data_PCD
#

_chem_comp.id                                   PCD
_chem_comp.name                                 "(MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C19 H26 Mo N8 O16 P2 S2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "MOLYBDENUM COFACTOR; MOCO"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    1999-07-08
_chem_comp.pdbx_modified_date                   2020-06-17
_chem_comp.pdbx_ambiguous_flag                  Y
_chem_comp.pdbx_release_status                  REL
_chem_comp.pdbx_replaced_by                     ?
_chem_comp.pdbx_replaces                        ?
_chem_comp.formula_weight                       844.471
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    PCD
_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  Y
_chem_comp.pdbx_model_coordinates_db_code       ?
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 EBI
#   #
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
PCD  N1      N1      N   0  1  Y  N  N  55.344  123.432   96.085  ?  ?  ?  N1      PCD   1  
PCD  C2      C2      C   0  1  Y  N  N  56.485  122.822   96.521  ?  ?  ?  C2      PCD   2  
PCD  N3      N3      N   0  1  Y  N  N  56.611  122.574   97.843  ?  ?  ?  N3      PCD   3  
PCD  C4      C4      C   0  1  Y  N  N  55.698  122.881   98.781  ?  ?  ?  C4      PCD   4  
PCD  C5      C5      C   0  1  Y  N  N  54.482  123.555   98.236  ?  ?  ?  C5      PCD   5  
PCD  C6      C6      C   0  1  Y  N  N  54.344  123.806   96.900  ?  ?  ?  C6      PCD   6  
PCD  O2      O2      O   0  1  N  N  N  57.440  122.456   95.818  ?  ?  ?  O2      PCD   7  
PCD  N4      N4      N   0  1  N  N  N  55.857  122.620  100.052  ?  ?  ?  N4      PCD   8  
PCD  "C1'"   C1*     C   0  1  N  N  R  55.198  123.671   94.661  ?  ?  ?  "C1'"   PCD   9  
PCD  C2D     C2*     C   0  1  N  N  R  54.250  122.857   93.765  ?  ?  ?  C2D     PCD  10  
PCD  "O2'"   O2*     O   0  1  N  N  N  54.398  121.445   93.823  ?  ?  ?  "O2'"   PCD  11  
PCD  "C3'"   C3*     C   0  1  N  N  S  53.220  123.476   92.782  ?  ?  ?  "C3'"   PCD  12  
PCD  C4D     C4*     C   0  1  N  N  R  53.603  124.916   93.293  ?  ?  ?  C4D     PCD  13  
PCD  O4D     O4*     O   0  1  N  N  N  54.731  124.925   94.181  ?  ?  ?  O4D     PCD  14  
PCD  "O3'"   O3*     O   0  1  N  N  N  54.057  123.138   91.713  ?  ?  ?  "O3'"   PCD  15  
PCD  "C5'"   C5*     C   0  1  N  N  N  52.374  125.704   93.848  ?  ?  ?  "C5'"   PCD  16  
PCD  "O5'"   O5*     O   0  1  N  N  N  52.075  124.765   94.903  ?  ?  ?  "O5'"   PCD  17  
