data_COD
# 
_chem_comp.id                                    COD 
_chem_comp.name                                  "DEPHOSPHO COENZYME A" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H35 N7 O13 P2 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1999-07-29 
_chem_comp.pdbx_modified_date                    2024-10-29 
_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                        687.554 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     COD 
_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   N 
_chem_comp.pdbx_model_coordinates_db_code        1B6T 
_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 
COD N1   N1   N 0 1 Y N N N N N 23.897 20.397 42.164 3.959  1.483  -9.333  N1   COD 1  
COD C2   C2   C 0 1 Y N N N N N 23.164 21.557 42.427 2.710  1.273  -9.710  C2   COD 2  
COD N3   N3   N 0 1 Y N N N N N 22.107 21.952 41.625 1.777  0.873  -8.872  N3   COD 3  
COD C4   C4   C 0 1 Y N N N N N 21.758 21.174 40.520 2.064  0.657  -7.592  C4   COD 4  
COD C5   C5   C 0 1 Y N N N N N 22.467 20.007 40.216 3.377  0.872  -7.140  C5   COD 5  
COD C6   C6   C 0 1 Y N N N N N 23.596 19.598 41.083 4.338  1.298  -8.073  C6   COD 6  
COD N7   N7   N 0 1 N N N N N N 24.272 18.487 40.801 5.648  1.520  -7.688  N7   COD 7  
COD N8   N8   N 0 1 Y N N N N N 22.045 19.394 39.179 3.395  0.589  -5.816  N8   COD 8  
COD C9   C9   C 0 1 Y N N N N N 20.961 20.175 38.711 2.204  0.228  -5.434  C9   COD 9  
COD N10  N10  N 0 1 Y N N N N N 20.855 21.275 39.611 1.346  0.257  -6.493  N10  COD 10 
COD C11  C11  C 0 1 N N R N N N 19.870 22.349 39.540 -0.078 -0.082 -6.464  C11  COD 11 
COD C12  C12  C 0 1 N N R N N N 19.787 23.156 38.202 -0.282 -1.608 -6.643  C12  COD 12 
COD O13  O13  O 0 1 N N N N N N 20.869 24.090 38.052 -0.327 -1.957 -8.028  O13  COD 13 
COD C14  C14  C 0 1 N N S N N N 18.400 23.798 38.324 -1.663 -1.831 -5.972  C14  COD 14 
COD O15  O15  O 0 1 N N N N N N 18.536 25.002 39.105 -2.698 -1.867 -6.956  O15  COD 15 
COD C16  C16  C 0 1 N N R N N N 17.633 22.728 39.056 -1.830 -0.610 -5.046  C16  COD 16 
COD O17  O17  O 0 1 N N N N N N 18.547 21.860 39.771 -0.637 0.182  -5.160  O17  COD 17 
COD C18  C18  C 0 1 N N N N N N 16.827 21.907 38.057 -2.011 -1.075 -3.600  C18  COD 18 
COD O19  O19  O 0 1 N N N N N N 17.710 21.309 37.076 -2.158 0.063  -2.749  O19  COD 19 
COD P20  P20  P 0 1 N N S N N N 17.134 20.471 35.811 -2.343 -0.496 -1.251  P20  COD 20 
COD O21  O21  O 0 1 N N N N N N 18.227 20.281 34.729 -3.651 -1.432 -1.185  O21  COD 21 
COD O22  O22  O 0 1 N N N N N N 16.555 19.097 36.267 -1.151 -1.286 -0.869  O22  COD 22 
COD O23  O23  O 0 1 N N N N N N 15.982 21.427 35.312 -2.516 0.739  -0.233  O23  COD 23 
COD P24  P24  P 0 1 N N R N N N 16.093 22.588 34.282 -2.695 0.110  1.237   P24  COD 24 
COD O25  O25  O 0 1 N N N N N N 17.178 23.591 34.708 -3.997 -0.836 1.261   O25  COD 25 
COD O26  O26  O 0 1 N N N N N N 16.414 21.965 32.905 -1.498 -0.689 1.580   O26  COD 26 
COD O27  O27  O 0 1 N N N N N N 14.626 23.183 34.254 -2.874 1.296  2.310   O27  COD 27 
COD C28  C28  C 0 1 N N N N N N 14.177 24.256 33.473 -3.027 0.677  3.589   C28  COD 28 
COD C29  C29  C 0 1 N N N N N N 12.661 24.394 33.806 -3.202 1.755  4.660   C29  COD 29 
COD C30  C30  C 0 1 N N N N N N 12.000 23.009 33.462 -1.970 2.662  4.677   C30  COD 30 
COD C31  C31  C 0 1 N N N N N N 12.453 24.684 35.353 -4.445 2.590  4.345   C31  COD 31 
COD C32  C32  C 0 1 N N R N N N 12.095 25.571 32.914 -3.367 1.092  6.029   C32  COD 32 
COD O33  O33  O 0 1 N N N N N N 12.307 25.287 31.515 -4.590 0.354  6.057   O33  COD 33 
COD C34  C34  C 0 1 N N N N N N 10.547 25.805 33.126 -2.211 0.158  6.276   C34  COD 34 
