data_3CD
#

_chem_comp.id                                   3CD
_chem_comp.name                                 "3-(CHLOROACETYL) PYRIDINE ADENINE DINUCLEOTIDE"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C22 H28 Cl N6 O14 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        3-CAPAD
_chem_comp.pdbx_formal_charge                   1
_chem_comp.pdbx_initial_date                    2010-02-10
_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                       697.890
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    3CD
_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  N
_chem_comp.pdbx_model_coordinates_db_code       2XF8
_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
3CD  O1A   O1A   O   0  1  N  N  N  -38.433  53.115  50.690   2.671  -4.082   0.890  O1A   3CD   1  
3CD  PA    PA    P   0  1  N  N  N  -38.929  52.401  51.923   2.052  -3.440  -0.451  PA    3CD   2  
3CD  O2A   O2A   O   0  1  N  N  N  -40.175  51.567  51.833   2.066  -4.450  -1.533  O2A   3CD   3  
3CD  O3    O3    O   0  1  N  N  N  -37.735  51.461  52.468   0.536  -2.973  -0.172  O3    3CD   4  
3CD  PN    PN    P   0  1  N  N  N  -36.900  51.712  53.829  -0.862  -3.754  -0.008  PN    3CD   5  
3CD  O1N   O1N   O   0  1  N  N  N  -35.776  50.705  53.827  -0.672  -4.927   0.873  O1N   3CD   6  
3CD  O2N   O2N   O   0  1  N  N  N  -37.876  51.764  54.989  -1.375  -4.246  -1.453  O2N   3CD   7  
3CD  O5D   O5D   O   0  1  N  N  N  -36.219  53.161  53.626  -1.955  -2.766   0.641  O5D   3CD   8  
3CD  C5D   C5D   C   0  1  N  N  N  -36.206  54.148  54.660  -3.268  -3.192   1.010  C5D   3CD   9  
3CD  C4D   C4D   C   0  1  N  N  R  -34.826  54.317  55.301  -4.043  -2.010   1.594  C4D   3CD  10  
3CD  C3D   C3D   C   0  1  N  N  S  -33.693  54.633  54.318  -5.422  -2.474   2.114  C3D   3CD  11  
3CD  O3D   O3D   O   0  1  N  N  N  -33.187  55.944  54.577  -5.380  -2.679   3.528  O3D   3CD  12  
3CD  C2D   C2D   C   0  1  N  N  R  -32.599  53.630  54.623  -6.369  -1.305   1.764  C2D   3CD  13  
3CD  O2D   O2D   O   0  1  N  N  N  -31.309  54.252  54.606  -6.942  -0.752   2.950  O2D   3CD  14  
3CD  O4D   O4D   O   0  1  N  N  N  -34.414  53.144  56.009  -4.345  -1.046   0.561  O4D   3CD  15  
3CD  C1D   C1D   C   0  1  N  N  R  -32.990  53.247  56.037  -5.451  -0.272   1.073  C1D   3CD  16  
3CD  N1N   N1N   N   1  1  Y  N  N  -32.255  52.131  56.652  -6.162   0.389  -0.024  N1N   3CD  17  
3CD  C6N   C6N   C   0  1  Y  N  N  -31.845  52.397  57.902  -6.274  -0.234  -1.182  C6N   3CD  18  
3CD  C5N   C5N   C   0  1  Y  N  N  -31.126  51.481  58.657  -6.937   0.350  -2.247  C5N   3CD  19  
3CD  C4N   C4N   C   0  1  Y  N  N  -30.838  50.263  58.082  -7.491   1.609  -2.093  C4N   3CD  20  
3CD  C2N   C2N   C   0  1  Y  N  N  -31.971  50.948  56.062  -6.675   1.584   0.176  C2N   3CD  21  
3CD  C3N   C3N   C   0  1  Y  N  N  -31.245  49.985  56.784  -7.356   2.246  -0.851  C3N   3CD  22  
3CD  C7N   C7N   C   0  1  N  N  N  -30.880  48.638  56.210  -7.926   3.585  -0.631  C7N   3CD  23  
3CD  O7N   O7N   O   0  1  N  N  N  -31.615  48.100  55.381  -7.803   4.126   0.448  O7N   3CD  24  
