data_ZNA # _chem_comp.id ZNA _chem_comp.name "[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-bis(oxidanyl)thiolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H28 N7 O13 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2018-08-15 _chem_comp.pdbx_modified_date 2024-05-08 _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 680.499 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ZNA _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 6EDR _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.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 ZNA N01 N1 N 0 1 N N N N N N -17.634 -0.787 -1.646 -2.871 -7.199 0.981 N01 ZNA 1 ZNA C02 C1 C 0 1 N N N N N N -16.549 -0.012 -1.822 -3.758 -6.280 0.550 C02 ZNA 2 ZNA O03 O1 O 0 1 N N N N N N -16.462 1.083 -1.260 -4.813 -6.636 0.062 O03 ZNA 3 ZNA C04 C2 C 0 1 Y N N N N N -15.493 -0.477 -2.644 -3.448 -4.840 0.672 C04 ZNA 4 ZNA C44 C3 C 0 1 Y N N N N N -15.331 -1.827 -3.004 -4.358 -3.878 0.229 C44 ZNA 5 ZNA C05 C4 C 0 1 Y N N N N N -14.533 0.431 -3.130 -2.240 -4.417 1.238 C05 ZNA 6 ZNA C06 C5 C 0 1 Y N N N N N -13.466 0.008 -3.931 -1.998 -3.057 1.328 C06 ZNA 7 ZNA C07 C6 C 0 1 Y N N N N N -13.323 -1.332 -4.284 -2.949 -2.168 0.861 C07 ZNA 8 ZNA N08 N2 N 1 1 Y N N N N N -14.268 -2.256 -3.832 -4.082 -2.596 0.337 N08 ZNA 9 ZNA C09 C7 C 0 1 N N R N N N -14.204 -3.716 -4.127 -5.058 -1.615 -0.144 C09 ZNA 10 ZNA S10 S1 S 0 1 N N N N N N -13.417 -4.399 -2.643 -4.319 -0.540 -1.441 S10 ZNA 11 ZNA C42 C8 C 0 1 N N R N N N -13.289 -4.268 -5.274 -5.413 -0.605 0.967 C42 ZNA 12 ZNA O43 O2 O 0 1 N N N N N N -13.908 -5.453 -5.793 -6.615 -1.030 1.612 O43 ZNA 13 ZNA C40 C9 C 0 1 N N S N N N -11.903 -4.676 -4.705 -5.614 0.807 0.432 C40 ZNA 14 ZNA O41 O3 O 0 1 N N N N N N -11.194 -5.499 -5.658 -6.938 1.238 0.752 O41 ZNA 15 ZNA C11 C10 C 0 1 N N R N N N -12.208 -5.496 -3.449 -5.416 0.896 -1.095 C11 ZNA 16 ZNA C12 C11 C 0 1 N N N N N N -10.982 -5.704 -2.555 -4.730 2.208 -1.479 C12 ZNA 17 ZNA O13 O4 O 0 1 N N N N N N -11.049 -4.944 -1.333 -3.505 2.334 -0.754 O13 ZNA 18 ZNA P14 P1 P 0 1 N N N N N N -11.447 -5.586 0.108 -2.520 3.598 -0.910 P14 ZNA 19 ZNA O15 O5 O 0 1 N N N N N N -10.420 -5.151 1.075 -3.260 4.924 -0.375 O15 ZNA 20 ZNA O16 O6 O 0 1 N N N N N N -11.764 -7.032 -0.014 -2.164 3.773 -2.336 O16 ZNA 21 ZNA O17 O7 O 0 1 N N N N N N -12.852 -4.831 0.415 -1.182 3.346 -0.050 O17 ZNA 22 ZNA P18 P2 P 0 1 N N N N N N -13.044 -3.502 1.308 0.273 4.035 -0.017 