3 N3 N 0 1 Y N N -1.762 -26.880 -19.975 -0.894 1.828 -4.158 N3 VLO 6 VLO C4 C4 C 0 1 Y N N -1.822 -28.174 -19.743 -1.454 1.803 -2.984 C4 VLO 7 VLO N4 N4 N 0 1 Y N N -0.612 -28.806 -19.950 -0.629 1.181 -2.092 N4 VLO 8 VLO C5 C5 C 0 1 N N R -0.330 -30.253 -19.763 -0.902 0.956 -0.671 C5 VLO 9 VLO O1 O1 O 0 1 N N N 0.742 -30.373 -18.853 -2.326 0.964 -0.425 O1 VLO 10 VLO C6 C6 C 0 1 N N R 1.673 -31.400 -19.278 -2.467 1.234 0.987 C6 VLO 11 VLO C7 C7 C 0 1 N N N 3.001 -30.740 -19.559 -3.868 1.767 1.290 C7 VLO 12 VLO O2 O2 O 0 1 N N N 3.998 -31.722 -19.951 -4.832 0.741 1.044 O2 VLO 13 VLO P1 P1 P 0 1 N N N 5.398 -31.111 -20.449 -6.413 0.953 1.258 P1 VLO 14 VLO O3 O3 O 0 1 N N N 6.285 -32.198 -20.965 -6.714 1.203 2.820 O3 VLO 15 VLO O4 O4 O 0 1 N N N 5.141 -29.920 -21.310 -6.865 2.125 0.476 O4 VLO 16 VLO O5 O5 O 0 1 N N N 5.980 -30.584 -19.055 -7.203 -0.359 0.763 O5 VLO 17 VLO P2 P2 P 0 1 N N N 7.440 -30.221 -18.515 -8.725 -0.651 0.328 P2 VLO 18 VLO O6 O6 O 0 1 N N N 7.411 -28.888 -17.830 -8.951 -0.167 -1.191 O6 VLO 19 VLO O7 O7 O 0 1 N N N 8.447 -30.472 -19.589 -9.644 0.087 1.223 O7 VLO 20 VLO O8 O8 O 0 1 N N N 7.563 -31.377 -17.413 -9.022 -2.230 0.438 O8 VLO 21 VLO P3 P3 P 0 1 N N N 7.588 -32.990 -17.482 -10.365 -3.117 0.450 P3 VLO 22 VLO O9 O9 O 0 1 N N N 8.777 -33.395 -16.649 -10.050 -4.558 1.096 O9 VLO 23 VLO O10 O10 O 0 1 N N N 7.737 -33.413 -18.925 -11.401 -2.432 1.255 O10 VLO 24 VLO O11 O11 O 0 1 N N N 6.264 -33.410 -16.889 -10.895 -3.309 -1.058 O11 VLO 25 VLO C8 C8 C 0 1 N N R 0.991 -32.108 -20.458 -1.402 2.312 1.291 C8 VLO 26 VLO O12 O12 O 0 1 N N N 0.306 -33.278 -20.024 -0.816 2.088 2.575 O12 VLO 27 VLO C9 C9 C 0 1 N N R 0.057 -31.035 -21.017 -0.349 2.124 0.175 C9 VLO 28 VLO O13 O13 O 0 1 N N N -1.087 -31.665 -21.618 0.919 1.779 0.736 O13 VLO 29 VLO P4 P4 P 0 1 N N N -1.533 -31.230 -23.104 2.249 2.657 0.504 P4 VLO 30 VLO O14 O14 O 0 1 N N N -1.990 -29.796 -23.115 2.063 4.103 1.186 O14 VLO 31 VLO O15 O15 O 0 1 N N N -2.496 -32.263 -23.629 2.483 2.822 -0.948 O15 VLO 32 VLO O16 O16 O 0 1 N N N -0.172 -31.313 -23.958 3.509 1.907 1.168 O16 VLO 33 VLO C10 C10 C 0 1 N N N 0.608 -32.537 -24.027 4.852 2.382 1.042 C10 VLO 34 VLO C11 C11 C 0 1 N N R 2.010 -32.209 -24.481 5.797 1.439 1.790 C11 VLO 35 VLO O17 O17 O 0 1 