data_AH5 # _chem_comp.id AH5 _chem_comp.name "Molybdopterin cytosine dinucleotide dioxo molybdenum" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H24 Mo N8 O15 P2 S2" _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 826.456 _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 1DGJ _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 AH5 MO MO1 MO ? 0 N N N N N N -5.263 53.025 74.900 -4.459 -4.292 -2.098 MO AH5 1 AH5 OT1 O1 O -2 1 N N N N N N -5.388 54.432 73.991 -4.366 -3.260 -3.394 OT1 AH5 2 AH5 OT2 O2 O -2 1 N N N N N N -6.366 53.250 76.182 -5.443 -5.303 -2.973 OT2 AH5 3 AH5 N1 N1 N 0 1 N N N N N N 6.645 48.058 70.202 7.565 -1.139 -0.567 N1 AH5 4 AH5 C2 C1 C 0 1 N N N N N N 7.907 47.479 69.922 8.908 -1.471 -0.805 C2 AH5 5 AH5 N3 N2 N 0 1 N N N N N N 7.923 46.109 69.717 9.839 -0.487 -0.806 N3 AH5 6 AH5 C4 C2 C 0 1 N N N N N N 6.827 45.367 69.775 9.494 0.789 -0.579 C4 AH5 7 AH5 C5 C3 C 0 1 N N N N N N 5.510 45.955 70.067 8.140 1.144 -0.332 C5 AH5 8 AH5 C6 C4 C 0 1 N N N N N N 5.517 47.311 70.266 7.225 0.164 -0.333 C6 AH5 9 AH5 O2 O3 O 0 1 N N N N N N 8.950 48.170 69.863 9.223 -2.651 -1.012 O2 AH5 10 AH5 N4 N3 N 0 1 N N N N N N 6.798 44.025 69.578 10.454 1.708 -0.593 N4 AH5 11 AH5 "C1'" C5 C 0 1 N N R N N N 6.604 49.510 70.428 6.551 -2.244 -0.566 "C1'" AH5 12 AH5 C2D C6 C 0 1 N N R N N N 5.785 50.258 69.342 6.294 -2.837 0.830 C2D AH5 13 AH5 "O2'" O4 O 0 1 N N N N N N 6.616 50.616 68.242 6.357 -4.252 0.763 "O2'" AH5 14 AH5 "C3'" C7 C 0 1 N N S N N N 5.262 51.475 70.077 4.905 -2.276 1.183 "C3'" AH5 15 AH5 C4D C8 C 0 1 N N R N N N 5.035 50.950 71.484 4.242 -2.098 -0.190 C4D AH5 16 AH5 O4D O5 O 0 1 N N N N N N 5.862 49.753 71.635 5.329 -1.758 -1.078 O4D AH5 17 AH5 "O3'" O6 O 0 1 N N N N N N 6.301 52.466 70.174 4.163 -3.170 2.006 "O3'" AH5 18 AH5 "C5'" C9 C 0 1 N N N N N N 3.594 50.637 71.739 3.159 -1.047 -0.282 "C5'" AH5 19 AH5 "O5'" O7 O 0 1 N N N N N N 3.047 49.831 70.514 1.969 -1.507 0.403 "O5'" AH5 20 AH5 PA P1 P 0 1 N N N N N N 1.560 49.320 70.490 0.837 -0.536 0.948 PA AH5 21 AH5 O2A O9 O 0 1 N N N N N N 1.253 48.754 69.046 -0.294 -1.223 1.608 O2A AH5 22 AH5 O1A O8 O 0 1 N N N N N N 1.342 48.327 71.601 1.487 0.538 1.811 O1A AH5 23 AH5 O3A O10 O 0 1 N N N N N N 0.625 50.596 70.858 0.297 0.233 -0.341 O3A AH5 24 AH5 PB P2 P 0 1 N N N N N N 0.307 51.972 70.090 -0.521 1.587 -0.525 PB AH5 25 AH5 O2B O12 O 0 1 N N N N N N -1.069 51.770 69.472 -0.532 1.965 -1.956 O2B AH5 26 AH5 O1B O11 O 0 1 N N N N N N 1.433 