P18 ZNA 23 ZNA O19 O8 O 0 1 N N N N N N -12.361 -3.688 2.604 0.201 5.398 0.836 O19 ZNA 24 ZNA O20 O9 O 0 1 N N N N N N -14.489 -3.194 1.299 0.706 4.339 -1.399 O20 ZNA 25 ZNA O21 O10 O 0 1 N N N N N N -12.224 -2.326 0.498 1.327 3.028 0.667 O21 ZNA 26 ZNA C22 C12 C 0 1 N N N N N N -12.795 -1.529 -0.561 2.726 3.306 0.751 C22 ZNA 27 ZNA C23 C13 C 0 1 N N R N N N -12.435 -0.029 -0.435 3.435 2.148 1.456 C23 ZNA 28 ZNA O24 O11 O 0 1 N N N N N N -12.544 0.527 0.894 3.365 0.965 0.643 O24 ZNA 29 ZNA C38 C14 C 0 1 N N S N N N -10.975 0.228 -0.776 4.926 2.485 1.647 C38 ZNA 30 ZNA O39 O12 O 0 1 N N N N N N -10.710 0.046 -2.188 5.265 2.485 3.035 O39 ZNA 31 ZNA C36 C15 C 0 1 N N R N N N -10.869 1.688 -0.370 5.671 1.347 0.908 C36 ZNA 32 ZNA O37 O13 O 0 1 N N N N N N -11.315 2.544 -1.442 6.812 0.916 1.652 O37 ZNA 33 ZNA C25 C16 C 0 1 N N R N N N -11.829 1.800 0.836 4.592 0.234 0.855 C25 ZNA 34 ZNA N26 N3 N 0 1 Y N N N N N -11.085 2.046 2.118 4.848 -0.680 -0.261 N26 ZNA 35 ZNA C27 C17 C 0 1 Y N N N N N -10.391 1.107 2.757 4.297 -0.608 -1.505 C27 ZNA 36 ZNA N28 N4 N 0 1 Y N N N N N -9.858 1.649 3.848 4.746 -1.578 -2.247 N28 ZNA 37 ZNA C29 C18 C 0 1 Y N N N N N -10.215 2.931 3.900 5.610 -2.333 -1.528 C29 ZNA 38 ZNA C35 C19 C 0 1 Y N N N N N -10.982 3.180 2.821 5.691 -1.763 -0.246 C35 ZNA 39 ZNA N34 N5 N 0 1 Y N N N N N -11.490 4.415 2.614 6.487 -2.320 0.660 N34 ZNA 40 ZNA C33 C20 C 0 1 Y N N N N N -11.217 5.448 3.533 7.194 -3.391 0.365 C33 ZNA 41 ZNA N32 N6 N 0 1 Y N N N N N -10.412 5.154 4.649 7.154 -3.960 -0.826 N32 ZNA 42 ZNA C30 C21 C 0 1 Y N N N N N -9.939 3.900 4.793 6.381 -3.478 -1.794 C30 ZNA 43 ZNA N31 N7 N 0 1 N N N N N N -9.171 3.564 5.831 6.347 -4.081 -3.039 N31 ZNA 44 ZNA H1 H1 H 0 1 N N N N N N -18.379 -0.477 -1.055 -3.075 -8.144 0.901 H1 ZNA 45 ZNA H2 H2 H 0 1 N N N N N N -17.696 -1.673 -2.106 -2.028 -6.915 1.367 H2 ZNA 46 ZNA H3 H3 H 0 1 N N N N N N -16.038 -2.556 -2.638 -5.297 -4.189 -0.205 H3 ZNA 47 ZNA H4 H4 H 0 1 N N N N N N -14.622 1.478 -2.879 -1.515 -5.134 1.595 H4 ZNA 48 ZNA H5 H5 H 0 1 N N N N N N -12.743 0.731 -4.280 -1.077 -2.694 1.759 H5 ZNA 49 ZNA H6 H6 H 0 1 N N N N N N -12.494 -1.652 -4.898 -2.763 -1.107 0.931 H6 ZNA 50 ZNA H7 H7 H 0 1 N N N N N N -15.210 -4.155 -4.198 -5.953 -2.113 -0.517 H7 ZNA 51 ZNA H8 H8 H 0 1 N N N N N N -13.164 -3.500 -6.052 -4.608 -0.592 1.702 H8 ZNA 52 ZNA H9 H9 H 0 1 N N N N N N -14.761 -5.235 -6.150 -6.869 -0.486 2.370 H9 ZNA 53 ZNA H10 H10 H 0 1 N N N N N