data_MGD # _chem_comp.id MGD _chem_comp.name "2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H26 N10 O13 P2 S2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2021-03-01 _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 740.557 _chem_comp.one_letter_code ? _chem_comp.three_letter_code MGD _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1AA6 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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.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 MGD PB PB P 0 1 N N R 76.024 41.615 32.763 -0.098 1.311 -1.069 PB MGD 1 MGD O1B O1B O 0 1 N N N 74.800 41.012 33.335 0.513 2.551 -0.541 O1B MGD 2 MGD O2B O2B O 0 1 N N N 76.113 41.838 31.285 -1.630 1.598 -1.471 O2B MGD 3 MGD O3B O3B O 0 1 N N N 77.408 40.855 33.124 -0.044 0.163 0.058 O3B MGD 4 MGD O3A O3A O 0 1 N N N 77.488 38.506 32.888 -0.861 -0.387 2.495 O3A MGD 5 MGD PA PA P 0 1 N N S 77.853 39.635 34.007 -0.873 0.715 1.323 PA MGD 6 MGD O1A O1A O 0 1 N N N 79.306 39.702 34.233 -0.249 1.964 1.815 O1A MGD 7 MGD O2A O2A O 0 1 N N N 76.931 39.441 35.189 -2.392 1.012 0.881 O2A MGD 8 MGD "O5'" "O5'" O 0 1 N N N 76.425 42.939 33.641 0.715 0.823 -2.370 "O5'" MGD 9 MGD "C5'" "C5'" C 0 1 N N N 76.583 42.816 35.057 0.631 1.879 -3.329 "C5'" MGD 10 MGD "C4'" "C4'" C 0 1 N N R 75.969 43.939 35.880 1.388 1.478 -4.597 "C4'" MGD 11 MGD "O4'" "O4'" O 0 1 N N N 76.726 45.121 35.769 0.787 0.307 -5.175 "O4'" MGD 12 MGD "C3'" "C3'" C 0 1 N N S 74.551 44.309 35.448 1.298 2.607 -5.641 "C3'" MGD 13 MGD "O3'" "O3'" O 0 1 N N N 73.688 43.940 36.542 2.599 3.090 -5.980 "O3'" MGD 14 MGD "C2'" "C2'" C 0 1 N N R 74.599 45.870 35.239 0.633 1.932 -6.869 "C2'" MGD 15 MGD "O2'" "O2'" O 0 1 N N N 73.471 46.524 35.856 1.249 2.364 -8.084 "O2'" MGD 16 MGD "C1'" "C1'" C 0 1 N N R 75.849 46.215 36.034 0.918 0.431 -6.608 "C1'" MGD 17 MGD N9 N9 N 0 1 Y N N 76.474 47.493 35.621 -0.067 -0.411 -7.290 N9 MGD 18 MGD C8 C8 C 0 1 Y N N 76.374 48.134 34.407 -1.291 -0.773 -6.808 C8 MGD 19 MGD N7 N7 N 0 1 Y N N 77.100 49.214 34.337 -1.903 -1.523 -7.676 N7 MGD 20 MGD C5 C5 C 0 1 Y N N 77.708 49.305 35.580 -1.111 -1.688 -8.764 C5 MGD 21 MGD C6 C6 C 0 1 N N N 78.594 50.272 36.102 -1.250 -2.384 -9.987 C6 MGD 22 MGD O6 O6 O 0 1 N N N 78.855 51.303 35.488 -2.263 -3.016 -10.235 O6 MGD 23 MGD N1 N1 N 0 1 N N N 79.026 50.033 37.392 -0.232 -2.333 -10.874 N1 MGD 24 MGD C2 C2 C 0 1 N N N 78.613 48.938 38.114 0.895 -1.623 -10.587 C2 MGD 25 MGD N2 N2 N 0 1 N N N 79.060 48.762 39.332 