data_F5K # _chem_comp.id F5K _chem_comp.name "Molybdopterin cytosine dinucleotide hydroxy-oxo-sulfido-molybdenum" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H25 Mo N8 O15 P2 S3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge ? _chem_comp.pdbx_initial_date 2026-06-03 _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 859.529 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ? _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 5G5G _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y _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 _chem_comp_atom.pdbx_residue_numbering _chem_comp_atom.pdbx_polymer_type _chem_comp_atom.pdbx_component_id F5K N1 N1 N 0 1 N N N N N N 211.878 -98.936 172.437 7.309 0.913 -1.066 N1 F5K 1 1 non-polymer 2 F5K C2 C1 C 0 1 N N N N N N 212.550 -97.646 172.628 8.492 0.698 -1.790 C2 F5K 2 1 non-polymer 2 F5K N3 N2 N 0 1 N N N N N N 213.685 -97.680 171.606 9.684 0.894 -1.176 N3 F5K 3 1 non-polymer 2 F5K C4 C2 C 0 1 N N N N N N 214.151 -98.618 170.798 9.744 1.282 0.106 C4 F5K 4 1 non-polymer 2 F5K C5 C3 C 0 1 N N N N N N 213.220 -99.795 170.701 8.557 1.500 0.857 C5 F5K 5 1 non-polymer 2 F5K C6 C4 C 0 1 N N N N N N 212.229 -99.913 171.535 7.382 1.305 0.241 C6 F5K 6 1 non-polymer 2 F5K O2 O1 O 0 1 N N N N N N 212.308 -96.796 173.312 8.433 0.337 -2.973 O2 F5K 7 1 non-polymer 2 F5K N4 N3 N 0 1 N N N N N N 215.198 -98.599 170.053 10.944 1.457 0.651 N4 F5K 8 1 non-polymer 2 F5K "C1'" C5 C 0 1 N N R N N N 210.879 -99.167 173.468 6.000 0.688 -1.762 "C1'" F5K 9 1 non-polymer 2 F5K C2D C6 C 0 1 N N R N N N 209.563 -98.345 173.200 5.432 -0.727 -1.553 C2D F5K 10 1 non-polymer 2 F5K "O2'" O2 O 0 1 N N N N N N 208.890 -98.102 174.433 5.061 -1.278 -2.806 "O2'" F5K 11 1 non-polymer 2 F5K "C3'" C7 C 0 1 N N S N N N 208.870 -99.315 172.386 4.256 -0.479 -0.592 "C3'" F5K 12 1 non-polymer 2 F5K C4D C8 C 0 1 N N R N N N 209.083 -100.796 172.939 3.830 0.958 -0.922 C4D F5K 13 1 non-polymer 2 F5K O4D O3 O 0 1 N N N N N N 210.478 -100.543 173.454 5.055 1.625 -1.294 O4D F5K 14 1 non-polymer 2 F5K "O3'" O4 O 0 1 N N N N N N 207.412 -99.181 172.222 3.189 -1.398 -0.806 "O3'" F5K 15 1 non-polymer 2 F5K "C5'" C9 C 0 1 N N N N N N 209.146 -101.957 172.135 3.148 1.728 0.186 "C5'" F5K 16 1 non-polymer 2 F5K "O5'" O5 O 0 1 N N N N N N 209.563 -101.709 170.813 1.798 1.237 0.367 "O5'" F5K 17 1 non-polymer 2 F5K PA P1 P 0 1 N N N N N N 210.053 -102.905 169.957 0.498 2.033 -0.068 PA F5K 18 1 non-polymer 2 F5K O1A O6 O 0 1 N N N N N N 210.113 -102.413 168.512 0.572 3.508 0.023 