3CD  C8N   C8N   C   0  1  N  N  N  -29.757  48.018  56.596  -8.661   4.284  -1.745  C8N   3CD  25  
3CD  O5B   O5B   O   0  1  N  N  N  -39.190  53.494  53.071   2.933  -2.168  -0.894  O5B   3CD  26  
3CD  C5B   C5B   C   0  1  N  N  N  -39.627  54.813  52.747   4.296  -2.272  -1.311  C5B   3CD  27  
3CD  C4B   C4B   C   0  1  N  N  R  -41.106  54.813  52.389   4.830  -0.881  -1.659  C4B   3CD  28  
3CD  C3B   C3B   C   0  1  N  N  S  -41.302  54.860  50.880   6.261  -0.983  -2.231  C3B   3CD  29  
3CD  O3B   O3B   O   0  1  N  N  N  -41.628  53.557  50.376   6.234  -0.933  -3.659  O3B   3CD  30  
3CD  C2B   C2B   C   0  1  N  N  R  -42.406  55.878  50.641   6.983   0.259  -1.660  C2B   3CD  31  
3CD  O2B   O2B   O   0  1  N  N  N  -43.653  55.255  50.325   7.424   1.112  -2.717  O2B   3CD  32  
3CD  C1B   C1B   C   0  1  N  N  R  -42.551  56.625  51.958   5.902   0.963  -0.810  C1B   3CD  33  
3CD  O4B   O4B   O   0  1  N  N  N  -41.735  55.973  52.939   4.966  -0.081  -0.464  O4B   3CD  34  
3CD  N9A   N9A   N   0  1  Y  N  N  -42.169  58.048  51.776   6.498   1.535   0.400  N9A   3CD  35  
3CD  C4A   C4A   C   0  1  Y  N  N  -42.822  59.089  52.301   7.104   2.761   0.504  C4A   3CD  36  
3CD  C5A   C5A   C   0  1  Y  N  N  -42.162  60.240  51.895   7.518   2.876   1.842  C5A   3CD  37  
3CD  N7A   N7A   N   0  1  Y  N  N  -41.121  59.864  51.128   7.149   1.736   2.474  N7A   3CD  38  
3CD  C8A   C8A   C   0  1  Y  N  N  -41.132  58.514  51.060   6.546   0.950   1.630  C8A   3CD  39  
3CD  N3A   N3A   N   0  1  Y  N  N  -43.921  59.183  53.097   7.351   3.761  -0.336  N3A   3CD  40  
3CD  C2A   C2A   C   0  1  Y  N  N  -44.367  60.388  53.490   7.973   4.846   0.076  C2A   3CD  41  
3CD  N1A   N1A   N   0  1  Y  N  N  -43.743  61.517  53.106   8.381   4.999   1.322  N1A   3CD  42  
3CD  C6A   C6A   C   0  1  Y  N  N  -42.642  61.475  52.314   8.179   4.053   2.234  C6A   3CD  43  
3CD  N6A   N6A   N   0  1  N  N  N  -42.019  62.618  51.932   8.609   4.223   3.538  N6A   3CD  44  
3CD  CL1   CL1   CL  ?  0  N  Y  N  -28.648  48.661  57.681  -9.235   5.893  -1.170  CL1   3CD  45  
3CD  H89   H89   H   ?  1  N  N  N  -30.098  47.083  57.064  -7.990   4.419  -2.594  H89   3CD  46  
3CD  H1A   H1A   H   0  1  N  N  N  -38.329  54.040  50.880   2.693  -3.474   1.642  H1A   3CD  47  
3CD  H2N   H2N   H   0  1  N  N  N  -37.395  51.775  55.808  -1.521  -3.527  -2.084  H2N   3CD  48  
3CD  H5D1  H5D1  H   0  0  N  N  N  -36.506  55.112  54.223  -3.789  -3.569   0.129  H5D1  3CD  49  
3CD  H5D2  H5D2  H   0  0  N  N  N  -36.900  53.816  55.446  -3.197  -3.984   1.756  H5D2  3CD  50  
3CD  H4D   H4D   H   0  1  N  N  N  -34.975  55.176  55.971  -3.473  -1.542   2.396  H4D   3CD  51  
3CD  H3D   H3D   H   0  1  N  N  N  -34.037  54.583  53.274  -5.734  -3.387   1.607  H3D   3CD  52  
3CD  HA    HA    H   0  1  N  N  N  -33.075  56.061  55.513  -6.220  -2.971   3.908  HA    3CD  53  
3CD  H2D   H2D   H   0  1  N  N  N  -32.521  52.795  53.911  -7.152  -1.639   1.083  H2D   3CD  54  