N -11.326 -3.777 -4.442 -4.902 1.473 0.919 H10 ZNA 54 ZNA H11 H11 H 0 1 N N N N N N -10.348 -5.742 -5.300 -7.120 1.278 1.701 H11 ZNA 55 ZNA H12 H12 H 0 1 N N N N N N -12.708 -6.446 -3.689 -6.368 0.789 -1.615 H12 ZNA 56 ZNA H13 H13 H 0 1 N N N N N N -10.908 -6.772 -2.302 -4.521 2.210 -2.548 H13 ZNA 57 ZNA H14 H14 H 0 1 N N N N N N -10.084 -5.397 -3.112 -5.384 3.045 -1.235 H14 ZNA 58 ZNA H15 H15 H 0 1 N N N N N N -10.069 -5.909 1.527 -3.522 4.881 0.554 H15 ZNA 59 ZNA H16 H16 H 0 1 N N N N N N -12.986 -3.577 3.311 -0.076 5.274 1.754 H16 ZNA 60 ZNA H17 H17 H 0 1 N N N N N N -13.890 -1.633 -0.529 3.134 3.424 -0.253 H17 ZNA 61 ZNA H18 H18 H 0 1 N N N N N N -12.419 -1.902 -1.525 2.881 4.225 1.316 H18 ZNA 62 ZNA H19 H19 H 0 1 N N N N N N -13.068 0.541 -1.131 2.968 1.961 2.423 H19 ZNA 63 ZNA H20 H20 H 0 1 N N N N N N -10.316 -0.396 -0.154 5.161 3.449 1.196 H20 ZNA 64 ZNA H21 H21 H 0 1 N N N N N N -9.791 0.214 -2.363 6.193 2.691 3.214 H21 ZNA 65 ZNA H22 H22 H 0 1 N N N N N N -9.841 1.928 -0.060 5.958 1.658 -0.097 H22 ZNA 66 ZNA H23 H23 H 0 1 N N N N N N -11.243 3.452 -1.173 7.476 1.606 1.789 H23 ZNA 67 ZNA H24 H24 H 0 1 N N N N N N -12.536 2.624 0.656 4.557 -0.310 1.799 H24 ZNA 68 ZNA H25 H25 H 0 1 N N N N N N -10.280 0.080 2.443 3.593 0.144 -1.828 H25 ZNA 69 ZNA H26 H26 H 0 1 N N N N N N -11.616 6.441 3.384 7.831 -3.819 1.124 H26 ZNA 70 ZNA H27 H27 H 0 1 N N N N N N -9.036 4.362 6.419 5.786 -3.713 -3.740 H27 ZNA 71 ZNA H28 H28 H 0 1 N N N N N N -9.616 2.837 6.353 6.883 -4.870 -3.211 H28 ZNA 72 # 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 ZNA O43 C42 SING N N 1 ZNA O41 C40 SING N N 2 ZNA C42 C40 SING N N 3 ZNA C42 C09 SING N N 4 ZNA C40 C11 SING N N 5 ZNA C07 C06 DOUB Y N 6 ZNA C07 N08 SING Y N 7 ZNA C09 N08 SING N N 8 ZNA C09 S10 SING N N 9 ZNA C06 C05 SING Y N 10 ZNA N08 C44 DOUB Y N 11 ZNA C11 S10 SING N N 12 ZNA C11 C12 SING N N 13 ZNA C05 C04 DOUB Y N 14 ZNA C44 C04 SING Y N 15 ZNA C04 C02 SING N N 16 ZNA C12 O13 SING N N 17 ZNA O39 C38 SING N N 18 ZNA C02 N01 SING N N 19 ZNA C02 O03 DOUB N N 20 ZNA O37 C36 SING N N 21 ZNA O13 P14 SING N N 22 ZNA C38 C23 SING N N 23 ZNA C38 C36 SING N N 24 ZNA C22 C23 SING N N 25 ZNA C22 O21 SING N N 26 ZNA C23 O24 SING N N 27 ZNA C36 C25 SING N N 28 ZNA O16 P14 DOUB N N 29 ZNA P14 O17 SING N N 30 ZNA P14 O15 SING N N 31 ZNA O17 P18 SING N N 32 ZNA O21 P18 SING N N 33 ZNA C25 O24 SING N N 34 ZNA C25 N26 SING N N 35 ZNA O20 P18 DOUB N N 36 ZNA P18 O19 SING