O1A F5K 19 1 non-polymer 2 F5K O2A O7 O 0 1 N N N N N N 211.231 -103.551 170.598 0.081 1.521 -1.438 O2A F5K 20 1 non-polymer 2 F5K O3A O8 O 0 1 N N N N N N 208.793 -104.019 170.066 -0.634 1.518 0.927 O3A F5K 21 1 non-polymer 2 F5K PB P2 P 0 1 N N N N N N 207.493 -103.963 169.168 -0.637 0.499 2.154 PB F5K 22 1 non-polymer 2 F5K O1B O9 O 0 1 N N N N N N 207.708 -104.696 167.915 -0.240 1.219 3.383 O1B F5K 23 1 non-polymer 2 F5K O2B O10 O 0 1 N N N N N N 206.975 -102.563 169.121 0.327 -0.610 1.753 O2B F5K 24 1 non-polymer 2 F5K O3B O11 O 0 1 N N N N N N 206.524 -104.719 170.149 -2.107 -0.101 2.183 O3B F5K 25 1 non-polymer 2 F5K C10 C10 C 0 1 N N N N N N 206.489 -106.209 170.132 -2.723 -0.760 1.058 C10 F5K 26 1 non-polymer 2 F5K "C9'" C11 C 0 1 N N R N N N 207.241 -106.841 171.249 -3.591 -1.922 1.549 "C9'" F5K 27 1 non-polymer 2 F5K "C8'" C12 C 0 1 N N N N N N 207.212 -108.443 170.978 -3.700 -3.049 0.535 "C8'" F5K 28 1 non-polymer 2 F5K "S8'" S1 S -1 1 N N N N N N 207.493 -109.058 169.445 -2.360 -4.016 0.227 "S8'" F5K 29 1 non-polymer 2 F5K "C7'" C13 C 0 1 N N N N N N 206.787 -109.129 171.921 -4.847 -3.295 -0.129 "C7'" F5K 30 1 non-polymer 2 F5K "S7'" S2 S -1 1 N N N N N N 206.491 -110.884 171.750 -4.901 -4.466 -1.326 "S7'" F5K 31 1 non-polymer 2 F5K "C6'" C14 C 0 1 N N R N N N 206.708 -108.611 173.390 -6.148 -2.551 0.167 "C6'" F5K 32 1 non-polymer 2 F5K C7 C15 C 0 1 N N R N N N 207.408 -107.170 173.366 -6.137 -1.835 1.556 C7 F5K 33 1 non-polymer 2 F5K "O9'" O12 O 0 1 N N N N N N 206.863 -106.338 172.424 -4.845 -1.309 1.913 "O9'" F5K 34 1 non-polymer 2 F5K "N5'" N4 N 0 1 N N N N N N 205.182 -108.387 173.592 -6.452 -1.646 -0.942 "N5'" F5K 35 1 non-polymer 2 F5K C4A C16 C 0 1 N N N N N N 204.737 -107.534 174.740 -7.134 -0.453 -0.779 C4A F5K 36 1 non-polymer 2 F5K "N8'" N5 N 0 1 N N N N N N 207.126 -106.539 174.673 -7.060 -0.706 1.619 "N8'" F5K 37 1 non-polymer 2 F5K C4B C17 C 0 1 N N N N N N 205.874 -106.547 175.177 -7.447 -0.003 0.519 C4B F5K 38 1 non-polymer 2 F5K "N1'" N6 N 0 1 N N N N N N 205.618 -105.803 176.329 -8.103 1.163 0.743 "N1'" F5K 39 1 non-polymer 2 F5K "C2'" C18 C 0 1 N N N N N N 204.321 -105.552 176.790 -8.480 1.885 -0.316 "C2'" F5K 40 1 non-polymer 2 F5K "N2'" N7 N 0 1 N N N N N N 204.083 -104.903 177.826 -9.135 3.027 -0.122 "N2'" F5K 41 1 non-polymer 2 F5K "N3'" N8 N 0 1 N N N N N N 203.386 -106.455 176.364 -8.223 1.507 -1.604 "N3'" F5K 42 1 non-polymer 2 F5K "C4'" C19 C 0 1 N N N N N N 203.384 -107.305 175.270 -7.541 0.336 -1.916 "C4'" F5K 43 1 non-polymer 2 F5K "O4'" O13 O 0 1 N N N N N N 202.560 -108.096 174.773 -7.342 0.043 -3.090 "O4'" F5K 44 1 non-polymer 2 F5K MO MO1 MO ? 