N N N 1.957 -31.083 -25.391 5.887 0.170 1.106 O17 VLO 36 VLO C12 C12 C 0 1 N N R 3.068 -30.233 -25.208 7.118 -0.426 1.570 C12 VLO 37 VLO N5 N5 N 0 1 Y N N 2.572 -28.886 -24.905 7.576 -1.449 0.627 N5 VLO 38 VLO C13 C13 C 0 1 Y N N 1.304 -28.523 -24.514 7.258 -1.526 -0.696 C13 VLO 39 VLO N6 N6 N 0 1 Y N N 1.186 -27.226 -24.332 7.840 -2.562 -1.229 N6 VLO 40 VLO C14 C14 C 0 1 Y N N 2.445 -26.712 -24.623 8.561 -3.207 -0.283 C14 VLO 41 VLO C15 C15 C 0 1 N N N 2.920 -25.367 -24.598 9.379 -4.364 -0.280 C15 VLO 42 VLO O18 O18 O 0 1 N N N 2.300 -24.349 -24.304 9.551 -5.012 -1.298 O18 VLO 43 VLO N7 N7 N 0 1 N N N 4.273 -25.317 -24.967 9.964 -4.729 0.882 N7 VLO 44 VLO C16 C16 C 0 1 N N N 5.033 -26.377 -25.295 9.766 -4.001 2.010 C16 VLO 45 VLO N8 N8 N 0 1 N N N 4.613 -27.618 -25.323 9.016 -2.934 2.024 N8 VLO 46 VLO C17 C17 C 0 1 Y N N 3.303 -27.728 -24.977 8.405 -2.499 0.913 C17 VLO 47 VLO C18 C18 C 0 1 N N R 3.947 -30.829 -24.109 8.126 0.744 1.626 C18 VLO 48 VLO O19 O19 O 0 1 N N N 5.074 -31.489 -24.645 8.990 0.606 2.755 O19 VLO 49 VLO C19 C19 C 0 1 N N S 2.998 -31.788 -23.384 7.237 1.999 1.774 C19 VLO 50 VLO O20 O20 O 0 1 N N N 3.702 -32.907 -22.856 7.526 2.675 2.999 O20 VLO 51 VLO C20 C20 C 0 1 N N N 0.212 -25.442 -20.705 1.344 0.969 -5.030 C20 VLO 52 VLO O21 O21 O 0 1 N N N -0.268 -24.302 -20.775 1.228 1.317 -6.193 O21 VLO 53 VLO N9 N9 N 0 1 N N N 1.560 -25.657 -21.008 2.458 0.333 -4.606 N9 VLO 54 VLO H1 H1 H 0 1 N N N 4.015 -27.741 -21.273 3.815 -0.986 -1.980 H1 VLO 55 VLO H2 H2 H 0 1 N N N 3.956 -26.032 -21.546 4.420 -0.889 -3.544 H2 VLO 56 VLO H3 H3 H 0 1 N N N -2.719 -28.685 -19.426 -2.425 2.212 -2.750 H3 VLO 57 VLO H4 H4 H 0 1 N N N -1.225 -30.727 -19.335 -0.467 0.010 -0.346 H4 VLO 58 VLO H5 H5 H 0 1 N N N 1.808 -32.131 -18.467 -2.270 0.333 1.567 H5 VLO 59 VLO H6 H6 H 0 1 N N N 3.344 -30.221 -18.652 -3.922 2.074 2.335 H6 VLO 60 VLO H7 H7 H 0 1 N N N 2.875 -30.011 -20.373 -4.078 2.624 0.649 H7 VLO 61 VLO H8 H8 H 0 1 N N N 6.590 -31.972 -21.836 -6.443 0.474 3.395 H8 VLO 62 VLO H9 H9 H 0 1 N N N 8.088 -28.330 -18.194 -8.381 -0.610 -1.834 H9 VLO 63 VLO H10 H10 H 0 1 N N N 9.408 -33.848 -17.196 -10.816 -5.147 1.136 H10 VLO 64 VLO H11 H11 H 0 1 N N N 5.756 -33.873 -17.544 -10.266 -3.753 -1.643 H11 VLO 65 VLO H12 H12 H 