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 2023-09-23
_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 Corina
_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 N N N 55.344 123.432 96.085 ? ? ? N1 PCD 1
PCD C2 C2 C 0 1 N N N 56.485 122.822 96.521 ? ? ? C2 PCD 2
PCD N3 N3 N 0 1 N N N 56.611 122.574 97.843 ? ? ? N3 PCD 3
PCD C4 C4 C 0 1 N N N 55.698 122.881 98.781 ? ? ? C4 PCD 4
PCD C5 C5 C 0 1 N N N 54.482 123.555 98.236 ? ? ? C5 PCD 5
PCD C6 C6 C 0 1 N 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'A" 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'A" C 0 1 N N R 53.603 124.916 93.293 ? ? ? C4D PCD 13
PCD O4D "O4'A" 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 N 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 N 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 53.694 123.851 98.913 ? ? ? H5 PCD 49
PCD H6 H6 H 0 1 N N N 53.460 124.289 96.512 ? ? ? H6 PCD 50
PCD H42 H42 H 0 1 N N N 56.691 122.169 100.369 ? ? ? H42 PCD 51
PCD H41 H41 H 0 1 N N N 55.144 122.871 100.707 ? ? ? H41 PCD 52
PCD "H1'" "H1'" H 0 1 N N N 56.198 123.526 94.226 ? ? ? "H1'" PCD 53
PCD "H2'" "H2'" H 0 1 N N N 53.494 122.828 94.564 ? ? ? "H2'" PCD 54
PCD H2O1 H2O1 H 0 0 N N N 53.771 121.036 93.238 ? ? ? H2O1 PCD 55
PCD "H3'" "H3'" H 0 1 N N N 52.168 123.158 92.837 ? ? ? "H3'" PCD 56
PCD H4D "H4'A" H 0 1 N N N 53.912 125.465 92.391 ? ? ? H4D PCD 57
PCD H3O1 H3O1 H 0 0 N N N 53.658 123.416 90.897 ? ? ? H3O1 PCD 58
PCD "H5'2" "H5'2" H 0 0 N N N 52.642 126.701 94.227 ? ? ? "H5'2" PCD 59
PCD "H5'1" "H5'1" H 0 0 N N N 51.559 125.797 93.115 ? ? ? "H5'1" PCD 60
PCD HOA2 HOA2 H 0 0 N N N 50.890 125.589 97.675 ? ? ? HOA2 PCD 61
PCD HOB2 HOB2 H 0 0 N N N 49.415 123.757 92.683 ? ? ? HOB2 PCD 62
PCD H102 H102 H 0 0 N N N 46.989 127.952 92.253 ? ? ? H102 PCD 63
PCD H101 H101 H 0 0 N N N 46.961 127.453 93.979 ? ? ? H101 PCD 64
PCD "H9'" "H9'" H 0 1 N N N 48.581 129.094 94.556 ? ? ? "H9'" PCD 65
PCD "H6'" "H6'" H 0 1 N N N 48.757 132.730 92.296 ? ? ? "H6'" PCD 66
PCD H7 H7 H 0 1 N N N 49.975 131.089 93.657 ? ? ? H7 PCD 67
PCD "H5'" "H5'" H 0 1 N N N 47.412 130.683 90.694 ? ? ? "H5'" PCD 68
PCD "H8'" "H8'" H 0 1 N N N 50.830 132.026 91.803 ? ? ? "H8'" PCD 69
PCD "H2'2" "H2'2" H 0 0 N N N 53.110 130.678 88.114 ? ? ? "H2'2" PCD 70
PCD "H2'1" "H2'1" H 0 0 N N N 52.394 129.949 86.840 ? ? ? "H2'1" PCD 71
PCD "H4'" "H4'" H 0 1 N N N 48.084 131.416 86.937 ? ? ? "H4'" PCD 72
PCD HR11 HR11 H 0 0 N N N 42.414 133.684 94.742 ? ? ? HR11 PCD 73
PCD HR12 HR12 H 0 0 N N N 43.727 134.275 94.167 ? ? ? 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 N N 1
PCD N1 C6 SING N N 2
PCD N1 "C1'" SING N N 3
PCD C2 N3 SING N N 4
PCD C2 O2 DOUB N N 5
PCD N3 C4 DOUB N N 6
PCD C4 C5 SING N N 7
PCD C4 N4 SING N N 8
PCD C5 C6 DOUB N 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 1.06 "InChI=1S/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"
PCD InChIKey InChI 1.06 YEBYDVFRFUQMER-MQPNXHJTSA-L
PCD SMILES_CANONICAL CACTVS 3.385 "O.NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]4Nc5nc(N)nc(O)c5N[C@H]4C6=C3S[Mo](=O)(=O)S6)[C@@H](O)[C@H]2O"
PCD SMILES CACTVS 3.385 "O.NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]4Nc5nc(N)nc(O)c5N[CH]4C6=C3S[Mo](=O)(=O)S6)[CH](O)[CH]2O"
PCD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "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" 2.0.7 "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_identifier.comp_id PCD
_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-13-$l^{3}-oxidanyl-7-oxidanyl-13,13-bis(oxidanylidene)-17-oxa-12,14-dithia-2,4,6,9-tetraza-13$l^{7}-molybdatetracyclo[8.7.0.0^{3,8}.0^{11,15}]heptadeca-3(8),4,6,11(15)-tetraen-16-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate"
#
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 ? ?
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
PCD "Modify synonyms" 2020-06-11 PDBE
PCD "Modify descriptor" 2023-09-23 RCSB
#