0 N N N N N N 206.554 -111.197 169.464 -2.687 -4.720 -1.972 MO F5K 45 2 non-polymer 3 F5K S S3 S -2 1 N N N N N N 206.643 -113.508 169.613 -3.239 -5.455 -4.275 S F5K 46 2 non-polymer 3 F5K O1 O14 O -2 1 N N N N N N 204.814 -111.101 169.066 -2.709 -6.337 -1.449 O1 F5K 47 2 non-polymer 3 F5K O21 O15 O -1 1 N N N N N N 207.431 -111.644 167.615 -1.031 -4.849 -2.335 O21 F5K 48 2 non-polymer 3 F5K H1 H1 H 0 1 N N N N N N 213.375 -100.543 169.938 8.594 1.774 1.758 H1 F5K 49 1 non-polymer 2 F5K H2 H2 H 0 1 N N N N N N 211.652 -100.826 171.518 6.586 1.441 0.719 H2 F5K 50 1 non-polymer 2 F5K H3 H3 H 0 1 N N N N N N 215.786 -97.790 170.037 11.666 1.318 0.173 H3 F5K 51 1 non-polymer 2 F5K H4 H4 H 0 1 N N N N N N 215.425 -99.393 169.489 11.023 1.710 1.487 H4 F5K 52 1 non-polymer 2 F5K H5 H5 H 0 1 N N N N N N 211.276 -98.888 174.455 6.114 0.831 -2.738 H5 F5K 53 1 non-polymer 2 F5K H6 H6 H 0 1 N N N N N N 209.791 -97.420 172.650 6.104 -1.299 -1.119 H6 F5K 54 1 non-polymer 2 F5K H7 H7 H 0 1 N N N N N N 208.097 -97.606 174.269 4.846 -2.087 -2.725 H7 F5K 55 1 non-polymer 2 F5K H8 H8 H 0 1 N N N N N N 209.319 -99.296 171.382 4.579 -0.550 0.345 H8 F5K 56 1 non-polymer 2 F5K H9 H9 H 0 1 N N N N N N 208.402 -100.948 173.789 3.221 0.948 -1.706 H9 F5K 57 1 non-polymer 2 F5K H10 H10 H 0 1 N N N N N N 207.090 -99.881 171.666 2.619 -1.344 -0.190 H10 F5K 58 1 non-polymer 2 F5K H11 H11 H 0 1 N N N N N N 209.855 -102.661 172.596 3.130 2.691 -0.048 H11 F5K 59 1 non-polymer 2 F5K H12 H12 H 0 1 N N N N N N 208.145 -102.412 172.104 3.659 1.625 1.031 H12 F5K 60 1 non-polymer 2 F5K H13 H13 H 0 1 N N N N N N 211.950 -103.586 169.978 -0.644 1.920 -1.754 H13 F5K 61 1 non-polymer 2 F5K H14 H14 H 0 1 N N N N N N 206.840 -102.305 168.217 0.406 -1.243 2.368 H14 F5K 62 1 non-polymer 2 F5K H15 H15 H 0 1 N N N N N N 205.439 -106.532 170.195 -2.033 -1.098 0.447 H15 F5K 63 1 non-polymer 2 F5K H16 H16 H 0 1 N N N N N N 206.923 -106.555 169.182 -3.282 -0.124 0.560 H16 F5K 64 1 non-polymer 2 F5K H17 H17 H 0 1 N N N N N N 208.293 -106.560 171.093 -3.168 -2.303 2.364 H17 F5K 65 1 non-polymer 2 F5K H28 H28 H 0 1 N N N N N N 203.138 -104.750 178.114 -9.392 3.516 -0.804 H28 F5K 66 1 non-polymer 2 F5K H29 H29 H 0 1 N N N N N N 204.837 -104.535 178.370 -9.315 3.299 0.693 H29 F5K 67 1 non-polymer 2 F5K H20 H20 H 0 1 N N N N N N 207.157 -109.295 174.125 -6.870 -3.228 0.211 H20 F5K 68 1 non-polymer 2 F5K H21 H21 H 0 1 N N N N N N 208.491 -107.303 