3CD  HB    HB    H   0  1  N  N  N  -31.035  54.390  53.707  -7.479  -1.377   3.456  HB    3CD  55  
3CD  H1D   H1D   H   0  1  N  N  N  -32.670  54.020  56.751  -5.097   0.463   1.795  H1D   3CD  56  
3CD  H6N   H6N   H   0  1  N  N  N  -32.083  53.357  58.335  -5.841  -1.216  -1.301  H6N   3CD  57  
3CD  HC    HC    H   0  1  N  N  N  -32.297  50.746  55.052  -6.567   2.059   1.140  HC    3CD  58  
3CD  H5N   H5N   H   0  1  N  N  N  -30.803  51.715  59.661  -7.020  -0.170  -3.190  H5N   3CD  59  
3CD  H4N   H4N   H   0  1  N  N  N  -30.292  49.520  58.644  -8.013   2.088  -2.908  H4N   3CD  60  
3CD  H8N   H8N   H   0  1  N  N  N  -29.175  48.023  55.663  -9.516   3.681  -2.050  H8N   3CD  61  
3CD  H5B1  H5B1  H   0  0  N  N  N  -39.467  55.469  53.615   4.891  -2.698  -0.503  H5B1  3CD  62  
3CD  H5B2  H5B2  H   0  0  N  N  N  -39.052  55.176  51.883   4.359  -2.915  -2.188  H5B2  3CD  63  
3CD  H4B   H4B   H   0  1  N  N  N  -41.547  53.891  52.795   4.169  -0.389  -2.373  H4B   3CD  64  
3CD  H3B   H3B   H   0  1  N  N  N  -40.388  55.159  50.345   6.745  -1.898  -1.891  H3B   3CD  65  
3CD  HD    HD    H   0  1  N  N  N  -41.700  53.592  49.429   7.107  -0.993  -4.071  HD    3CD  66  
3CD  H2B   H2B   H   0  1  N  N  N  -42.150  56.528  49.792   7.825  -0.043  -1.037  H2B   3CD  67  
3CD  HE    HE    H   0  1  N  N  N  -44.150  55.117  51.123   8.059   0.699  -3.318  HE    3CD  68  
3CD  H1B   H1B   H   0  1  N  N  N  -43.596  56.611  52.302   5.407   1.739  -1.393  H1B   3CD  69  
3CD  H8A   H8A   H   0  1  N  N  N  -40.422  57.908  50.518   6.144  -0.024   1.869  H8A   3CD  70  
3CD  H2A   H2A   H   0  1  N  N  N  -45.239  60.452  54.124   8.158   5.640  -0.632  H2A   3CD  71  
3CD  H66   H66   H   ?  1  N  N  N  -41.866  63.198  52.732   8.455   3.525   4.194  H66   3CD  72  
3CD  H67   H67   H   ?  1  N  N  N  -41.141  62.394  51.510   9.064   5.040   3.796  H67   3CD  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
3CD  O1A  PA    SING  N  N   1  
3CD  PA   O2A   DOUB  N  N   2  
3CD  PA   O3    SING  N  N   3  
3CD  PA   O5B   SING  N  N   4  
3CD  O3   PN    SING  N  N   5  
3CD  PN   O1N   DOUB  N  N   6  
3CD  PN   O2N   SING  N  N   7  
3CD  PN   O5D   SING  N  N   8  
3CD  O5D  C5D   SING  N  N   9  
3CD  C5D  C4D   SING  N  N  10  
3CD  C4D  C3D   SING  N  N  11  
3CD  C4D  O4D   SING  N  N  12  
3CD  C3D  O3D   SING  N  N  13  
3CD  C3D  C2D   SING  N  N  14  
3CD  C2D  O2D   SING  N  N  15  
3CD  C2D  C1D   SING  N  N  16  
3CD  O4D  C1D   SING  N  N  17  
3CD  C1D  N1N   SING  N  N  18  
3CD  N1N  C6N   SING  Y  N  19  
3CD  N1N  C2N   DOUB  Y  N  20  
3CD  C6N  C5N   DOUB  Y  N  21  
3CD  C5N  C4N   SING  Y  N  22  
3CD  C4N  C3N   DOUB  Y  N  23  
3CD  C2N  C3N   SING  Y  N  24  
3CD  C3N  C7N   SING  N  N  25  
3CD  C7N  O7N   DOUB  N  N  26  
3CD  C7N  C8N   SING  N  N  27  
3CD  C8N  CL1   SING  N  N  28  
3CD  C8N  H89   SING  N  N  29  
3CD  O5B  C5B   SING  N  N  30  
3CD  C5B  C4B   SING  N  N  31  
3CD  C4B  C3B   SING  N  N  32  
3CD  C4B  O4B   SING  N  N  33  
3CD  C3B  O3B   SING  N  N  34  
3CD  C3B  C2B   SING  N  N  35  