52.447 69.317 0.180 2.596 0.371 O1B AH5 27 AH5 O3B O13 O 0 1 N N N N N N 0.236 52.942 71.404 -1.938 1.280 0.114 O3B AH5 28 AH5 C10 C10 C 0 1 N N N N N N -0.996 52.975 72.204 -2.968 0.537 -0.567 C10 AH5 29 AH5 "C9'" C11 C 0 1 N N R N N N -0.771 52.446 73.613 -3.651 -0.416 0.416 "C9'" AH5 30 AH5 "C8'" C12 C 0 1 N N N N N N -2.029 52.717 74.329 -4.248 -1.639 -0.261 "C8'" AH5 31 AH5 "S8'" S1 S -1 1 N N N N N N -3.389 52.092 73.569 -3.220 -2.832 -0.847 "S8'" AH5 32 AH5 "C7'" C13 C 0 1 N N N N N N -2.046 53.371 75.481 -5.580 -1.794 -0.393 "C7'" AH5 33 AH5 "S7'" S2 S -1 1 N N N N N N -3.429 53.741 76.371 -6.209 -3.082 -1.259 "S7'" AH5 34 AH5 "C6'" C14 C 0 1 N N R N N N -0.806 53.763 76.262 -6.583 -0.846 0.265 "C6'" AH5 35 AH5 C7 C15 C 0 1 N N R N N N 0.392 53.079 75.629 -5.936 -0.054 1.442 C7 AH5 36 AH5 "O9'" O14 O 0 1 N N N N N N 0.392 53.097 74.211 -4.607 0.400 1.126 "O9'" AH5 37 AH5 "N5'" N4 N 0 1 N N N N N N -0.576 55.223 76.163 -7.198 0.041 -0.723 "N5'" AH5 38 AH5 C4A C16 C 0 1 N N N N N N 0.753 55.621 76.518 -7.710 1.286 -0.387 C4A AH5 39 AH5 "N8'" N5 N 0 1 N N N N N N 1.682 53.415 76.076 -6.718 1.122 1.804 "N8'" AH5 40 AH5 C4B C17 C 0 1 N N N N N N 1.808 54.684 76.480 -7.471 1.807 0.901 C4B AH5 41 AH5 "N1'" N6 N 0 1 N N N N N N 3.082 55.037 76.818 -7.930 3.023 1.289 "N1'" AH5 42 AH5 "C2'" C18 C 0 1 N N N N N N 3.408 56.347 77.232 -8.653 3.728 0.415 "C2'" AH5 43 AH5 "N2'" N7 N 0 1 N N N N N N 4.654 56.749 77.569 -9.126 4.918 0.776 "N2'" AH5 44 AH5 "N3'" N8 N 0 1 N N N N N N 2.347 57.316 77.282 -8.936 3.285 -0.847 "N3'" AH5 45 AH5 "C4'" C19 C 0 1 N N N N N N 1.071 56.971 76.961 -8.484 2.060 -1.326 "C4'" AH5 46 AH5 "O4'" O15 O 0 1 N N N N N N 0.179 57.879 77.041 -8.773 1.709 -2.466 "O4'" AH5 47 AH5 H3 H3 H 0 1 N N N N N N 4.608 45.364 70.120 7.892 2.039 -0.172 H3 AH5 48 AH5 H4 H4 H 0 1 N N N N N N 4.582 47.806 70.483 6.327 0.376 -0.170 H4 AH5 49 AH5 H5 H5 H 0 1 N N N N N N 7.643 43.531 69.373 11.284 1.472 -0.748 H5 AH5 50 AH5 H6 H6 H 0 1 N N N N N N 5.931 43.530 69.638 10.266 2.553 -0.449 H6 AH5 51 AH5 H7 H7 H 0 1 N N N N N N 7.619 49.930 70.486 6.860 -2.978 -1.160 H7 AH5 52 AH5 H8 H8 H 0 1 N N N N N N 4.945 49.626 69.018 6.963 -2.500 1.467 H8 AH5 53 AH5 H9 H9 H 0 1 N N N N N N 6.098 51.072 67.589 6.323 -4.590 1.532 H9 AH5 54 AH5 H10 H10 H 0 1 N N N N N N 4.335 51.861 69.628 5.012 -1.403 1.644 H10 AH5 55 AH5 H11 H11 H 0 1 N N N N N N 5.366 51.715 72.202 3.851 -2.964 -0.480 H11 AH5 56 AH5 H12 H12 H 0 1 N N N N N N 5.970 