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 
# 
