data_ZW6 # _chem_comp.id ZW6 _chem_comp.name "Molybdopterin cytidine dinucleotide hydroxy-oxo-selenol-molybdenum" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H27 Mo N8 O15 P2 S2 Se" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge ? _chem_comp.pdbx_initial_date 2026-04-20 _chem_comp.pdbx_modified_date 2026-08-07 _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 908.440 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ZW6 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details MetalCoord _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 3HRD _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm ? _chem_comp.pdbx_comp_type "metal-containing ligand" # 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 ZW6 N1 N1 N 0 1 N N N N N N -5.493 13.746 -32.387 7.340 0.805 -0.970 N1 ZW6 1 ZW6 C2 C1 C 0 1 N N N N N N -4.432 14.551 -32.797 8.536 0.586 -1.672 C2 ZW6 2 ZW6 N3 N2 N 0 1 N N N N N N -3.168 14.047 -32.778 9.717 0.796 -1.041 N3 ZW6 3 ZW6 C4 C2 C 0 1 N N N N N N -2.954 12.745 -32.353 9.753 1.202 0.236 C4 ZW6 4 ZW6 C5 C3 C 0 1 N N N N N N -3.987 11.928 -31.948 8.553 1.424 0.964 C5 ZW6 5 ZW6 C6 C4 C 0 1 N N N N N N -5.252 12.433 -31.966 7.389 1.215 0.332 C6 ZW6 6 ZW6 O21 O3 O 0 1 N N N N N N -4.571 15.747 -33.191 8.497 0.209 -2.851 O21 ZW6 7 ZW6 N4 N3 N 0 1 N N N N N N -1.693 12.279 -32.336 10.943 1.390 0.798 N4 ZW6 8 ZW6 "C1'" C5 C 0 1 N N R N N N -6.923 14.296 -32.376 6.044 0.563 -1.685 "C1'" ZW6 9 ZW6 C2D C6 C 0 1 N N R N N N -7.444 14.430 -33.791 5.487 -0.856 -1.479 C2D ZW6 10 ZW6 "O2'" O4 O 0 1 N N N N N N -8.231 15.560 -34.027 5.142 -1.416 -2.735 "O2'" ZW6 11 ZW6 "C3'" C7 C 0 1 N N S N N N -8.182 13.141 -33.937 4.292 -0.615 -0.538 "C3'" ZW6 12 ZW6 C4D C8 C 0 1 N N R N N N -8.701 12.851 -32.518 3.858 0.816 -0.884 C4D ZW6 13 ZW6 O4D O5 O 0 1 N N N N N N -7.804 13.587 -31.631 5.083 1.493 -1.236 O4D ZW6 14 ZW6 "O3'" O6 O 0 1 N N N N N N -9.229 13.234 -34.916 3.239 -1.546 -0.765 "O3'" ZW6 15 ZW6 "C5'" C9 C 0 1 N N N N N N -8.733 11.406 -32.081 3.146 1.583 0.207 "C5'" ZW6 16 ZW6 "O5'" O7 O 0 1 N N N N N N -7.803 10.616 -32.829 1.764 1.160 0.277 "O5'" ZW6 17 ZW6 PA P1 P 0 1 N N N N N N -7.606 9.079 -32.571 0.540 2.125 -0.012 PA ZW6 18 ZW6 O1A O8 O 0 1 N N N N N N -6.736 8.626 -33.699 0.696 3.523 0.449 O1A ZW6 19 ZW6 O2A O9 O 0 1 N N N N N N -7.186 8.837 -31.171 0.183 1.995 -1.484 O2A ZW6 20 ZW6 O3A O10 O 0 1 N N N N N N -9.030 8.395 -32.627 -0.675 1.456 0.768 O3A ZW6 21 ZW6 PB P2 P 0 1 N N N N N N -10.073 8.241 -33.818 -0.760 0.590 2.104 PB ZW6 22 ZW6 O1B O11 O 0 1 N N N N N N -10.078 6.846 -34.306 -0.613 1.485 3.272 O1B ZW6 23 ZW6 O2B O12 O 0 1 N N N N N N -9.870 9.340 -34.837 0.351 -0.446 1.981 O2B ZW6 24 ZW6 O3B O13 O 0 1 N N N N N N -11.435 8.626 -33.127 -2.159 -0.152 2.011 O3B ZW6 25 ZW6 C10 C10 C 0 1 N N N N N N -12.279 7.706 -32.469 -2.522 -1.038 0.935 C10 ZW6 26 ZW6 "C9'" C11 C 0 1 N N R N N N -12.209 7.884 -30.974 -3.625 -1.989 1.398 "C9'" ZW6 27 ZW6 "C8'" C12 C 0 1 N N N N N N -12.994 6.850 -30.254 -3.893 -3.147 0.449 "C8'" ZW6 28 ZW6 "S8'" S1 S -1 1 N N N N N N -12.645 5.128 -30.520 -2.682 -4.263 0.109 "S8'" ZW6 29 ZW6 "C7'" C13 C 0 1 N N N N N N -14.004 7.191 -29.357 -5.102 -3.327 -0.128 "C7'" ZW6 30 ZW6 "S7'" S2 S -1 1 N N N N N N -14.920 5.971 -28.517 -5.349 -4.569 -1.224 "S7'" ZW6 31 ZW6 "C6'" C14 C 0 1 N N R N N N -14.335 8.600 -29.075 -6.312 -2.447 0.191 "C6'" ZW6 32 ZW6 C7 C15 C 0 1 N N R N N N -13.110 9.501 -29.348 -6.110 -1.605 1.488 C7 ZW6 33 ZW6 "O9'" O14 O 0 1 N N N N N N -12.633 9.279 -30.701 -4.759 -1.122 1.597 "O9'" ZW6 34 ZW6 "N5'" N4 N 0 1 N N N N N N -15.552 9.052 -29.752 -6.651 -1.617 -0.966 "N5'" ZW6 35 ZW6 C4A C16 C 0 1 N N N N N N -15.710 10.414 -29.955 -7.263 -0.379 -0.850 C4A ZW6 36 ZW6 "N8'" N5 N 0 1 N N N N N N -13.471 10.872 -29.120 -6.986 -0.442 1.544 "N8'" ZW6 37 ZW6 C4B C17 C 0 1 N N N N N N -14.661 11.366 -29.633 -7.440 0.190 0.427 C4B ZW6 38 ZW6 "N1'" N6 N 0 1 N N N N N N -14.755 12.698 -29.798 -8.019 1.403 0.607 "N1'" ZW6 39 ZW6 "C2'" C18 C 0 1 N N N N N N -15.901 13.200 -30.307 -8.455 2.056 -0.474 "C2'" ZW6 40 ZW6 "N2'" N7 N 0 1 N N N N N N -16.020 14.541 -30.472 -9.039 3.242 -0.322 "N2'" ZW6 41 ZW6 "N3'" N8 N 0 1 N N N N N N -16.930 12.335 -30.648 -8.330 1.564 -1.742 "N3'" ZW6 42 ZW6 "C4'" C19 C 0 1 N N N N N N -16.906 10.963 -30.509 -7.731 0.338 -2.011 "C4'" ZW6 43 ZW6 "O4'" O15 O 0 1 N N N N N N -17.880 10.237 -30.836 -7.651 -0.059 -3.169 "O4'" ZW6 44 ZW6 MO MO1 MO ? 0 N N N N N N -14.573 3.861 -29.562 -3.276 -5.276 -1.840 MO ZW6 45 ZW6 O1 O1 O -1 1 N N N N N N -15.631 3.898 -30.872 -2.984 -3.851 -2.644 O1 ZW6 46 ZW6 O2 O2 O -1 1 N N N N N N -13.479 2.489 -29.791 -1.724 -5.754 -2.187 O2 ZW6 47 ZW6 SE SE1 SE -1 0 N N N N N N -15.860 2.863 -27.951 -4.020 -6.295 -3.764 SE ZW6 48 ZW6 H4 H4 H 0 1 N N N N N N -3.799 10.915 -31.625 