data_PGD # _chem_comp.id PGD _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 H24 N10 O13 P2 S2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2011-06-04 _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 738.541 _chem_comp.one_letter_code ? _chem_comp.three_letter_code PGD _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 1DMR _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 PGD PB PB P 0 1 N N R -8.957 54.093 36.016 -0.456 1.330 -1.010 PB PGD 1 PGD O1B O1B O 0 1 N N N -8.073 55.403 35.365 0.050 2.620 -0.490 O1B PGD 2 PGD O2B O2B O 0 1 N N N -8.063 53.046 37.008 -2.026 1.464 -1.340 O2B PGD 3 PGD O3B O3B O 0 1 N N N -9.468 53.295 34.704 -0.237 0.182 0.096 O3B PGD 4 PGD O3A O3A O 0 1 N N N -9.752 51.577 32.761 -0.884 -0.474 2.559 O3A PGD 5 PGD PA PA P 0 1 N N R -10.298 51.940 34.376 -1.060 0.634 1.404 PA PGD 6 PGD O1A O1A O 0 1 N N N -11.958 52.291 34.333 -2.494 0.768 1.063 O1A PGD 7 PGD O2A O2A O 0 1 N N N -9.822 50.766 35.488 -0.498 2.049 1.929 O2A PGD 8 PGD "O5'" "O5'" O 0 1 N N N -10.392 54.582 36.829 0.343 0.941 -2.352 "O5'" PGD 9 PGD "C5'" "C5'" C 0 1 N N N -11.308 55.291 36.066 0.110 1.992 -3.291 "C5'" PGD 10 PGD "C4'" "C4'" C 0 1 N N R -11.900 56.330 37.036 0.846 1.683 -4.596 "C4'" PGD 11 PGD "O4'" "O4'" O 0 1 N N N -12.313 55.668 38.216 0.350 0.456 -5.174 "O4'" PGD 12 PGD "C3'" "C3'" C 0 1 N N S -10.869 57.377 37.430 0.548 2.767 -5.655 "C3'" PGD 13 PGD "O3'" "O3'" O 0 1 N N N -11.244 58.617 36.888 1.607 3.725 -5.704 "O3'" PGD 14 PGD "C2'" "C2'" C 0 1 N N R -10.877 57.353 38.941 0.465 1.982 -6.985 "C2'" PGD 15 PGD "O2'" "O2'" O 0 1 N N N -10.841 58.638 39.524 1.469 2.432 -7.896 "O2'" PGD 16 PGD "C1'" "C1'" C 0 1 N N R -12.222 56.696 39.215 0.720 0.516 -6.569 "C1'" PGD 17 PGD N9 N9 N 0 1 Y N N -12.288 56.058 40.524 -0.117 -0.390 -7.358 N9 PGD 18 PGD C8 C8 C 0 1 Y N N -11.270 55.580 41.294 -1.384 -0.791 -7.051 C8 PGD 19 PGD N7 N7 N 0 1 Y N N -11.702 55.023 42.456 -1.827 -1.597 -7.971 N7 PGD 20 PGD C5 C5 C 0 1 Y N N -13.039 55.161 42.400 -0.874 -1.761 -8.920 C5 PGD 21 PGD C6 C6 C 0 1 N N N -14.031 54.780 43.294 -0.798 -2.504 -10.122 C6 PGD 22 PGD O6 O6 O 0 1 N N N -13.866 54.215 44.367 -1.736 -3.189 -10.493 O6 PGD 23 PGD N1 N1 N 0 1 N N N -15.320 55.052 42.939 0.337 -2.432 -10.850 N1 PGD 24 PGD C2 C2 C 0 1 N N N -15.642 55.701 41.765 1.381 -1.667 -10.423 C2 PGD 25 PGD N2 N2 N 0 1 N N N -17.002 55.946 41.493 2.524 -1.617 -11.180 N2 PGD 26 PGD N3 N3 N 0 1 N N N -14.668 56.070 40.874 1.323 -0.973 -9.308 N3 PGD 27 PGD C4 C4 C 0 1 Y N N -13.385 55.779 41.239 0.229 -0.991 -8.538 C4 PGD 28 PGD C10 C10 C 0 1 N N N -8.455 51.091 32.836 -1.633 -0.018 3.687 C10 PGD 29 PGD C11 C11 C 0 1 N N R -8.085 50.766 31.365 -1.508 -1.032 4.826 C11 PGD 30 PGD O11 O11 O 0 1 N N N -7.613 51.970 30.813 -0.134 -1.176 5.177 O11 PGD 31 PGD C12 C12 C 0 1 N N N -7.050 49.667 31.356 -2.309 -0.554 6.003 C12 PGD 32 PGD S12 S12 S 0 1 N N N -7.335 48.042 32.119 -3.858 0.233 5.713 S12 PGD 33 PGD C13 C13 C 0 1 N N N -5.947 49.751 30.583 -1.887 -0.698 7.250 C13 PGD 34 PGD S13 S13 S 0 1 N N N -4.768 48.408 30.612 -2.878 -0.111 8.583 S13 PGD 35 