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 2024-09-27 _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 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 ? 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 ? 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 ? 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 # _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 ? #