53.228 70.635 3.470 -2.796 2.304 H12 AH5 57 AH5 H13 H13 H 0 1 N N N N N N 3.500 50.034 72.654 2.950 -0.873 -1.234 H13 AH5 58 AH5 H14 H14 H 0 1 N N N N N N 3.025 51.571 71.855 3.477 -0.200 0.126 H14 AH5 59 AH5 H15 H15 H 0 1 N N N N N N 1.047 47.501 71.235 0.905 1.110 2.155 H15 AH5 60 AH5 H16 H16 H 0 1 N N N N N N 1.161 52.595 68.419 -0.193 3.400 0.349 H16 AH5 61 AH5 H17 H17 H 0 1 N N N N N N -1.352 54.014 72.267 -2.580 0.023 -1.309 H17 AH5 62 AH5 H18 H18 H 0 1 N N N N N N -1.758 52.356 71.709 -3.636 1.152 -0.941 H18 AH5 63 AH5 H19 H19 H 0 1 N N N N N N -0.603 51.360 73.563 -2.966 -0.743 1.058 H19 AH5 64 AH5 H26 H26 H 0 1 N N N N N N 5.415 56.101 77.533 -8.962 5.232 1.580 H26 AH5 65 AH5 H27 H27 H 0 1 N N N N N N 4.815 57.694 77.854 -9.603 5.398 0.217 H27 AH5 66 AH5 H20 H20 H 0 1 N N N N N N -0.907 53.456 77.313 -7.301 -1.402 0.663 H20 AH5 67 AH5 H21 H21 H 0 1 N N N N N N 0.264 52.020 75.898 -5.889 -0.642 2.236 H21 AH5 68 AH5 H22 H22 H 0 1 N N N N N N -0.749 55.507 75.220 -7.253 -0.213 -1.553 H22 AH5 69 AH5 H25 H25 H 0 1 N N N N N N 1.914 52.817 76.843 -6.710 1.403 2.643 H25 AH5 70 AH5 H1 H1 H 0 1 N N N N N N 2.550 58.256 77.556 -9.417 3.792 -1.381 H1 AH5 71 # 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 AH5 MO OT1 DOUB N N 1 Y N AH5 MO "S8'" SING N N 2 Y N AH5 MO OT2 DOUB N N 3 Y N AH5 MO "S7'" SING N N 4 Y N AH5 N1 C6 SING N N 5 N N AH5 N1 C2 SING N N 6 N N AH5 N1 "C1'" SING N N 7 N N AH5 C2 N3 SING N N 8 N N AH5 C2 O2 DOUB N N 9 N N AH5 N3 C4 DOUB N N 10 N N AH5 C4 N4 SING N N 11 N N AH5 C4 C5 SING N N 12 N N AH5 C5 C6 DOUB N N 13 N N AH5 "C1'" C2D SING N N 14 N N AH5 "C1'" O4D SING N N 15 N N AH5 C2D "O2'" SING N N 16 N N AH5 C2D "C3'" SING N N 17 N N AH5 "C3'" C4D SING N N 18 N N AH5 "C3'" "O3'" SING N N 19 N N AH5 C4D "C5'" SING N N 20 N N AH5 C4D O4D SING N N 21 N N AH5 "C5'" "O5'" SING N N 22 N N AH5 "O5'" PA SING N N 23 N N AH5 PA O2A DOUB N N 24 N N AH5 PA O1A SING N N 25 N N AH5 PA O3A SING N N 26 N N AH5 O3A PB SING N N 27 N N AH5 PB O2B DOUB N N 28 N N AH5 PB O1B SING N N 29 N N AH5 PB O3B SING N N 30 N N AH5 O3B C10 SING N N 31 N N AH5 C10 "C9'" SING N N 32 N N AH5 "C9'" "C8'" SING N N 33 N N AH5 "C9'" "O9'" SING N N 34 N N AH5 "C8'" "S8'" SING N N 35 N N AH5 "C8'" "C7'" DOUB N N 36 N N AH5 "C7'" "S7'" SING N N 37 N N AH5 "C7'" "C6'" SING N N 38 N N AH5 "C6'" C7 SING N N 39 N N AH5 "C6'" "N5'" SING N N 40 N N AH5 C7 "O9'" SING N N 41 N N AH5 C7 "N8'" SING N N 42 N N AH5 "N5'" C4A SING N N 43 N N AH5 