0 1 N N N 1.749 -32.359 -21.215 -1.841 3.308 1.240 H12 VLO 66 VLO H13 H13 H 0 1 N N N 0.934 -33.907 -19.688 -1.445 2.134 3.307 H13 VLO 67 VLO H14 H14 H 0 1 N N N 0.592 -30.388 -21.728 -0.268 3.027 -0.429 H14 VLO 68 VLO H15 H15 H 0 1 N N N -2.869 -29.746 -23.471 1.906 4.071 2.139 H15 VLO 69 VLO H16 H16 H 0 1 N N N 0.142 -33.230 -24.743 5.128 2.413 -0.011 H16 VLO 70 VLO H17 H17 H 0 1 N N N 0.644 -33.007 -23.033 4.925 3.382 1.468 H17 VLO 71 VLO H18 H18 H 0 1 N N N 2.425 -33.084 -25.003 5.457 1.297 2.816 H18 VLO 72 VLO H19 H19 H 0 1 N N N 3.660 -30.194 -26.134 6.981 -0.858 2.561 H19 VLO 73 VLO H20 H20 H 0 1 N N N 0.496 -29.225 -24.372 6.620 -0.832 -1.223 H20 VLO 74 VLO H21 H21 H 0 1 N N N 4.709 -24.417 -24.988 10.528 -5.518 0.911 H21 VLO 75 VLO H22 H22 H 0 1 N N N 6.065 -26.192 -25.554 10.244 -4.315 2.925 H22 VLO 76 VLO H23 H23 H 0 1 N N N 4.253 -30.031 -23.417 8.705 0.793 0.704 H23 VLO 77 VLO H24 H24 H 0 1 N N N 5.598 -31.847 -23.938 9.644 1.314 2.839 H24 VLO 78 VLO H25 H25 H 0 1 N N N 2.460 -31.247 -22.592 7.377 2.668 0.925 H25 VLO 79 VLO H26 H26 H 0 1 N N N 4.303 -32.614 -22.182 8.417 3.046 3.043 H26 VLO 80 VLO H27 H27 H 0 1 N N N 2.104 -24.862 -21.277 3.176 0.148 -5.231 H27 VLO 81 # 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 VLO O17 C12 SING N N 1 VLO O17 C11 SING N N 2 VLO N8 C16 DOUB N N 3 VLO N8 C17 SING N N 4 VLO C16 N7 SING N N 5 VLO C12 N5 SING N N 6 VLO C12 C18 SING N N 7 VLO C17 N5 SING Y N 8 VLO C17 C14 DOUB Y N 9 VLO N7 C15 SING N N 10 VLO N5 C13 SING Y N 11 VLO O19 C18 SING N N 12 VLO C14 C15 SING N N 13 VLO C14 N6 SING Y N 14 VLO C15 O18 DOUB N N 15 VLO C13 N6 DOUB Y N 16 VLO C11 C10 SING N N 17 VLO C11 C19 SING N N 18 VLO C18 C19 SING N N 19 VLO C10 O16 SING N N 20 VLO O16 P4 SING N N 21 VLO O15 P4 DOUB N N 22 VLO C19 O20 SING N N 23 VLO O14 P4 SING N N 24 VLO P4 O13 SING N N 25 VLO O13 C9 SING N N 26 VLO O4 P1 DOUB N N 27 VLO N1 C1 SING N N 28 VLO C9 C8 SING N N 29 VLO C9 C5 SING N N 30 VLO N9 C1 SING N N 31 VLO N9 C20 SING N N 32 VLO C1 N2 DOUB N N 33 VLO O3 P1 SING N N 34 VLO O21 C20 DOUB N N 35 VLO C20 C3 SING N N 36 VLO N2 C2 SING N N 37 VLO C8 O12 SING N N 38 VLO C8 C6 SING N N 39 VLO P1 O2 SING N N 40 VLO P1 O5 SING N N 41 VLO C3 C2 DOUB Y N 42 VLO C3 N3 SING Y N 43 VLO C2 N4 SING