PGD C14 C14 C 0 1 N N R -5.619 50.990 29.814 -0.567 -1.365 7.541 C14 PGD 36 PGD N15 N15 N 0 1 N N N -4.658 51.830 30.542 0.399 -0.357 7.986 N15 PGD 37 PGD C16 C16 C 0 1 N N N -4.533 53.195 30.109 1.658 -0.455 7.746 C16 PGD 38 PGD C17 C17 C 0 1 N N N -3.440 54.007 30.432 2.647 0.552 8.222 C17 PGD 39 PGD O17 O17 O 0 1 N N N -2.525 53.603 31.135 2.303 1.531 8.860 O17 PGD 40 PGD N18 N18 N 0 1 N N N -3.392 55.289 29.972 3.933 0.332 7.916 N18 PGD 41 PGD C19 C19 C 0 1 N N N -4.382 55.799 29.199 4.315 -0.723 7.222 C19 PGD 42 PGD N19 N19 N 0 1 N N N -4.335 57.136 28.730 5.655 -0.867 6.967 N19 PGD 43 PGD N20 N20 N 0 1 N N N -5.446 55.027 28.866 3.490 -1.661 6.750 N20 PGD 44 PGD C21 C21 C 0 1 N N N -5.533 53.745 29.318 2.196 -1.596 6.957 C21 PGD 45 PGD N22 N22 N 0 1 N N N -6.684 52.986 28.925 1.314 -2.523 6.478 N22 PGD 46 PGD C23 C23 C 0 1 N N R -6.971 51.727 29.595 -0.075 -2.078 6.282 C23 PGD 47 PGD HOB2 2HOB H 0 0 N N N -8.554 52.317 37.369 -2.316 0.605 -1.675 HOB2 PGD 48 PGD HOA2 2HOA H 0 0 N N N -10.308 49.972 35.296 0.436 1.917 2.140 HOA2 PGD 49 PGD "H5'1" "1H5'" H 0 0 N N N -10.880 55.730 35.135 0.477 2.933 -2.881 "H5'1" PGD 50 PGD "H5'2" "2H5'" H 0 0 N N N -12.071 54.652 35.563 -0.958 2.074 -3.488 "H5'2" PGD 51 PGD "H4'" "H4'" H 0 1 N N N -12.752 56.833 36.523 1.919 1.612 -4.418 "H4'" PGD 52 PGD "H3'" "H3'" H 0 1 N N N -9.840 57.183 37.045 -0.400 3.259 -5.441 "H3'" PGD 53 PGD "HO3'" "'HO3" H 0 0 N N N -10.600 59.270 37.134 1.366 4.374 -6.379 "HO3'" PGD 54 PGD "H2'" "H2'" H 0 1 N N N -9.985 56.836 39.366 -0.525 2.085 -7.428 "H2'" PGD 55 PGD "HO2'" "'HO2" H 0 0 N N N -10.846 58.622 40.473 1.290 3.367 -8.069 "HO2'" PGD 56 PGD "H1'" "H1'" H 0 1 N N N -13.037 57.455 39.191 1.773 0.264 -6.694 "H1'" PGD 57 PGD H8 H8 H 0 1 N N N -10.206 55.637 41.006 -1.937 -0.485 -6.175 H8 PGD 58 PGD HN1 HN1 H 0 1 N N N -16.066 54.761 43.570 0.412 -2.932 -11.678 HN1 PGD 59 PGD HN21 1HN2 H 0 0 N N N -17.240 56.425 40.625 3.274 -1.075 -10.891 HN21 PGD 60 PGD HN22 2HN2 H 0 0 N N N -17.413 56.452 42.277 2.584 -2.128 -12.003 HN22 PGD 61 PGD H101 1H10 H 0 0 N N N -7.738 51.776 33.346 -1.245 0.946 4.015 H101 PGD 62 PGD H102 2H10 H 0 0 N N N -8.327 50.235 33.539 -2.682 0.087 3.408 H102 PGD 63 PGD H11 H11 H 0 1 N N N -8.945 50.394 30.760 -1.896 -1.994 4.494 H11 PGD 64 PGD H12 H12 H 0 1 N N N -6.683 47.350 32.113 -4.685 -0.816 5.859 H12 PGD 65 PGD H13 H13 H 0 1 N N N -3.991 48.467 30.067 -3.861 0.495 7.895 H13 PGD 66 PGD H14 H14 H 0 1 N N N -5.132 50.747 28.840 -0.704 -2.104 8.329 H14 PGD 67 PGD H191 1H19 H 0 0 N N N -5.079 57.519 28.148 6.284 -0.205 7.293 H191 PGD 68 PGD H192 2H19 H 0 0 N N N -3.451 57.266 28.237 5.973 -1.630 6.460 H192 PGD 69 PGD H22 H22 H 0 1 N N N -6.636 52.817 27.920 1.590 -3.430 6.277 H22 PGD 70 PGD H23 H23 H 0 1 N N N -7.650 51.094 28.977 -0.709 -2.942 6.081 H23 PGD 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 PGD PB O1B DOUB N N 1 PGD PB O2B SING N N 2 PGD PB O3B SING N N 3 PGD PB "O5'" SING N N 4 PGD O2B HOB2 SING N N 5 PGD O3B PA SING N N 6 PGD O3A PA SING N N 7 PGD O3A C10 SING N N 8 PGD PA O1A DOUB N N 9 PGD PA O2A SING N N 10 PGD