C4A "C4'" SING N N 44 N N AH5 C4A C4B DOUB N N 45 N N AH5 "N8'" C4B SING N N 46 N N AH5 C4B "N1'" SING N N 47 N N AH5 "N1'" "C2'" DOUB N N 48 N N AH5 "C2'" "N3'" SING N N 49 N N AH5 "C2'" "N2'" SING N N 50 N N AH5 "N3'" "C4'" SING N N 51 N N AH5 "C4'" "O4'" DOUB N N 52 N N AH5 C5 H3 SING N N 53 N N AH5 C6 H4 SING N N 54 N N AH5 N4 H5 SING N N 55 N N AH5 N4 H6 SING N N 56 N N AH5 "C1'" H7 SING N N 57 N N AH5 C2D H8 SING N N 58 N N AH5 "O2'" H9 SING N N 59 N N AH5 "C3'" H10 SING N N 60 N N AH5 C4D H11 SING N N 61 N N AH5 "O3'" H12 SING N N 62 N N AH5 "C5'" H13 SING N N 63 N N AH5 "C5'" H14 SING N N 64 N N AH5 O1A H15 SING N N 65 N N AH5 O1B H16 SING N N 66 N N AH5 C10 H17 SING N N 67 N N AH5 C10 H18 SING N N 68 N N AH5 "C9'" H19 SING N N 69 N N AH5 "C6'" H20 SING N N 70 N N AH5 C7 H21 SING N N 71 N N AH5 "N5'" H22 SING N N 72 N N AH5 "N8'" H25 SING N N 73 N N AH5 "N2'" H26 SING N N 74 N N AH5 "N2'" H27 SING N N 75 N N AH5 H1 "N3'" SING N N 76 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 AH5 InChI InChI 1.06 "InChI=1S/C19H26N8O13P2S2.Mo.2O/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);;;/q;+2;;/p-2/t5-,6-,8+,10-,11-,16-,17-;;;/m1.../s1" AH5 InChIKey InChI 1.06 KGCKMLSJAXDKBP-RRNIHQQDSA-L AH5 SMILES_CANONICAL CACTVS 3.385 "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" AH5 SMILES CACTVS 3.385 "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" AH5 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)(=O)S4)O)O" AH5 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)(=O)S4)O)O" # _pdbx_chem_comp_identifier.comp_id AH5 _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~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(1~{R},10~{R},16~{R})-5-azanyl-7,13,13-tris(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]methyl hydrogen phosphate" # _pdbx_chem_comp_atom_coordination.geometry_id 1 _pdbx_chem_comp_atom_coordination.comp_id AH5 _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 1DGJ # _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 AH5 _pdbx_chem_comp_atom_coordination_sphere.atom_id MO _pdbx_chem_comp_atom_coordination_sphere.descriptor "@SQP{Mo,O,O,S,S,O}" _pdbx_chem_comp_atom_coordination_sphere.provenance MetalCoord _pdbx_chem_comp_atom_coordination_sphere.representative_entry_id 1DGJ # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site AH5 "Create component" 2026-04-20 RCSB AH5 "Other modification" 2026-07-31 RCSB AH5 "Initial release" 2026-08-12 RCSB #