8.573 1.710 1.862 H4 ZW6 49 ZW6 H5 H5 H 0 1 N N N N N N -6.079 11.813 -31.652 6.585 1.353 0.795 H5 ZW6 50 ZW6 H6 H6 H 0 1 N N N N N N -0.938 12.868 -32.625 11.674 1.249 0.335 H6 ZW6 51 ZW6 H7 H7 H 0 1 N N N N N N -1.510 11.343 -32.034 11.007 1.655 1.632 H7 ZW6 52 ZW6 H8 H8 H 0 1 N N N N N N -6.860 15.315 -31.968 6.172 0.704 -2.661 H8 ZW6 53 ZW6 H9 H9 H 0 1 N N N N N N -6.585 14.422 -34.478 6.157 -1.419 -1.031 H9 ZW6 54 ZW6 H10 H10 H 0 1 N N N N N N -8.514 15.566 -34.934 4.934 -2.227 -2.654 H10 ZW6 55 ZW6 H11 H11 H 0 1 N N N N N N -7.473 12.349 -34.220 4.600 -0.677 0.404 H11 ZW6 56 ZW6 H12 H12 H 0 1 N N N N N N -9.716 13.266 -32.432 3.264 0.796 -1.679 H12 ZW6 57 ZW6 H13 H13 H 0 1 N N N N N N -9.676 12.398 -34.982 2.657 -1.495 -0.159 H13 ZW6 58 ZW6 H14 H14 H 0 1 N N N N N N -8.474 11.349 -31.013 3.194 2.554 0.009 H14 ZW6 59 ZW6 H15 H15 H 0 1 N N N N N N -9.747 11.007 -32.235 3.592 1.423 1.080 H15 ZW6 60 ZW6 H16 H16 H 0 1 N N N N N N -6.349 8.388 -31.164 -0.500 2.505 -1.724 H16 ZW6 61 ZW6 H17 H17 H 0 1 N N N N N N -9.768 8.957 -35.700 0.398 -0.991 2.678 H17 ZW6 62 ZW6 H18 H18 H 0 1 N N N N N N -13.315 7.866 -32.802 -1.739 -1.554 0.648 H18 ZW6 63 ZW6 H19 H19 H 0 1 N N N N N N -11.965 6.683 -32.725 -2.844 -0.520 0.165 H19 ZW6 64 ZW6 H20 H20 H 0 1 N N N N N N -11.156 7.783 -30.673 -3.354 -2.377 2.272 H20 ZW6 65 ZW6 H24 H24 H 0 1 N N N N N N -15.265 15.145 -30.218 -9.134 3.587 0.480 H24 ZW6 66 ZW6 H25 H25 H 0 1 N N N N N N -16.863 14.926 -30.848 -9.332 3.688 -1.019 H25 ZW6 67 ZW6 H21 H21 H 0 1 N N N N N N -14.527 8.670 -27.994 -7.079 -3.050 0.367 H21 ZW6 68 ZW6 H22 H22 H 0 1 N N N N N N -12.319 9.214 -28.640 -6.309 -2.173 2.273 H22 ZW6 69 ZW6 H23 H23 H 0 1 N N N N N N -13.507 11.001 -28.129 -7.240 -0.132 2.333 H23 ZW6 70 ZW6 H26 H26 H 0 1 N N N N N N -15.575 8.612 -30.650 -6.469 -1.904 -1.767 H26 ZW6 71 ZW6 H27 H27 H 0 1 N N N N N N -17.761 12.741 -31.027 -8.636 2.038 -2.418 H27 ZW6 72 ZW6 H3 H3 H 0 1 N N N N N N -12.833 2.705 -30.453 -1.693 -6.617 -2.241 H3 ZW6 73 ZW6 H2 H2 H 0 1 N N N N N N -15.376 4.336 -31.676 -3.647 -3.628 -3.154 H2 ZW6 74 ZW6 H1 H1 H 0 1 N N N N N N -15.090 2.745 -26.716 -5.523 -6.302 -3.777 H1 ZW6 75 # 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 _chem_comp_bond.pdbx_metal_coordination_flag _chem_comp_bond.pdbx_metal_pi_flag ZW6 SE MO SING N N 1 Y N ZW6 MO O1 DOUB N N 2 Y N ZW6 MO "S8'" SING N N 3 Y N ZW6 MO O2 SING N N 4 