O2A HOA2 SING N N 11 PGD "O5'" "C5'" SING N N 12 PGD "C5'" "C4'" SING N N 13 PGD "C5'" "H5'1" SING N N 14 PGD "C5'" "H5'2" SING N N 15 PGD "C4'" "O4'" SING N N 16 PGD "C4'" "C3'" SING N N 17 PGD "C4'" "H4'" SING N N 18 PGD "O4'" "C1'" SING N N 19 PGD "C3'" "O3'" SING N N 20 PGD "C3'" "C2'" SING N N 21 PGD "C3'" "H3'" SING N N 22 PGD "O3'" "HO3'" SING N N 23 PGD "C2'" "O2'" SING N N 24 PGD "C2'" "C1'" SING N N 25 PGD "C2'" "H2'" SING N N 26 PGD "O2'" "HO2'" SING N N 27 PGD "C1'" N9 SING N N 28 PGD "C1'" "H1'" SING N N 29 PGD N9 C8 SING Y N 30 PGD N9 C4 SING Y N 31 PGD C8 N7 DOUB Y N 32 PGD C8 H8 SING N N 33 PGD N7 C5 SING Y N 34 PGD C5 C6 SING N N 35 PGD C5 C4 DOUB Y N 36 PGD C6 O6 DOUB N N 37 PGD C6 N1 SING N N 38 PGD N1 C2 SING N N 39 PGD N1 HN1 SING N N 40 PGD C2 N2 SING N N 41 PGD C2 N3 DOUB N N 42 PGD N2 HN21 SING N N 43 PGD N2 HN22 SING N N 44 PGD N3 C4 SING N N 45 PGD C10 C11 SING N N 46 PGD C10 H101 SING N N 47 PGD C10 H102 SING N N 48 PGD C11 O11 SING N N 49 PGD C11 C12 SING N N 50 PGD C11 H11 SING N N 51 PGD O11 C23 SING N N 52 PGD C12 S12 SING N N 53 PGD C12 C13 DOUB N N 54 PGD S12 H12 SING N N 55 PGD C13 S13 SING N N 56 PGD C13 C14 SING N N 57 PGD S13 H13 SING N N 58 PGD C14 N15 SING N N 59 PGD C14 C23 SING N N 60 PGD C14 H14 SING N N 61 PGD N15 C16 DOUB N N 62 PGD C16 C17 SING N N 63 PGD C16 C21 SING N N 64 PGD C17 O17 DOUB N N 65 PGD C17 N18 SING N N 66 PGD N18 C19 DOUB N N 67 PGD C19 N19 SING N N 68 PGD C19 N20 SING N N 69 PGD N19 H191 SING N N 70 PGD N19 H192 SING N N 71 PGD N20 C21 DOUB N N 72 PGD C21 N22 SING N N 73 PGD N22 C23 SING N N 74 PGD N22 H22 SING N N 75 PGD C23 H23 SING N N 76 # 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 PGD SMILES ACDLabs 10.04 "O=C6N=C(N=C1C6=NC2C(S)=C(S)C(OC2N1)COP(=O)(O)OP(=O)(O)OCC5OC(n4cnc3c4N=C(N)NC3=O)C(O)C5O)N" PGD SMILES_CANONICAL CACTVS 3.341 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]5NC6=NC(=NC(=O)C6=N[C@H]5C(=C4S)S)N)[C@@H](O)[C@H]3O" PGD SMILES CACTVS 3.341 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]5NC6=NC(=NC(=O)C6=N[CH]5C(=C4S)S)N)[CH](O)[CH]3O" PGD 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=NC(=NC(=O)C6=N5)N)S)S)O)O)N=C(NC2=O)N" PGD SMILES "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(=C(C5C(O4)NC6=NC(=NC(=O)C6=N5)N)S)S)O)O)N=C(NC2=O)N" PGD InChI InChI 1.03 ;InChI=1S/C20H24N10O13P2S2/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/h3-6,9-10,17-18,31-32,46-47H,1-2H2,(H,35,36)(H,37,38)(H3,22,27,29,34)(H3,21,25,26,28,33)/t4-,5-,6+,9-,10-,17-,18-/m1/s1 ; PGD InChIKey InChI 1.03 SOFMTHSWCZNJTQ-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 PGD "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(R)-{[(R)-{[(5aR,8R,9aR)-2-amino-4-oxo-6,7-disulfanyl-5a,8,9a,10-tetrahydro-4H-pyrano[3,2-g]pteridin-8-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine" PGD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(5aR,8R,9aR)-2-amino-4-oxo-6,7-bis-sulfanyl-5a,8,9a,10-tetrahydropyrano[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 PGD "Create component" 1999-07-08 RCSB PGD "Modify descriptor" 2011-06-04 RCSB #