data_EAK # _chem_comp.id EAK _chem_comp.name "Molybdopterin oxo thio molybdenum" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H13 Mo N5 O7 P S3" _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 538.348 _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 3BDJ _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 EAK N1 N1 N 0 1 N N N N N N 102.228 42.727 123.967 -3.143 -1.354 0.608 N1 EAK 1 1 non-polymer 2 EAK C2 C1 C 0 1 N N N N N N 103.479 42.102 123.969 -3.968 -0.902 1.556 C2 EAK 2 1 non-polymer 2 EAK N2 N2 N 0 1 N N N N N N 103.961 41.653 125.129 -4.729 -1.768 2.220 N2 EAK 3 1 non-polymer 2 EAK N3 N3 N 0 1 N N N N N N 104.108 42.005 122.783 -4.077 0.422 1.877 N3 EAK 4 1 non-polymer 2 EAK C4 C2 C 0 1 N N N N N N 103.563 42.487 121.602 -3.324 1.407 1.248 C4 EAK 5 1 non-polymer 2 EAK O4 O1 O 0 1 N N N N N N 104.176 42.388 120.406 -3.467 2.581 1.573 O4 EAK 6 1 non-polymer 2 EAK N5 N4 N 0 1 N N N N N N 101.596 43.648 120.377 -1.622 1.799 -0.492 N5 EAK 7 1 non-polymer 2 EAK C6 C3 C 0 1 N N R N N N 100.581 44.700 120.580 -0.844 1.389 -1.663 C6 EAK 8 1 non-polymer 2 EAK C7 C4 C 0 1 N N R N N N 99.575 44.330 121.702 -0.517 -0.137 -1.661 C7 EAK 9 1 non-polymer 2 EAK N8 N5 N 0 1 N N N N N N 100.296 43.897 122.903 -1.537 -0.946 -1.006 N8 EAK 10 1 non-polymer 2 EAK C9 C5 C 0 1 N N N N N N 102.308 43.116 121.575 -2.435 0.929 0.217 C9 EAK 11 1 non-polymer 2 EAK C10 C6 C 0 1 N N N N N N 101.603 43.240 122.866 -2.367 -0.454 -0.045 C10 EAK 12 1 non-polymer 2 EAK "C1'" C7 C 0 1 N N N N N N 99.789 44.987 119.335 0.411 2.262 -1.800 "C1'" EAK 13 1 non-polymer 2 EAK "S1'" S1 S -1 1 N N N N N N 100.462 46.158 118.112 0.174 3.897 -2.083 "S1'" EAK 14 1 non-polymer 2 EAK "C2'" C8 C 0 1 N N N N N N 98.583 44.400 119.097 1.667 1.761 -1.735 "C2'" EAK 15 1 non-polymer 2 EAK "S2'" S2 S -1 1 N N N N N N 97.609 44.797 117.578 2.938 2.812 -2.070 "S2'" EAK 16 1 non-polymer 2 EAK "C3'" C9 C 0 1 N N R N N N 97.950 43.406 119.990 1.930 0.303 -1.391 "C3'" EAK 17 1 non-polymer 2 EAK "O3'" O2 O 0 1 N N N N N N 98.821 43.155 121.191 0.731 -0.391 -0.990 "O3'" EAK 18 1 non-polymer 2 EAK "C4'" C10 C 0 1 N N N N N N 97.811 42.122 119.209 2.917 0.086 -0.241 "C4'" EAK 19 1 non-polymer 2 EAK "O4'" O3 O 0 1 N N N N N N 97.403 40.996 119.946 3.119 -1.319 -0.006 "O4'" EAK 20 1 non-polymer 2 EAK P P1 P 0 1 N N N N N N 95.896 40.712 120.421 4.106 -1.844 1.099 P EAK 21 1 non-polymer 2 EAK O1P O4 O 0 1 N N N N N N 94.979 40.927 119.242 3.767 -1.331 2.457 O1P EAK 22 1 non-polymer 2 EAK O2P O5 O 0 1 N N N N N N 95.563 41.612 121.573 5.528 -1.441 0.656 O2P EAK 23 1 non-polymer 2 EAK O3P O6 O 0 1 N N N N N N 95.768 39.296 120.926 4.046 -3.384 1.026 O3P EAK 24 1 non-polymer 2 EAK MO1 MO1 MO ? 0 N N N N N N 99.143 45.894 116.126 2.170 4.927 -1.701 MO1 EAK 25 2 non-polymer 3 EAK S1 S3 S -1 1 N N N N N N 99.926 48.034 115.398 1.206 7.062 -1.342 S1 EAK 26 2 non-polymer 3 EAK O1 O7 O -2 1 N N N N N N 99.786 44.697 115.145 2.035 4.595 -0.080 O1 EAK 27 2 non-polymer 3 EAK H1 H1 H 0 1 N N N N N N 103.430 41.767 125.969 -4.686 -2.626 2.034 H1 EAK 28 1 non-polymer 2 EAK H2 H2 H 0 1 N N N N N N 104.853 41.202 125.159 -5.277 -1.492 2.847 H2 EAK 29 1 non-polymer 2 EAK H4 H4 H 0 1 N N N N N N 105.006 41.567 122.752 -4.641 0.664 2.508 H4 EAK 30 1 non-polymer 2 EAK H3 H3 H 0 1 N N N N N N 102.290 44.020 119.761 -1.584 2.625 -0.220 H3 EAK 31 1 non-polymer 2 EAK H5 H5 H 0 1 N N N N N N 101.092 45.626 120.883 -1.401 1.551 -2.466 H5 EAK 32 1 non-polymer 2 EAK H6 H6 H 0 1 N N N N N N 98.905 45.177 121.912 -0.444 -0.448 -2.598 H6 EAK 33 1 non-polymer 2 EAK H7 H7 H 0 1 N N N N N N 100.419 44.719 123.460 -1.627 -1.794 -1.240 H7 EAK 34 1 non-polymer 2 EAK H9 H9 H 0 1 N N N N N N 96.959 43.758 120.312 2.300 -0.131 -2.205 H9 EAK 35 1 non-polymer 2 EAK H10 H10 H 0 1 N N N N N N 97.071 42.290 118.413 2.566 0.516 0.569 H10 EAK 36 1 non-polymer 2 EAK H11 H11 H 0 1 N N N N N N 98.788 41.894 118.759 3.773 0.510 -0.463 H11 EAK 37 1 non-polymer 2 EAK H12 H12 H 0 1 N N N N N N 94.823 42.161 121.343 5.709 -1.813 -0.128 H12 EAK 38 1 non-polymer 2 EAK H13 H13 H 0 1 N N N N N N 95.134 38.827 120.397 4.590 -3.730 1.634 H13 EAK 39 1 non-polymer 2 EAK H14 H14 H 0 1 N N N N N N 99.326 48.166 114.252 0.014 6.934 -1.092 H14 EAK 40 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 EAK N1 C10 SING N N 1 N N EAK N1 C2 DOUB N N 2 N N EAK C2 N2 SING N N 3 N N EAK C2 N3 SING N N 4 N N EAK N3 C4 SING N N 5 N N EAK C4 C9 SING N N 6 N N EAK C4 O4 DOUB N N 7 N N EAK N5 C9 SING N N 8 N N EAK N5 C6 SING N N 9 N N EAK C6 "C1'" SING N N 10 N N EAK C6 C7 SING N N 11 N N EAK C7 "O3'" SING N N 12 N N EAK C7 N8 SING N N 13 N N EAK N8 C10 SING N N 14 N N EAK C9 C10 DOUB N N 15 N N EAK "C1'" "C2'" DOUB N N 16 N N EAK "C1'" "S1'" SING N N 17 N N EAK "S1'" MO1 SING N N 18 Y N EAK "C2'" "S2'" SING N N 19 N N EAK "C2'" "C3'" SING N N 20 N N EAK "S2'" MO1 SING N N 21 Y N EAK "C3'" "C4'" SING N N 22 N N EAK "C3'" "O3'" SING N N 23 N N EAK "C4'" "O4'" SING N N 24 N N EAK "O4'" P SING N N 25 N N EAK P O1P DOUB N N 26 N N EAK P O3P SING N N 27 N N EAK P O2P SING N N 28 N N EAK MO1 O1 DOUB N N 29 Y N EAK MO1 S1 SING N N 30 Y N EAK N2 H1 SING N N 31 N N EAK N2 H2 SING N N 32 N N EAK N5 H3 SING N N 33 N N EAK C6 H5 SING N N 34 N N EAK C7 H6 SING N N 35 N N EAK N8 H7 SING N N 36 N N EAK "C3'" H9 SING N N 37 N N EAK "C4'" H10 SING N N 38 N N EAK "C4'" H11 SING N N 39 N N EAK O2P H12 SING N N 40 N N EAK O3P H13 SING N N 41 N N EAK S1 H14 SING N N 42 N N EAK H4 N3 SING N N 43 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 EAK InChI InChI 1.06 "InChI=1S/C10H14N5O6PS2.Mo.O.H2S/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" EAK InChIKey InChI 1.06 XGOBUXBIBAURDT-JSUDGWJLSA-K EAK 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](S)(=O)S4)C(=O)N1" EAK SMILES CACTVS 3.385 "NC1=NC2=C(N[CH]3[CH](N2)O[CH](CO[P](O)(O)=O)C4=C3S[Mo](S)(=O)S4)C(=O)N1" EAK 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)(S2)S)OP(=O)(O)O" EAK SMILES "OpenEye OEToolkits" 2.0.7 "C(C1C2=C(C3C(O1)NC4=C(N3)C(=O)NC(=N4)N)S[Mo](=O)(S2)S)OP(=O)(O)O" # _pdbx_chem_comp_identifier.comp_id EAK _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-7,13-bis(oxidanylidene)-13-sulfanyl-17-oxa-12,14-dithia-2,4,6,9-tetraza-13$l^{5}-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 EAK _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 3BDJ # _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 EAK _pdbx_chem_comp_atom_coordination_sphere.atom_id MO1 _pdbx_chem_comp_atom_coordination_sphere.descriptor "@SQP{Mo,N,S,S,S,O}" _pdbx_chem_comp_atom_coordination_sphere.provenance MetalCoord _pdbx_chem_comp_atom_coordination_sphere.representative_entry_id 3BDJ # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site EAK "Create component" 2026-04-20 RCSB EAK "Other modification" 2026-07-31 RCSB EAK "Initial release" 2026-08-12 RCSB #