Y N ZW6 MO "S7'" SING N N 5 Y N ZW6 N1 C6 SING N N 6 N N ZW6 N1 C2 SING N N 7 N N ZW6 N1 "C1'" SING N N 8 N N ZW6 C2 O21 DOUB N N 9 N N ZW6 C2 N3 SING N N 10 N N ZW6 N3 C4 DOUB N N 11 N N ZW6 C4 C5 SING N N 12 N N ZW6 C4 N4 SING N N 13 N N ZW6 C5 C6 DOUB N N 14 N N ZW6 "C1'" C2D SING N N 15 N N ZW6 "C1'" O4D SING N N 16 N N ZW6 C2D "O2'" SING N N 17 N N ZW6 C2D "C3'" SING N N 18 N N ZW6 "C3'" "O3'" SING N N 19 N N ZW6 "C3'" C4D SING N N 20 N N ZW6 C4D "C5'" SING N N 21 N N ZW6 C4D O4D SING N N 22 N N ZW6 "C5'" "O5'" SING N N 23 N N ZW6 "O5'" PA SING N N 24 N N ZW6 PA O1A DOUB N N 25 N N ZW6 PA O3A SING N N 26 N N ZW6 PA O2A SING N N 27 N N ZW6 O3A PB SING N N 28 N N ZW6 PB O1B DOUB N N 29 N N ZW6 PB O2B SING N N 30 N N ZW6 PB O3B SING N N 31 N N ZW6 O3B C10 SING N N 32 N N ZW6 C10 "C9'" SING N N 33 N N ZW6 "C9'" "O9'" SING N N 34 N N ZW6 "C9'" "C8'" SING N N 35 N N ZW6 "C8'" "S8'" SING N N 36 N N ZW6 "C8'" "C7'" DOUB N N 37 N N ZW6 "C7'" "S7'" SING N N 38 N N ZW6 "C7'" "C6'" SING N N 39 N N ZW6 "C6'" "N5'" SING N N 40 N N ZW6 "C6'" C7 SING N N 41 N N ZW6 C7 "O9'" SING N N 42 N N ZW6 C7 "N8'" SING N N 43 N N ZW6 "N5'" C4A SING N N 44 N N ZW6 C4A "C4'" SING N N 45 N N ZW6 C4A C4B DOUB N N 46 N N ZW6 "N8'" C4B SING N N 47 N N ZW6 C4B "N1'" SING N N 48 N N ZW6 "N1'" "C2'" DOUB N N 49 N N ZW6 "C2'" "N3'" SING N N 50 N N ZW6 "C2'" "N2'" SING N N 51 N N ZW6 "N3'" "C4'" SING N N 52 N N ZW6 "C4'" "O4'" DOUB N N 53 N N ZW6 SE H1 SING N N 54 N N ZW6 O1 H2 SING N N 55 N N ZW6 O2 H3 SING N N 56 N N ZW6 C5 H4 SING N N 57 N N ZW6 C6 H5 SING N N 58 N N ZW6 N4 H6 SING N N 59 N N ZW6 N4 H7 SING N N 60 N N ZW6 "C1'" H8 SING N N 61 N N ZW6 C2D H9 SING N N 62 N N ZW6 "O2'" H10 SING N N 63 N N ZW6 "C3'" H11 SING N N 64 N N ZW6 C4D H12 SING N N 65 N N ZW6 "O3'" H13 SING N N 66 N N ZW6 "C5'" H14 SING N N 67 N N ZW6 "C5'" H15 SING N N 68 N N ZW6 O2A H16 SING N N 69 N N ZW6 O2B H17 SING N N 70 N N ZW6 C10 H18 SING N N 71 N N ZW6 C10 H19 SING N N 72 N N ZW6 "C9'" H20 SING N N 73 N N ZW6 "C6'" H21 SING N N 74 N N ZW6 C7 H22 SING N N 75 N N ZW6 "N8'" H23 SING N N 76 N N ZW6 "N2'" H24 SING N N 77 N N ZW6 "N2'" H25 SING N N 78 N N ZW6 "N5'" H26 SING N N 79 N N ZW6 "N3'" H27 SING N N 80 N N # 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 ZW6 InChI InChI 1.06 "InChI=1S/C19H26N8O13P2S2.Mo.2H2O.H2Se/c20-7-1-2-27(19(31)22-7)17-11(29)10(28)5(39-17)3-36-41(32,33)40-42(34,35)37-4-6-12(43)13(44)8-16(38-6)24-14-9(23-8)15(30)26-18(21)25-14;;;;/h1-2,5-6,8,10-11,16-17,23,28-29,43-44H,3-4H2,(H,32,33)(H,34,35)(H2,20,22,31)(H4,21,24,25,26,30);;3*1H2/q;+5;;;/p-5/t5-,6-,8+,10-,11-,16-,17-;;;;/m1..../s1" ZW6 InChIKey InChI 1.06 INJMIBMQZDSMML-MQPNXHJTSA-I ZW6 SMILES_CANONICAL CACTVS 3.385 "O.NC1=NC2=C(N[C@@H]3[C@H](N2)O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)N5C=CC(=NC5=O)N)C6=C3S[Mo](O)([SeH])S6)C(=O)N1" ZW6 SMILES CACTVS 3.385 "O.NC1=NC2=C(N[CH]3[CH](N2)O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)N5C=CC(=NC5=O)N)C6=C3S[Mo](O)([SeH])S6)C(=O)N1" ZW6 SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OC[C@@H]3C4=C([C@H]5[C@@H](O3)NC6=C(N5)C(=O)NC(=N6)N)S[Mo](=[OH])(S4)(O)[SeH])O)O" ZW6 SMILES "OpenEye OEToolkits" 3.1.0.0 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C4=C(C5C(O3)NC6=C(N5)C(=O)NC(=N6)N)S[Mo](=[OH])(S4)(O)[SeH])O)O" # _pdbx_chem_comp_identifier.comp_id ZW6 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 3.1.0.0 _pdbx_chem_comp_identifier.identifier "[[(1~{R},10~{R},16~{R})-5-azanyl-13-$l^{3}-oxidanylidene-13-oxidanyl-7-oxidanylidene-13-selanyl-17-oxa-12,14-dithia-2,4,6,9-tetraza-13$l^{6}-molybdatetracyclo[8.7.0.0^{3,8}.0^{11,15}]heptadeca-3(8),4,11(15)-trien-16-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate" # _pdbx_chem_comp_atom_coordination.geometry_id 1 _pdbx_chem_comp_atom_coordination.comp_id ZW6 _pdbx_chem_comp_atom_coordination.atom_id MO _pdbx_chem_comp_atom_coordination.number 5 _pdbx_chem_comp_atom_coordination.geometry_calculated square-pyramid _pdbx_chem_comp_atom_coordination.geometry_generic "square pyramidal" _pdbx_chem_comp_atom_coordination.geometry_abbr SQP _pdbx_chem_comp_atom_coordination.provenance MetalCoord _pdbx_chem_comp_atom_coordination.representative_entry_id 3HRD # _pdbx_chem_comp_atom_coordination_sphere.id 1 _pdbx_chem_comp_atom_coordination_sphere.geometry_id 1 _pdbx_chem_comp_atom_coordination_sphere.comp_id ZW6 _pdbx_chem_comp_atom_coordination_sphere.atom_id MO _pdbx_chem_comp_atom_coordination_sphere.descriptor "@SQP{Mo,O,S,S,Se,O}" _pdbx_chem_comp_atom_coordination_sphere.provenance MetalCoord _pdbx_chem_comp_atom_coordination_sphere.representative_entry_id 3HRD # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site ZW6 "Create component" 2026-04-20 RCSB ZW6 "Other modification" 2026-07-31 RCSB ZW6 "Initial release" 2026-08-12 RCSB #