N N 37 ZNA N26 C27 SING Y N 38 ZNA N26 C35 SING Y N 39 ZNA N34 C35 DOUB Y N 40 ZNA N34 C33 SING Y N 41 ZNA C27 N28 DOUB Y N 42 ZNA C35 C29 SING Y N 43 ZNA C33 N32 DOUB Y N 44 ZNA N28 C29 SING Y N 45 ZNA C29 C30 DOUB Y N 46 ZNA N32 C30 SING Y N 47 ZNA C30 N31 SING N N 48 ZNA N01 H1 SING N N 49 ZNA N01 H2 SING N N 50 ZNA C44 H3 SING N N 51 ZNA C05 H4 SING N N 52 ZNA C06 H5 SING N N 53 ZNA C07 H6 SING N N 54 ZNA C09 H7 SING N N 55 ZNA C42 H8 SING N N 56 ZNA O43 H9 SING N N 57 ZNA C40 H10 SING N N 58 ZNA O41 H11 SING N N 59 ZNA C11 H12 SING N N 60 ZNA C12 H13 SING N N 61 ZNA C12 H14 SING N N 62 ZNA O15 H15 SING N N 63 ZNA O19 H16 SING N N 64 ZNA C22 H17 SING N N 65 ZNA C22 H18 SING N N 66 ZNA C23 H19 SING N N 67 ZNA C38 H20 SING N N 68 ZNA O39 H21 SING N N 69 ZNA C36 H22 SING N N 70 ZNA O37 H23 SING N N 71 ZNA C25 H24 SING N N 72 ZNA C27 H25 SING N N 73 ZNA C33 H26 SING N N 74 ZNA N31 H27 SING N N 75 ZNA N31 H28 SING N N 76 # 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 ZNA SMILES ACDLabs 12.01 "Nc1ncnc2c1ncn2C1OC(COP(=O)(O)OP(=O)(O)OCC2SC([n+]3cc(ccc3)C(N)=O)C(O)C2O)C(O)C1O" ZNA InChI InChI 1.06 "InChI=1S/C21H27N7O13P2S/c22-17-12-19(25-7-24-17)28(8-26-12)20-15(31)13(29)10(40-20)5-38-42(34,35)41-43(36,37)39-6-11-14(30)16(32)21(44-11)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/p+1/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1" ZNA InChIKey InChI 1.06 YLEHCOOOOOOSDX-NNYOXOHSSA-O ZNA SMILES_CANONICAL CACTVS 3.385 "NC(=O)c1ccc[n+](c1)[C@@H]2S[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O" ZNA SMILES CACTVS 3.385 "NC(=O)c1ccc[n+](c1)[CH]2S[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O" ZNA SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](S2)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N" ZNA SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(c[n+](c1)C2C(C(C(S2)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N" # 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 ZNA "SYSTEMATIC NAME" ACDLabs 12.01 "1-[(2R,3R,4S,5R)-5-({[(R)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxythiolan-2-yl]-3-carbamoylpyridin-1-ium (non-preferred name)" ZNA "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-bis(oxidanyl)thiolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl 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 ZNA "Create component" 2018-08-15 RCSB ZNA "Initial release" 2018-11-21 RCSB ZNA "Modify charge" 2024-05-08 RCSB #