173.227 -6.412 -2.485 2.248 H21 F5K 69 1 non-polymer 2 F5K H22 H22 H 0 1 N N N N N N 204.831 -107.965 172.756 -6.204 -1.859 -1.749 H22 F5K 70 1 non-polymer 2 F5K H25 H25 H 0 1 N N N N N N 207.709 -106.996 175.345 -7.388 -0.465 2.405 H25 F5K 71 1 non-polymer 2 F5K H30 H30 H 0 1 N N N N N N 202.568 -106.511 176.937 -8.495 2.023 -2.264 H30 F5K 72 1 non-polymer 2 F5K H18 H18 H 0 1 N N N N N N 207.533 -112.585 167.532 -0.882 -4.514 -3.120 H18 F5K 73 2 non-polymer 3 # 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 F5K N1 C6 SING N N 1 N N F5K N1 C2 SING N N 2 N N F5K N1 "C1'" SING N N 3 N N F5K C2 N3 SING N N 4 N N F5K C2 O2 DOUB N N 5 N N F5K N3 C4 DOUB N N 6 N N F5K C4 C5 SING N N 7 N N F5K C4 N4 SING N N 8 N N F5K C5 C6 DOUB N N 9 N N F5K "C1'" O4D SING N N 10 N N F5K "C1'" C2D SING N N 11 N N F5K C2D "O2'" SING N N 12 N N F5K C2D "C3'" SING N N 13 N N F5K "C3'" C4D SING N N 14 N N F5K "C3'" "O3'" SING N N 15 N N F5K C4D "C5'" SING N N 16 N N F5K C4D O4D SING N N 17 N N F5K "C5'" "O5'" SING N N 18 N N F5K "O5'" PA SING N N 19 N N F5K PA O1A DOUB N N 20 N N F5K PA O3A SING N N 21 N N F5K PA O2A SING N N 22 N N F5K O3A PB SING N N 23 N N F5K PB O1B DOUB N N 24 N N F5K PB O3B SING N N 25 N N F5K PB O2B SING N N 26 N N F5K O3B C10 SING N N 27 N N F5K C10 "C9'" SING N N 28 N N F5K "C9'" "C8'" SING N N 29 N N F5K "C9'" "O9'" SING N N 30 N N F5K "C8'" "C7'" DOUB N N 31 N N F5K "C8'" "S8'" SING N N 32 N N F5K "S8'" MO SING N N 33 Y N F5K "C7'" "S7'" SING N N 34 N N F5K "C7'" "C6'" SING N N 35 N N F5K "S7'" MO SING N N 36 Y N F5K "C6'" "N5'" SING N N 37 N N F5K "C6'" C7 SING N N 38 N N F5K C7 "O9'" SING N N 39 N N F5K C7 "N8'" SING N N 40 N N F5K "N5'" C4A SING N N 41 N N F5K C4A "C4'" SING N N 42 N N F5K C4A C4B DOUB N N 43 N N F5K "N8'" C4B SING N N 44 N N F5K C4B "N1'" SING N N 45 N N F5K "N1'" "C2'" DOUB N N 46 N N F5K "C2'" "N3'" SING N N 47 N N F5K "C2'" "N2'" SING N N 48 N N F5K "N3'" "C4'" SING N N 49 N N F5K "C4'" "O4'" DOUB N N 50 N N F5K MO O1 DOUB N N 51 Y N F5K MO O21 SING N N 52 Y N F5K MO S SING N N 53 Y N F5K C5 H1 SING N N 54 N N F5K C6 H2 SING N N 55 N N F5K N4 H3 SING N N 56 N N F5K N4 H4 SING N N 57 N N F5K "C1'" H5 SING N N 58 N N F5K C2D H6 SING N N 59 N N F5K "O2'" H7 SING N N 60 N N F5K "C3'" H8 SING N N 61 N N F5K C4D H9 SING N N 62 N N F5K "O3'" H10 SING N N 63 N N F5K "C5'" H11 SING N N 64 N N F5K "C5'" H12 SING N N 65 N N F5K O2A H13 SING N N 66 N N F5K O2B H14 SING N N 67 N N F5K C10 H15 SING N N 68 N N F5K C10 H16 SING N N 69 N N F5K "C9'" H17 SING N N 70 N N