data_DYI # _chem_comp.id DYI _chem_comp.name "Molybdopterin hydrox dioxo molybdenum" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H13 Mo N5 O9 P 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 538.282 _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 2E1Q _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 _chem_comp_atom.pdbx_residue_numbering _chem_comp_atom.pdbx_polymer_type _chem_comp_atom.pdbx_component_id DYI N1 N1 N 0 1 N N N N N N 35.544 11.518 155.166 4.985 -1.378 -0.603 N1 DYI 1 1 non-polymer 2 DYI C2 C1 C 0 1 N N N N N N 36.341 11.489 156.328 5.514 -2.109 0.382 C2 DYI 2 1 non-polymer 2 DYI N2 N2 N 0 1 N N N N N N 36.544 10.275 156.889 6.833 -2.113 0.549 N2 DYI 3 1 non-polymer 2 DYI N3 N3 N 0 1 N N N N N N 36.853 12.645 156.816 4.759 -2.867 1.233 N3 DYI 4 1 non-polymer 2 DYI C4 C2 C 0 1 N N N N N N 36.628 13.886 156.217 3.372 -2.927 1.148 C4 DYI 5 1 non-polymer 2 DYI O4 O1 O 0 1 N N N N N N 37.103 15.018 156.662 2.745 -3.629 1.935 O4 DYI 6 1 non-polymer 2 DYI N5 N4 N 0 1 N N N N N N 35.381 15.434 154.216 1.422 -2.109 -0.121 N5 DYI 7 1 non-polymer 2 DYI C6 C3 C 0 1 N N R N N N 34.026 15.244 153.327 0.812 -1.488 -1.298 C6 DYI 8 1 non-polymer 2 DYI C7 C4 C 0 1 N N R N N N 34.093 13.784 152.501 1.702 -0.357 -1.901 C7 DYI 9 1 non-polymer 2 DYI N8 N5 N 0 1 N N N N N N 34.408 12.598 153.272 3.128 -0.623 -1.756 N8 DYI 10 1 non-polymer 2 DYI C9 C5 C 0 1 N N N N N N 35.804 14.005 154.989 2.793 -2.147 0.082 C9 DYI 11 1 non-polymer 2 DYI C10 C6 C 0 1 N N N N N N 35.198 12.607 154.421 3.637 -1.377 -0.743 C10 DYI 12 1 non-polymer 2 DYI "C1'" C7 C 0 1 N N N N N N 33.764 16.341 152.466 -0.606 -1.006 -0.978 "C1'" DYI 13 1 non-polymer 2 DYI "S1'" S1 S -1 1 N N N N N N 32.897 17.552 153.184 -1.750 -2.191 -0.671 "S1'" DYI 14 1 non-polymer 2 DYI "C2'" C8 C 0 1 N N N N N N 34.296 16.251 151.083 -0.952 0.302 -0.977 "C2'" DYI 15 1 non-polymer 2 DYI "S2'" S2 S -1 1 N N N N N N 33.961 17.620 150.058 -2.580 0.692 -0.818 "S2'" DYI 16 1 non-polymer 2 DYI "C3'" C9 C 0 1 N N R N N N 35.113 14.999 150.568 0.086 1.403 -1.130 "C3'" DYI 17 1 non-polymer 2 DYI "O3'" O2 O 0 1 N N N N N N 35.156 13.908 151.521 1.433 0.907 -1.269 "O3'" DYI 18 1 non-polymer 2 DYI "C4'" C10 C 0 1 N N N N N N 36.343 15.623 150.273 0.164 2.362 0.058 "C4'" DYI 19 1 non-polymer 2 DYI "O4'" O3 O 0 1 N N N N N N 37.188 14.668 149.613 0.996 3.488 -0.274 "O4'" DYI 20 1 non-polymer 2 DYI P P1 P 0 1 N N N N N N 37.379 14.579 148.239 1.049 4.778 0.623 P DYI 21 1 non-polymer 2 DYI O2P O5 O 0 1 N N N N N N 36.415 13.644 147.608 1.462 4.479 2.024 O2P DYI 22 1 non-polymer 2 DYI O1P O4 O 0 1 N N N N N N 37.258 16.011 147.632 -0.345 5.434 0.547 O1P DYI 23 1 non-polymer 2 DYI O3P O6 O 0 1 N N N N N N 38.630 14.102 147.970 2.025 5.745 -0.079 O3P DYI 24 1 non-polymer 2 DYI MO1 MO1 MO ? 