PCD  PA      PA      P   0  1  N  N  R  50.718  125.131   95.669  ?  ?  ?  PA      PCD  18  
PCD  O1A     O1A     O   0  1  N  N  N  50.102  123.837   96.368  ?  ?  ?  O1A     PCD  19  
PCD  O2A     O2A     O   0  1  N  N  N  51.111  126.028   96.862  ?  ?  ?  O2A     PCD  20  
PCD  O3A     O3A     O   0  1  N  N  N  49.586  125.904   94.737  ?  ?  ?  O3A     PCD  21  
PCD  PB      PB      P   0  1  N  N  R  48.613  125.467   93.554  ?  ?  ?  PB      PCD  22  
PCD  O1B     O1B     O   0  1  N  N  N  47.305  125.129   94.336  ?  ?  ?  O1B     PCD  23  
PCD  O2B     O2B     O   0  1  N  N  N  49.660  124.674   92.711  ?  ?  ?  O2B     PCD  24  
PCD  O3B     O3B     O   0  1  N  N  N  48.598  126.881   92.904  ?  ?  ?  O3B     PCD  25  
PCD  C10     C10     C   0  1  N  N  N  47.595  127.831   93.163  ?  ?  ?  C10     PCD  26  
PCD  "C9'"   "C9'"   C   0  1  N  N  R  48.122  129.171   93.559  ?  ?  ?  "C9'"   PCD  27  
PCD  "C8'"   "C8'"   C   0  1  N  N  N  47.045  130.267   93.605  ?  ?  ?  "C8'"   PCD  28  
PCD  "S8'"   "S8'"   S   0  1  N  N  N  45.621  130.015   94.657  ?  ?  ?  "S8'"   PCD  29  
PCD  "C7'"   "C7'"   C   0  1  N  N  N  47.172  131.418   92.892  ?  ?  ?  "C7'"   PCD  30  
PCD  "S7'"   "S7'"   S   0  1  N  N  N  45.772  132.509   92.878  ?  ?  ?  "S7'"   PCD  31  
PCD  "C6'"   "C6'"   C   0  1  N  N  R  48.474  131.677   92.152  ?  ?  ?  "C6'"   PCD  32  
PCD  C7      C7      C   0  1  N  N  R  49.624  130.792   92.658  ?  ?  ?  C7      PCD  33  
PCD  "O9'"   "O9'"   O   0  1  N  N  N  49.122  129.457   92.585  ?  ?  ?  "O9'"   PCD  34  
PCD  "N5'"   "N5'"   N   0  1  N  N  N  48.005  131.486   90.754  ?  ?  ?  "N5'"   PCD  35  
PCD  C4A     C4A     C   0  1  Y  N  N  49.163  131.297   89.973  ?  ?  ?  C4A     PCD  36  
PCD  "N8'"   "N8'"   N   0  1  N  N  N  50.560  131.086   91.594  ?  ?  ?  "N8'"   PCD  37  
PCD  C4B     C4B     C   0  1  Y  N  N  50.551  131.084   90.178  ?  ?  ?  C4B     PCD  38  
PCD  "N1'"   "N1'"   N   0  1  Y  N  N  51.554  130.922   89.305  ?  ?  ?  "N1'"   PCD  39  
PCD  "C2'"   "C2'"   C   0  1  Y  N  N  51.205  130.963   87.973  ?  ?  ?  "C2'"   PCD  40  
PCD  "N2'"   "N2'"   N   0  1  N  N  N  52.415  130.776   87.401  ?  ?  ?  "N2'"   PCD  41  
PCD  "N3'"   "N3'"   N   0  1  Y  N  N  49.910  131.152   87.598  ?  ?  ?  "N3'"   PCD  42  
PCD  "C4'"   "C4'"   C   0  1  Y  N  N  49.018  131.300   88.607  ?  ?  ?  "C4'"   PCD  43  
PCD  "O4'"   "O4'"   O   0  1  N  N  N  47.871  131.461   87.862  ?  ?  ?  "O4'"   PCD  44  
PCD  MO      MO      MO  0  0  N  N  N  43.903  131.550   93.855  ?  ?  ?  MO      PCD  45  