1.914 -1.589 -11.506 N2 MGD 26 MGD N3 N3 N 0 1 N N N 77.771 48.046 37.623 1.036 -0.972 -9.454 N3 MGD 27 MGD C4 C4 C 0 1 Y N N 77.348 48.267 36.365 0.068 -0.973 -8.530 C4 MGD 28 MGD C10 C10 C 0 1 N N N 78.150 38.282 31.647 -1.608 0.158 3.584 C10 MGD 29 MGD C11 C11 C 0 1 N N R 78.391 36.768 31.609 -1.636 -0.846 4.738 C11 MGD 30 MGD O11 O11 O 0 1 N N N 77.195 36.043 31.778 -0.297 -1.109 5.158 O11 MGD 31 MGD C12 C12 C 0 1 N N N 79.090 36.395 30.337 -2.471 -0.282 5.854 C12 MGD 32 MGD S12 S12 S 0 1 N N N 80.419 37.424 29.793 -3.976 0.546 5.464 S12 MGD 33 MGD C13 C13 C 0 1 N N N 78.726 35.256 29.602 -2.111 -0.390 7.139 C13 MGD 34 MGD S13 S13 S 0 1 N N N 79.582 34.826 28.123 -3.142 0.294 8.393 S13 MGD 35 MGD C14 C14 C 0 1 N N R 77.596 34.379 30.087 -0.823 -1.091 7.493 C14 MGD 36 MGD N15 N15 N 0 1 N N N 76.455 34.681 29.249 0.221 -0.081 7.729 N15 MGD 37 MGD C16 C16 C 0 1 N N N 75.237 34.342 29.774 1.575 -0.474 7.687 C16 MGD 38 MGD C17 C17 C 0 1 N N N 74.101 34.331 28.922 2.579 0.343 8.214 C17 MGD 39 MGD O17 O17 O 0 1 N N N 74.181 34.641 27.714 2.304 1.417 8.728 O17 MGD 40 MGD N18 N18 N 0 1 N N N 72.898 33.999 29.516 3.859 -0.082 8.147 N18 MGD 41 MGD C19 C19 C 0 1 N N N 72.815 33.718 30.854 4.153 -1.277 7.567 C19 MGD 42 MGD N19 N19 N 0 1 N N N 71.653 33.419 31.385 5.461 -1.686 7.503 N19 MGD 43 MGD N20 N20 N 0 1 N N N 73.868 33.744 31.625 3.213 -2.053 7.070 N20 MGD 44 MGD C21 C21 C 0 1 N N N 75.089 34.046 31.136 1.927 -1.688 7.113 C21 MGD 45 MGD N22 N22 N 0 1 N N N 76.155 33.995 31.985 0.940 -2.511 6.595 N22 MGD 46 MGD C23 C23 C 0 1 N N R 77.347 34.672 31.530 -0.384 -1.954 6.304 C23 MGD 47 MGD HOB2 2HOB H 0 0 N N N 76.898 42.225 30.917 -1.990 0.767 -1.809 HOB2 MGD 48 MGD HOA2 2HOA H 0 0 N N N 77.200 38.703 35.723 -2.761 0.175 0.568 HOA2 MGD 49 MGD "H5'1" "1H5'" H 0 0 N N N 76.191 41.830 35.401 -0.413 2.065 -3.574 "H5'1" MGD 50 MGD "H5'2" "2H5'" H 0 0 N N N 77.661 42.699 35.313 1.074 2.784 -2.913 "H5'2" MGD 51 MGD "H4'" "H4'" H 0 1 N N N 75.954 43.542 36.921 2.433 1.278 -4.357 "H4'" MGD 52 MGD "H3'" "H3'" H 0 1 N N N 74.184 43.807 34.522 0.675 3.421 -5.269 "H3'" MGD 53 MGD "HO3'" "'HO3" H 0 0 N N N 72.806 44.170 36.273 2.480 3.749 -6.678 "HO3'" MGD 54 MGD "H2'" "H2'" H 0 1 N N N 74.589 46.177 34.167 -0.439 2.126 -6.889 "H2'" MGD 55 MGD "HO2'" "'HO2" H 0 0 N N N 73.499 47.465 35.730 1.035 3.301 -8.188 "HO2'" MGD 56 MGD "H1'" "H1'" H 0 1 N N N 75.614 46.358 37.114 1.928 0.171 -6.925 "H1'" MGD 57 MGD H8 H8 H 0 1 N N N 75.757 47.806 33.553 -1.692 -0.480 -5.849 