0 N N N N N N 33.354 19.564 151.861 -3.624 -1.132 0.033 MO1 DYI 25 2 non-polymer 3 DYI OM3 O7 O -1 1 N N N N N N 32.268 20.385 152.920 -4.306 -2.522 0.633 OM3 DYI 26 2 non-polymer 3 DYI OM1 O8 O -2 1 N N N N N N 33.170 20.617 150.142 -4.958 -0.269 0.516 OM1 DYI 27 2 non-polymer 3 DYI OM2 O9 O -2 1 N N N N N N 34.764 20.523 152.062 -2.911 -0.850 1.505 OM2 DYI 28 2 non-polymer 3 DYI H1 H1 H 0 1 N N N N N N 36.137 9.460 156.478 7.347 -1.641 0.016 H1 DYI 29 1 non-polymer 2 DYI H2 H2 H 0 1 N N N N N N 37.101 10.193 157.715 7.201 -2.586 1.192 H2 DYI 30 1 non-polymer 2 DYI H4 H4 H 0 1 N N N N N N 37.417 12.608 157.641 5.161 -3.333 1.862 H4 DYI 31 1 non-polymer 2 DYI H3 H3 H 0 1 N N N N N N 35.223 16.143 154.904 0.913 -2.477 0.482 H3 DYI 32 1 non-polymer 2 DYI H5 H5 H 0 1 N N N N N N 33.197 15.147 154.043 0.735 -2.184 -2.000 H5 DYI 33 1 non-polymer 2 DYI H6 H6 H 0 1 N N N N N N 33.127 13.655 151.992 1.507 -0.278 -2.868 H6 DYI 34 1 non-polymer 2 DYI H7 H7 H 0 1 N N N N N N 33.528 12.213 153.550 3.690 -0.285 -2.349 H7 DYI 35 1 non-polymer 2 DYI H9 H9 H 0 1 N N N N N N 34.638 14.651 149.639 -0.153 1.927 -1.940 H9 DYI 36 1 non-polymer 2 DYI H10 H10 H 0 1 N N N N N N 36.173 16.487 149.614 0.535 1.886 0.833 H10 DYI 37 1 non-polymer 2 DYI H11 H11 H 0 1 N N N N N N 36.821 15.961 151.204 -0.737 2.670 0.291 H11 DYI 38 1 non-polymer 2 DYI H12 H12 H 0 1 N N N N N N 36.582 16.016 146.964 -0.527 5.644 -0.294 H12 DYI 39 1 non-polymer 2 DYI H13 H13 H 0 1 N N N N N N 38.562 13.306 147.456 2.089 6.493 0.393 H13 DYI 40 1 non-polymer 2 DYI H14 H14 H 0 1 N N N N N N 32.713 21.122 153.321 -5.020 -2.713 0.182 H14 DYI 41 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 DYI N1 C10 SING N N 1 N N DYI N1 C2 DOUB N N 2 N N DYI C2 N2 SING N N 3 N N DYI C2 N3 SING N N 4 N N DYI N3 C4 SING N N 5 N N DYI C4 C9 SING N N 6 N N DYI C4 O4 DOUB N N 7 N N DYI N5 C9 SING N N 8 N N DYI N5 C6 SING N N 9 N N DYI C6 C7 SING N N 10 N N DYI C6 "C1'" SING N N 11 N N DYI C7 "O3'" SING N N 12 N N DYI C7 N8 SING N N 13 N N DYI N8 C10 SING N N 14 N N DYI C9 C10 DOUB N N 15 N N DYI "C1'" "C2'" DOUB N N 