Y N 44 VLO N3 C4 DOUB Y N 45 VLO O2 C7 SING N N 46 VLO N4 C5 SING N N 47 VLO N4 C4 SING Y N 48 VLO C5 O1 SING N N 49 VLO O7 P2 DOUB N N 50 VLO C7 C6 SING N N 51 VLO C6 O1 SING N N 52 VLO O5 P2 SING N N 53 VLO O10 P3 DOUB N N 54 VLO P2 O6 SING N N 55 VLO P2 O8 SING N N 56 VLO P3 O8 SING N N 57 VLO P3 O11 SING N N 58 VLO P3 O9 SING N N 59 VLO N1 H1 SING N N 60 VLO N1 H2 SING N N 61 VLO C4 H3 SING N N 62 VLO C5 H4 SING N N 63 VLO C6 H5 SING N N 64 VLO C7 H6 SING N N 65 VLO C7 H7 SING N N 66 VLO O3 H8 SING N N 67 VLO O6 H9 SING N N 68 VLO O9 H10 SING N N 69 VLO O11 H11 SING N N 70 VLO C8 H12 SING N N 71 VLO O12 H13 SING N N 72 VLO C9 H14 SING N N 73 VLO O14 H15 SING N N 74 VLO C10 H16 SING N N 75 VLO C10 H17 SING N N 76 VLO C11 H18 SING N N 77 VLO C12 H19 SING N N 78 VLO C13 H20 SING N N 79 VLO N7 H21 SING N N 80 VLO C16 H22 SING N N 81 VLO C18 H23 SING N N 82 VLO O19 H24 SING N N 83 VLO C19 H25 SING N N 84 VLO O20 H26 SING N N 85 VLO N9 H27 SING N N 86 # 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 VLO InChI InChI 1.06 "InChI=1S/C20H27N9O21P4/c21-20-26-15-9(17(34)27-20)25-5-29(15)19-13(11(31)7(47-19)2-45-53(40,41)50-54(42,43)49-51(35,36)37)48-52(38,39)44-1-6-10(30)12(32)18(46-6)28-4-24-8-14(28)22-3-23-16(8)33/h3-7,10-13,18-19,30-32H,1-2H2,(H,38,39)(H,40,41)(H,42,43)(H,22,23,33)(H2,35,36,37)(H3,21,26,27,34)/t6-,7-,10-,11-,12-,13-,18-,19-/m1/s1" VLO InChIKey InChI 1.06 QIEFBLFMZQEZSF-INFSMZHSSA-N VLO 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](O)[C@H]3O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6C(=O)NC=Nc56" VLO 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](O)[CH]3O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6C(=O)NC=Nc56" VLO SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O[C@@H]4[C@@H]([C@H](O[C@H]4n5cnc6c5N=C(NC6=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)O)N=CNC2=O" VLO SMILES "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OC4C(C(OC4n5cnc6c5N=C(NC6=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)O)N=CNC2=O" # _pdbx_chem_comp_identifier.comp_id VLO _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~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VLO "Create component" 2022-08-30 RCSB VLO "Initial release" 2023-10-25 RCSB #