H8 MGD 58 MGD HN1 HN1 H 0 1 N N N 79.674 50.689 37.827 -0.303 -2.803 -11.720 HN1 MGD 59 MGD HN21 1HN2 H 0 0 N N N 78.753 47.949 39.867 2.722 -1.089 -11.316 HN21 MGD 60 MGD HN22 2HN2 H 0 0 N N N 78.863 49.602 39.875 1.824 -2.065 -12.347 HN22 MGD 61 MGD H101 1H10 H 0 0 N N N 77.601 38.678 30.760 -2.628 0.364 3.258 H101 MGD 62 MGD H102 2H10 H 0 0 N N N 79.071 38.893 31.505 -1.140 1.083 3.919 H102 MGD 63 MGD H11 H11 H 0 1 N N N 79.048 36.495 32.467 -2.088 -1.774 4.390 H11 MGD 64 MGD H12 H12 H 0 1 N N N 80.862 37.187 28.986 -4.446 0.772 6.704 H12 MGD 65 MGD H13 H13 H 0 1 N N N 79.335 34.055 27.625 -3.329 -0.792 9.162 H13 MGD 66 MGD H14 H14 H 0 1 N N N 77.824 33.290 30.013 -0.960 -1.709 8.381 H14 MGD 67 MGD H15 H15 H 0 1 N N N 76.571 34.252 28.330 -0.017 0.840 7.912 H15 MGD 68 MGD H18 H18 H 0 1 N N N 72.049 33.960 28.952 4.572 0.468 8.508 H18 MGD 69 MGD H191 1H19 H 0 0 N N N 71.591 33.209 32.381 5.684 -2.538 7.095 H191 MGD 70 MGD H192 2H19 H 0 0 N N N 71.249 32.640 30.864 6.164 -1.122 7.862 H192 MGD 71 MGD H22 H22 H 0 1 N N N 76.371 33.025 32.215 1.124 -3.448 6.424 H22 MGD 72 MGD H23 H23 H 0 1 N N N 78.242 34.306 32.084 -1.102 -2.756 6.132 H23 MGD 73 # # 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 MGD PB O1B DOUB N N 1 MGD PB O2B SING N N 2 MGD PB O3B SING N N 3 MGD PB "O5'" SING N N 4 MGD O2B HOB2 SING N N 5 MGD O3B PA SING N N 6 MGD O3A PA SING N N 7 MGD O3A C10 SING N N 8 MGD PA O1A DOUB N N 9 MGD PA O2A SING N N 10 MGD O2A HOA2 SING N N 11 MGD "O5'" "C5'" SING N N 12 MGD "C5'" "C4'" SING N N 13 MGD "C5'" "H5'1" SING N N 14 MGD "C5'" "H5'2" SING N N 15 MGD "C4'" "O4'" SING N N 16 MGD "C4'" "C3'" SING N N 17 MGD "C4'" "H4'" SING N N 18 MGD "O4'" "C1'" SING N N 19 MGD "C3'" "O3'" SING N N 20 MGD "C3'" "C2'" SING N N 21 MGD "C3'" "H3'" SING N N 22 MGD "O3'" "HO3'" SING N N 23 MGD "C2'" "O2'" SING N N 24 MGD "C2'" "C1'" SING N N 25 MGD "C2'" "H2'" SING N N 26 MGD "O2'" "HO2'" SING N N 27 MGD "C1'" N9 SING N N 28 MGD "C1'" "H1'" SING N N 29 MGD N9 C8 SING Y N 30 MGD N9 C4 SING Y N 31 MGD C8 N7 DOUB Y N 32 MGD C8 H8 SING N N 33 MGD N7 C5 SING Y N 34 MGD C5 C6 SING N N 35 MGD C5 C4 DOUB Y N 36 MGD C6 O6 DOUB N N 37 MGD C6 N1 SING N N 38 MGD N1 C2 SING N N 39 MGD N1 HN1 SING N N 40 MGD C2 N2 SING N N 41 MGD C2 N3 DOUB N N 42 MGD N2 HN21 SING N N 43 MGD N2 HN22 SING N N 44 MGD N3 C4 SING N N 45 MGD C10 C11 SING N N 46 MGD C10 H101 SING N N 47 MGD C10 H102 SING N N 48 MGD C11 O11 SING N N 49 MGD C11 C12 SING N N 50 MGD C11 H11 SING N N 51 