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                    2025-07-15 
_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 
_chem_comp.pdbx_pcm                              Y 
# 
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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 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 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 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 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 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 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 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 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 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 N N N -34.826 54.317 55.301 -4.043 -2.010 1.594  C4D  3CD 10 
3CD C3D  C3D  C  0 1 N N S N N N -33.693 54.633 54.318 -5.422 -2.474 2.114  C3D  3CD 11 
3CD O3D  O3D  O  0 1 N N N 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 N N N -32.599 53.630 54.623 -6.369 -1.305 1.764  C2D  3CD 13 
3CD O2D  O2D  O  0 1 N N N 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 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 N N N -32.990 53.247 56.037 -5.451 -0.272 1.073  C1D  3CD 16 
3CD N1N  N1N  N  1 1 Y N N N 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 N 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 N 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 N 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 N 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 N 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 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 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 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 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 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 N N N -41.106 54.813 52.389 4.830  -0.881 -1.659 C4B  3CD 28 
3CD C3B  C3B  C  0 1 N N S N N N -41.302 54.860 50.880 6.261  -0.983 -2.231 C3B  3CD 29 
3CD O3B  O3B  O  0 1 N N N 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 N N N -42.406 55.878 50.641 6.983  0.259  -1.660 C2B  3CD 31 
3CD O2B  O2B  O  0 1 N N N 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 N N N -42.551 56.625 51.958 5.902  0.963  -0.810 C1B  3CD 33 
3CD O4B  O4B  O  0 1 N N N 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 N 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 N 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 N 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 N 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 N 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 N 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 N 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 N 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 N 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 N N N -42.019 62.618 51.932 8.609  4.223  3.538  N6A  3CD 44 
3CD CL1  CL1  CL 0 0 N Y N N N N -28.648 48.661 57.681 -9.235 5.893  -1.170 CL1  3CD 45 
3CD H89  H89  H  0 1 N N N 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 N N N -45.239 60.452 54.124 8.158  5.640  -0.632 H2A  3CD 71 
3CD H66  H66  H  0 1 N N N N N N -41.866 63.198 52.732 8.455  3.525  4.194  H66  3CD 72 
3CD H67  H67  H  0 1 N N N 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 
3CD "Modify PCM"           2024-09-27 PDBE 
3CD "Other modification"   2025-07-15 RCSB 
# 
_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         ? 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            3CD 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C8N 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