PCD  OR1     OR1     O   0  1  N  N  N  43.027  133.651   94.017  ?  ?  ?  OR1     PCD  46  
PCD  OM2     OM2     O   0  1  N  N  N  42.993  131.008   95.181  ?  ?  ?  OM2     PCD  47  
PCD  OM1     OM1     O   0  1  N  N  N  43.322  130.697   92.531  ?  ?  ?  OM1     PCD  48  
PCD  H5      H5      H   0  1  N  N  N  53.634  123.887   98.858  ?  ?  ?  H5      PCD  49  
PCD  H6      H6      H   0  1  N  N  N  53.446  124.298   96.489  ?  ?  ?  H6      PCD  50  
PCD  H42     2H4     H   0  1  N  N  N  55.164  122.852  100.763  ?  ?  ?  H42     PCD  51  
PCD  H41     1H4     H   0  1  N  N  N  56.740  123.041  100.339  ?  ?  ?  H41     PCD  52  
PCD  "H1'"   H1*     H   0  1  N  N  N  56.283  123.429   94.582  ?  ?  ?  "H1'"   PCD  53  
PCD  "H2'"   H2*     H   0  1  N  N  N  53.521  123.691   93.887  ?  ?  ?  "H2'"   PCD  54  
PCD  H2O1    1H2O    H   0  0  N  N  N  53.812  120.942   93.269  ?  ?  ?  H2O1    PCD  55  
PCD  "H3'"   H3*     H   0  1  N  N  N  52.131  123.277   92.642  ?  ?  ?  "H3'"   PCD  56  
PCD  H4D     H4*     H   0  1  N  N  N  53.942  125.476   92.390  ?  ?  ?  H4D     PCD  57  
PCD  H3O1    1H3O    H   0  0  N  N  N  53.426  123.516   91.111  ?  ?  ?  H3O1    PCD  58  
PCD  "H5'2"  2H5*    H   0  0  N  N  N  52.527  126.771   94.132  ?  ?  ?  "H5'2"  PCD  59  
PCD  "H5'1"  1H5*    H   0  0  N  N  N  51.556  125.959   93.134  ?  ?  ?  "H5'1"  PCD  60  
PCD  HOA2    2HOA    H   0  0  N  N  N  50.305  126.245   97.316  ?  ?  ?  HOA2    PCD  61  
PCD  HOB2    2HOB    H   0  0  N  N  N  49.079  124.413   92.005  ?  ?  ?  HOB2    PCD  62  
PCD  H102    2H10    H   0  0  N  N  N  46.905  127.922   92.291  ?  ?  ?  H102    PCD  63  
PCD  H101    1H10    H   0  0  N  N  N  46.879  127.448   93.928  ?  ?  ?  H101    PCD  64  
PCD  "H9'"   "H9'"   H   0  1  N  N  N  48.520  129.152   94.600  ?  ?  ?  "H9'"   PCD  65  
PCD  "H6'"   "H6'"   H   0  1  N  N  N  48.956  132.672   92.293  ?  ?  ?  "H6'"   PCD  66  
PCD  H7      H7      H   0  1  N  N  N  50.040  130.935   93.682  ?  ?  ?  H7      PCD  67  
PCD  "H5'"   "H5'"   H   0  1  N  N  N  47.408  132.242   90.419  ?  ?  ?  "H5'"   PCD  68  
PCD  "H8'"   "H8'"   H   0  1  N  N  N  51.352  130.483   91.816  ?  ?  ?  "H8'"   PCD  69  
PCD  "H2'2"  "2H2'"  H   0  0  N  N  N  52.156  130.806   86.414  ?  ?  ?  "H2'2"  PCD  70  
PCD  "H2'1"  "1H2'"  H   0  0  N  N  N  52.922  129.943   87.700  ?  ?  ?  "H2'1"  PCD  71  
PCD  "H4'"   "H4'"   H   0  1  N  N  N  47.770  131.463   86.917  ?  ?  ?  "H4'"   PCD  72  
PCD  HR11    1HR1    H   0  0  N  N  N  42.358  134.249   93.705  ?  ?  ?  HR11    PCD  73  