16 N N DYI "C1'" "S1'" SING N N 17 N N DYI "S1'" MO1 SING N N 18 Y N DYI "C2'" "S2'" SING N N 19 N N DYI "C2'" "C3'" SING N N 20 N N DYI "S2'" MO1 SING N N 21 Y N DYI "C3'" "O3'" SING N N 22 N N DYI "C3'" "C4'" SING N N 23 N N DYI "C4'" "O4'" SING N N 24 N N DYI "O4'" P SING N N 25 N N DYI P O2P DOUB N N 26 N N DYI P O3P SING N N 27 N N DYI P O1P SING N N 28 N N DYI MO1 OM1 DOUB N N 29 Y N DYI MO1 OM2 DOUB N N 30 Y N DYI MO1 OM3 SING N N 31 Y N DYI N2 H1 SING N N 32 N N DYI N2 H2 SING N N 33 N N DYI N5 H3 SING N N 34 N N DYI C6 H5 SING N N 35 N N DYI C7 H6 SING N N 36 N N DYI N8 H7 SING N N 37 N N DYI "C3'" H9 SING N N 38 N N DYI "C4'" H10 SING N N 39 N N DYI "C4'" H11 SING N N 40 N N DYI O1P H12 SING N N 41 N N DYI O3P H13 SING N N 42 N N DYI OM3 H14 SING N N 43 N N DYI H4 N3 SING N N 44 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 DYI InChI InChI 1.06 "InChI=1S/C10H14N5O6PS2.Mo.H2O.2O/c11-10-14-7-4(8(16)15-10)12-3-6(24)5(23)2(21-9(3)13-7)1-20-22(17,18)19;;;;/h2-3,9,12,23-24H,1H2,(H2,17,18,19)(H4,11,13,14,15,16);;1H2;;/q;+3;;;/p-3/t2-,3+,9-;;;;/m1..../s1" DYI InChIKey InChI 1.06 KAYXRMRYSHVOTG-BKZHXLINSA-K DYI SMILES_CANONICAL CACTVS 3.385 "NC1=NC2=C(N[C@@H]3[C@H](N2)O[C@H](CO[P](O)(O)=O)C4=C3S[Mo](O)(=O)(=O)S4)C(=O)N1" DYI SMILES CACTVS 3.385 "NC1=NC2=C(N[CH]3[CH](N2)O[CH](CO[P](O)(O)=O)C4=C3S[Mo](O)(=O)(=O)S4)C(=O)N1" DYI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C([C@@H]1C2=C([C@H]3[C@@H](O1)NC4=C(N3)C(=O)NC(=N4)N)S[Mo](=O)(=O)(S2)O)OP(=O)(O)O" DYI SMILES "OpenEye OEToolkits" 2.0.7 "C(C1C2=C(C3C(O1)NC4=C(N3)C(=O)NC(=N4)N)S[Mo](=O)(=O)(S2)O)OP(=O)(O)O" # _pdbx_chem_comp_identifier.comp_id DYI _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-oxidanyl-7,13,13-tris(oxidanylidene)-17-oxa-12,14-dithia-2,4,6,9-tetraza-13$l^{7}-molybdatetracyclo[8.7.0.0^{3,8}.0^{11,15}]heptadeca-3(8),4,11(15)-trien-16-yl]methyl dihydrogen phosphate" # _pdbx_chem_comp_atom_coordination.geometry_id 1 _pdbx_chem_comp_atom_coordination.comp_id DYI _pdbx_chem_comp_atom_coordination.atom_id MO1 _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 2E1Q # _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 DYI _pdbx_chem_comp_atom_coordination_sphere.atom_id MO1 _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 2E1Q # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site DYI "Create component" 2026-04-20 RCSB DYI "Other modification" 2026-07-31 RCSB DYI "Initial release" 2026-08-12 RCSB #