3CD  C2B  O2B   SING  N  N  36  
3CD  C2B  C1B   SING  N  N  37  
3CD  C1B  O4B   SING  N  N  38  
3CD  C1B  N9A   SING  N  N  39  
3CD  N9A  C4A   SING  Y  N  40  
3CD  N9A  C8A   SING  Y  N  41  
3CD  C4A  C5A   SING  Y  N  42  
3CD  C4A  N3A   DOUB  Y  N  43  
3CD  C5A  N7A   SING  Y  N  44  
3CD  C5A  C6A   DOUB  Y  N  45  
3CD  N7A  C8A   DOUB  Y  N  46  
3CD  N3A  C2A   SING  Y  N  47  
3CD  C2A  N1A   DOUB  Y  N  48  
3CD  N1A  C6A   SING  Y  N  49  
3CD  O1A  H1A   SING  N  N  50  
3CD  O2N  H2N   SING  N  N  51  
3CD  C5D  H5D1  SING  N  N  52  
3CD  C5D  H5D2  SING  N  N  53  
3CD  C4D  H4D   SING  N  N  54  
3CD  C3D  H3D   SING  N  N  55  
3CD  O3D  HA    SING  N  N  56  
3CD  C2D  H2D   SING  N  N  57  
3CD  O2D  HB    SING  N  N  58  
3CD  C1D  H1D   SING  N  N  59  
3CD  C6N  H6N   SING  N  N  60  
3CD  C2N  HC    SING  N  N  61  
3CD  C5N  H5N   SING  N  N  62  
3CD  C4N  H4N   SING  N  N  63  
3CD  C8N  H8N   SING  N  N  64  
3CD  C5B  H5B1  SING  N  N  65  
3CD  C5B  H5B2  SING  N  N  66  
3CD  C4B  H4B   SING  N  N  67  
3CD  C3B  H3B   SING  N  N  68  
3CD  O3B  HD    SING  N  N  69  
3CD  C2B  H2B   SING  N  N  70  
3CD  O2B  HE    SING  N  N  71  
3CD  C1B  H1B   SING  N  N  72  
3CD  C8A  H8A   SING  N  N  73  
3CD  C2A  H2A   SING  N  N  74  
3CD  C6A  N6A   SING  N  N  75  
3CD  N6A  H66   SING  N  N  76  
3CD  N6A  H67   SING  N  N  77  
#   #
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
3CD  SMILES_CANONICAL  CACTVS                3.352  "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)[n+]5cccc(c5)C(=O)CCl)[C@@H](O)[C@H]3O"  
3CD  SMILES            CACTVS                3.352  "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)[n+]5cccc(c5)C(=O)CCl)[CH](O)[CH]3O"  
3CD  SMILES_CANONICAL  "OpenEye OEToolkits"  1.6.1  "c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)CCl"  
3CD  SMILES            "OpenEye OEToolkits"  1.6.1  "c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)CCl"  
3CD  InChI             InChI                 1.03   "InChI=1S/C22H27ClN6O14P2/c23-4-11(30)10-2-1-3-28(5-10)21-17(33)15(31)12(41-21)6-39-44(35,36)43-45(37,38)40-7-13-16(32)18(34)22(42-13)29-9-27-14-19(24)25-8-26-20(14)29/h1-3,5,8-9,12-13,15-18,21-22,31-34H,4,6-7H2,(H3-,24,25,26,35,36,37,38)/p+1/t12-,13-,15-,16-,17-,18-,21-,22-/m1/s1"  
3CD  InChIKey          InChI                 1.03   XIQCGHNADRRDKB-RBEMOOQDSA-O  
#
_pdbx_chem_comp_identifier.comp_id          3CD
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  1.6.1
_pdbx_chem_comp_identifier.identifier       "[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [[(2R,3S,4R,5R)-5-[3-(2-chloroethanoyl)pyridin-1-ium-1-yl]-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] 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
3CD  "Create component"      2010-02-10  EBI   
3CD  "Modify aromatic_flag"  2011-06-04  RCSB  
3CD  "Modify descriptor"     2011-06-04  RCSB  
3CD  "Modify synonyms"       2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     3CD
_pdbx_chem_comp_synonyms.name        3-CAPAD
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