PCD  HR12    2HR1    H   0  0  N  N  N  42.793  133.640   94.938  ?  ?  ?  HR12    PCD  74  
#   #
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
PCD  N1     C2      SING  Y  N   1  
PCD  N1     C6      SING  Y  N   2  
PCD  N1     "C1'"   SING  N  N   3  
PCD  C2     N3      SING  Y  N   4  
PCD  C2     O2      DOUB  N  N   5  
PCD  N3     C4      DOUB  Y  N   6  
PCD  C4     C5      SING  Y  N   7  
PCD  C4     N4      SING  N  N   8  
PCD  C5     C6      DOUB  Y  N   9  
PCD  C5     H5      SING  N  N  10  
PCD  C6     H6      SING  N  N  11  
PCD  N4     H42     SING  N  N  12  
PCD  N4     H41     SING  N  N  13  
PCD  "C1'"  C2D     SING  N  N  14  
PCD  "C1'"  O4D     SING  N  N  15  
PCD  "C1'"  "H1'"   SING  N  N  16  
PCD  C2D    "O2'"   SING  N  N  17  
PCD  C2D    "C3'"   SING  N  N  18  
PCD  C2D    "H2'"   SING  N  N  19  
PCD  "O2'"  H2O1    SING  N  N  20  
PCD  "C3'"  C4D     SING  N  N  21  
PCD  "C3'"  "O3'"   SING  N  N  22  
PCD  "C3'"  "H3'"   SING  N  N  23  
PCD  C4D    O4D     SING  N  N  24  
PCD  C4D    "C5'"   SING  N  N  25  
PCD  C4D    H4D     SING  N  N  26  
PCD  "O3'"  H3O1    SING  N  N  27  
PCD  "C5'"  "O5'"   SING  N  N  28  
PCD  "C5'"  "H5'2"  SING  N  N  29  
PCD  "C5'"  "H5'1"  SING  N  N  30  
PCD  "O5'"  PA      SING  N  N  31  
PCD  PA     O1A     DOUB  N  N  32  
PCD  PA     O2A     SING  N  N  33  
PCD  PA     O3A     SING  N  N  34  
PCD  O2A    HOA2    SING  N  N  35  
PCD  O3A    PB      SING  N  N  36  
PCD  PB     O1B     DOUB  N  N  37  
PCD  PB     O2B     SING  N  N  38  
PCD  PB     O3B     SING  N  N  39  
PCD  O2B    HOB2    SING  N  N  40  
PCD  O3B    C10     SING  N  N  41  
PCD  C10    "C9'"   SING  N  N  42  
PCD  C10    H102    SING  N  N  43  
PCD  C10    H101    SING  N  N  44  
PCD  "C9'"  "C8'"   SING  N  N  45  
PCD  "C9'"  "O9'"   SING  N  N  46  
PCD  "C9'"  "H9'"   SING  N  N  47  
PCD  "C8'"  "S8'"   SING  N  N  48  
PCD  "C8'"  "C7'"   DOUB  N  N  49  
PCD  "S8'"  MO      SING  N  N  50  
PCD  "C7'"  "S7'"   SING  N  N  51  
PCD  "C7'"  "C6'"   SING  N  N  52  
PCD  "S7'"  MO      SING  N  N  53  
PCD  "C6'"  C7      SING  N  N  54  
PCD  "C6'"  "N5'"   SING  N  N  55  
PCD  "C6'"  "H6'"   SING  N  N  56  
PCD  C7     "O9'"   SING  N  N  57  
PCD  C7     "N8'"   SING  N  N  58  
PCD  C7     H7      SING  N  N  59  
PCD  "N5'"  C4A     SING  N  N  60  
PCD  "N5'"  "H5'"   SING  N  N  61  
PCD  C4A    C4B     DOUB  Y  N  62  
PCD  C4A    "C4'"   SING  Y  N  63  
PCD  "N8'"  C4B     SING  N  N  64  