F5K "C6'" H20 SING N N 71 N N F5K C7 H21 SING N N 72 N N F5K "N5'" H22 SING N N 73 N N F5K "N8'" H25 SING N N 74 N N F5K "N2'" H29 SING N N 75 N N F5K "N3'" H30 SING N N 76 N N F5K H28 "N2'" SING N N 77 N N F5K H18 O21 SING N N 78 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 F5K InChI InChI 1.06 "InChI=1S/C19H26N8O13P2S2.Mo.H2O.O.H2S/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);;1H2;;1H2/q;+4;;;/p-4/t5-,6-,8+,10-,11-,16-,17-;;;;/m1..../s1" F5K InChIKey InChI 1.06 JTOUSFQUZZMIBU-MQPNXHJTSA-J F5K SMILES_CANONICAL CACTVS 3.385 "S.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)(=O)S6)C(=O)N1" F5K SMILES CACTVS 3.385 "S.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)(=O)S6)C(=O)N1" F5K SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "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](=O)(S4)(O)[S])O)O" F5K SMILES "OpenEye OEToolkits" 2.0.7 "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](=O)(S4)(O)[S])O)O" # _pdbx_chem_comp_identifier.comp_id F5K _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 "[[(1~{R},10~{R},16~{R})-5-azanyl-13-$l^{1}-sulfanyl-13-oxidanyl-7,13-bis(oxidanylidene)-17-oxa-12,14-dithia-2,4,6,9-tetraza-13$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 F5K _pdbx_chem_comp_atom_coordination.atom_id MO _pdbx_chem_comp_atom_coordination.number 6 _pdbx_chem_comp_atom_coordination.geometry_calculated octahedral _pdbx_chem_comp_atom_coordination.geometry_generic octahedral _pdbx_chem_comp_atom_coordination.geometry_abbr OCT _pdbx_chem_comp_atom_coordination.provenance MetalCoord _pdbx_chem_comp_atom_coordination.representative_entry_id 5G5G # _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 F5K _pdbx_chem_comp_atom_coordination_sphere.atom_id MO _pdbx_chem_comp_atom_coordination_sphere.descriptor "@OCT{Mo,O,O,O,S,S,S}" _pdbx_chem_comp_atom_coordination_sphere.provenance MetalCoord _pdbx_chem_comp_atom_coordination_sphere.representative_entry_id 5G5G # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id F5K _pdbx_chem_comp_pcm.modified_residue_id GLU _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Metal coordination" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom MO _pdbx_chem_comp_pcm.modified_residue_id_linking_atom OE2 _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? _pdbx_chem_comp_pcm.position "Amino-acid side chain" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site F5K "Create component" 2026-06-03 RCSB F5K "Other modification" 2026-07-31 RCSB F5K "Initial release" 2026-08-12 RCSB #