MGD O11 C23 SING N N 52 MGD C12 S12 SING N N 53 MGD C12 C13 DOUB N N 54 MGD S12 H12 SING N N 55 MGD C13 S13 SING N N 56 MGD C13 C14 SING N N 57 MGD S13 H13 SING N N 58 MGD C14 N15 SING N N 59 MGD C14 C23 SING N N 60 MGD C14 H14 SING N N 61 MGD N15 C16 SING N N 62 MGD N15 H15 SING N N 63 MGD C16 C17 SING N N 64 MGD C16 C21 DOUB N N 65 MGD C17 O17 DOUB N N 66 MGD C17 N18 SING N N 67 MGD N18 C19 SING N N 68 MGD N18 H18 SING N N 69 MGD C19 N19 SING N N 70 MGD C19 N20 DOUB N N 71 MGD N19 H191 SING N N 72 MGD N19 H192 SING N N 73 MGD N20 C21 SING N N 74 MGD C21 N22 SING N N 75 MGD N22 C23 SING N N 76 MGD N22 H22 SING N N 77 MGD C23 H23 SING N N 78 # # 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 MGD SMILES ACDLabs 10.04 "O=C1C=2NC3C(S)=C(S)C(OC3NC=2N=C(N)N1)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c5N=C(N)NC4=O)C(O)C6O" MGD SMILES_CANONICAL CACTVS 3.341 "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)n5cnc6C(=O)NC(=Nc56)N)C(=C3S)S)C(=O)N1" MGD SMILES CACTVS 3.341 "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)n5cnc6C(=O)NC(=Nc56)N)C(=C3S)S)C(=O)N1" MGD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4C(=C([C@H]5[C@@H](O4)NC6=C(N5)C(=O)NC(=N6)N)S)S)O)O)N=C(NC2=O)N" MGD SMILES "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(=C(C5C(O4)NC6=C(N5)C(=O)NC(=N6)N)S)S)O)O)N=C(NC2=O)N" MGD InChI InChI 1.03 "InChI=1S/C20H26N10O13P2S2/c21-19-26-13-7(15(33)28-19)24-6-12(47)11(46)5(41-17(6)25-13)2-40-45(37,38)43-44(35,36)39-1-4-9(31)10(32)18(42-4)30-3-23-8-14(30)27-20(22)29-16(8)34/h3-6,9-10,17-18,24,31-32,46-47H,1-2H2,(H,35,36)(H,37,38)(H3,22,27,29,34)(H4,21,25,26,28,33)/t4-,5-,6+,9-,10-,17-,18-/m1/s1" MGD InChIKey InChI 1.03 VQAGYJCYOLHZDH-ILXWUORBSA-N # # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier MGD "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(R)-{[(S)-{[(5aR,8R,9aR)-2-amino-4-oxo-6,7-disulfanyl-3,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine" MGD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(5aR,8R,9aR)-2-amino-4-oxo-6,7-bis-sulfanyl-3,5,5a,8,9a,10-hexahydropyrano[5,6-g]pteridin-8-yl]methoxy-hydroxy-phosphoryl] [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl hydrogen phosphate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site MGD "Create component" 1999-07-08 RCSB MGD "Modify descriptor" 2011-06-04 RCSB MGD "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id MGD _pdbx_chem_comp_synonyms.name "MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##