PCD  "N8'"  "H8'"   SING  N  N  65  
PCD  C4B    "N1'"   SING  Y  N  66  
PCD  "N1'"  "C2'"   DOUB  Y  N  67  
PCD  "C2'"  "N2'"   SING  N  N  68  
PCD  "C2'"  "N3'"   SING  Y  N  69  
PCD  "N2'"  "H2'2"  SING  N  N  70  
PCD  "N2'"  "H2'1"  SING  N  N  71  
PCD  "N3'"  "C4'"   DOUB  Y  N  72  
PCD  "C4'"  "O4'"   SING  N  N  73  
PCD  "O4'"  "H4'"   SING  N  N  74  
PCD  MO     OR1     SING  N  N  75  
PCD  MO     OM2     DOUB  N  N  76  
PCD  MO     OM1     DOUB  N  N  77  
PCD  OR1    HR11    SING  N  N  78  
PCD  OR1    HR12    SING  N  N  79  
#   #
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
PCD  InChI             InChI                 1.02b  "InChI=1/C19H26N8O13P2S2.Mo.H2O.2O/c20-7-1-2-27(19(31)22-7)17-11(29)10(28)5(39-17)3-36-41(32,33)40-42(34,35)37-4-6-12(43)13(44)8-16(38-6)24-14-9(23-8)15(30)26-18(21)25-14;;;;/h1-2,5-6,8,10-11,16-17,23,28-29,43-44H,3-4H2,(H,32,33)(H,34,35)(H2,20,22,31)(H4,21,24,25,26,30);;1H2;;/q;+2;;;/p-2/t5-,6-,8+,10-,11-,16-,17-;;;;/m1..../s1/fC19H24N8O13P2S2.Mo.H2O.2O/h43-44h,24,30,32,34H,20-21H2;;;;/q-2;m;;;/rC19H26MoN8O16P2S2/c21-7-1-2-28(19(32)23-7)17-11(30)10(29)5(43-17)3-40-45(36,37)44-46(38,39)41-4-6-12-13(48-20(33,34,35)47-12)8-16(42-6)25-14-9(24-8)15(31)27-18(22)26-14/h1-2,5-6,8,10-11,16-17,24,29-30H,3-4,33H2,(H,36,37)(H,38,39)(H2,21,23,32)(H4,22,25,26,27,31)/t5-,6-,8+,10-,11-,16-,17-/m1/s1/f/h25,31,36,38H,21-22H2"  
PCD  InChIKey          InChI                 1.02b  YEBYDVFRFUQMER-NBXMTLLYDD  
PCD  SMILES_CANONICAL  CACTVS                3.341  "O|[Mo]1(=O)(=O)SC2=C(S1)[C@@H]3Nc4c(O)nc(N)nc4N[C@@H]3O[C@@H]2CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]5O[C@H]([C@H](O)[C@@H]5O)n6ccc(N)nc6=O"  
PCD  SMILES            CACTVS                3.341  "O|[Mo]1(=O)(=O)SC2=C(S1)[CH]3Nc4c(O)nc(N)nc4N[CH]3O[CH]2CO[P](O)(=O)O[P](O)(=O)OC[CH]5O[CH]([CH](O)[CH]5O)n6ccc(N)nc6=O"  
PCD  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "C1=CN(C(=O)N=C1N)[C@H]2C([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]3C4=C([C@H]5[C@@H](O3)Nc6c(c(nc(n6)N)O)N5)S[Mo](=O)(=O)(S4)[OH2])O)O"  
PCD  SMILES            "OpenEye OEToolkits"  1.5.0  "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C4=C(C5C(O3)Nc6c(c(nc(n6)N)O)N5)S[Mo](=O)(=O)(S4)[OH2])O)O"  
#
_pdbx_chem_comp_audit.comp_id          PCD
_pdbx_chem_comp_audit.date             2020-06-11
_pdbx_chem_comp_audit.processing_site  PDBE
_pdbx_chem_comp_audit.action_type      "Modify synonyms"
#   #
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1  PCD  "MOLYBDENUM COFACTOR"  ?  ?  
2  PCD  MOCO                   ?  ?  
##