COD O35  O35  O 0 1 N N N N N N 10.153 26.642 33.997 -2.387 -1.041 6.263   O35  COD 35 
COD N36  N36  N 0 1 N N N N N N 9.709  25.069 32.339 -0.980 0.655  6.512   N36  COD 36 
COD C37  C37  C 0 1 N N N N N N 8.232  25.156 32.399 0.126  -0.249 6.833   C37  COD 37 
COD C38  C38  C 0 1 N N N N N N 7.725  26.058 31.248 1.402  0.565  7.054   C38  COD 38 
COD C39  C39  C 0 1 N N N N N N 7.960  27.525 31.567 2.541  -0.365 7.383   C39  COD 39 
COD O40  O40  O 0 1 N N N N N N 7.230  28.153 32.351 2.350  -1.561 7.436   O40  COD 40 
COD N41  N41  N 0 1 N N N N N N 9.000  28.086 30.957 3.771  0.132  7.619   N41  COD 41 
COD C42  C42  C 0 1 N N N N N N 9.449  29.539 31.109 4.878  -0.772 7.940   C42  COD 42 
COD C43  C43  C 0 1 N N N N N N 10.354 29.609 32.242 6.154  0.041  8.161   C43  COD 43 
COD S44  S44  S 0 1 N N N N N N 10.825 31.273 32.361 7.525  -1.078 8.558   S44  COD 44 
COD HC2  HC2  H 0 1 N N N N N N 23.428 22.181 43.296 2.445  1.436  -10.744 HC2  COD 45 
COD HN71 1HN7 H 0 0 N N N N N N 24.049 17.895 40.000 6.302  1.815  -8.341  HN71 COD 46 
COD HN72 2HN7 H 0 0 N N N N N N 24.254 17.897 41.633 5.913  1.382  -6.765  HN72 COD 47 
COD HC9  HC9  H 0 1 N N N N N N 20.330 19.969 37.829 1.935  -0.053 -4.426  HC9  COD 48 
COD HC11 HC11 H 0 0 N N N N N N 20.242 23.039 40.331 -0.618 0.470  -7.233  HC11 COD 49 
COD HC12 HC12 H 0 0 N N N N N N 19.896 22.541 37.278 0.497  -2.168 -6.127  HC12 COD 50 
COD HO13 HO13 H 0 0 N N N N N N 20.818 24.580 37.239 -0.456 -2.915 -8.070  HO13 COD 51 
COD HC14 HC14 H 0 0 N N N N N N 17.906 24.094 37.368 -1.659 -2.753 -5.390  HC14 COD 52 
COD HO15 HO15 H 0 0 N N N N N N 17.676 25.399 39.180 -2.504 -2.614 -7.538  HO15 COD 53 
COD HC16 HC16 H 0 0 N N N N N N 16.943 23.210 39.787 -2.695 -0.025 -5.358  HC16 COD 54 
COD H181 1H18 H 0 0 N N N N N N 16.188 21.145 38.562 -1.137 -1.649 -3.291  H181 COD 55 
COD H182 2H18 H 0 0 N N N N N N 16.018 22.508 37.579 -2.901 -1.700 -3.527  H182 COD 56 
COD HO21 HO21 H 0 0 N N N N N N 17.889 19.790 33.988 -4.403 -0.880 -1.440  HO21 COD 57 
COD HO25 HO25 H 0 0 N N N N N N 17.245 24.299 34.079 -4.753 -0.277 1.032   HO25 COD 58 
COD H281 1H28 H 0 0 N N N N N N 14.758 25.195 33.620 -2.141 0.083  3.813   H281 COD 59 
COD H282 2H28 H 0 0 N N N N N N 14.391 24.142 32.384 -3.905 0.031  3.576   H282 COD 60 
COD H301 1H30 H 0 0 N N N N N N 10.915 23.107 33.700 -1.072 2.053  4.778   H301 COD 61 
COD H302 2H30 H 0 0 N N N N N N 12.193 22.675 32.415 -1.923 3.228  3.747   H302 COD 62 
COD H303 3H30 H 0 0 N N N N N N 12.487 22.147 33.974 -2.038 3.351  5.519   H303 COD 63 
COD H311 1H31 H 0 0 N N N N N N 11.368 24.782 35.591 -5.331 1.957  4.399   H311 COD 64 
COD H312 2H31 H 0 0 N N N N N N 12.947 23.913 35.988 -4.533 3.400  5.069   H312 COD 65 
COD H313 3H31 H 0 0 N N N N N N 13.033 25.574 35.688 -4.358 3.007  3.342   H313 COD 66 
COD HC32 HC32 H 0 0 N N N N N N 12.644 26.488 33.227 -3.387 1.859  6.804   HC32 COD 67 
COD HO33 HO33 H 0 0 N N N N N N 11.967 25.994 30.979 -4.531 -0.310 5.358   HO33 COD 68 
COD HN36 HN36 H 0 0 N N N N N N 10.194 24.443 31.695 -0.828 1.612  6.470   HN36 COD 69 
COD H371 1H37 H 0 0 N N N N N N 7.749  24.151 32.392 -0.111 -0.806 7.739   H371 COD 70 
COD H372 2H37 H 0 0 N N N N N N 7.869  25.499 33.395 0.277  -0.944 6.007   H372 COD 71 
COD H381 1H38 H 0 0 N N N N N N 8.176  25.771 30.269 1.639  1.122  6.148   H381 COD 72 
COD H382 2H38 H 0 0 N N N N N N 6.655  25.855 31.005 1.251  1.260  7.879   H382 COD 73 
COD HN41 HN41 H 0 0 N N N N N N 9.458  27.393 30.365 3.923  1.089  7.577   HN41 COD 74 
COD H421 1H42 H 0 0 N N N N N N 9.893  29.954 30.174 4.641  -1.329 8.846   H421 COD 75 
COD H422 2H42 H 0 0 N N N N N N 8.593  30.249 31.194 5.029  -1.468 7.114   H422 COD 76 
COD H431 1H43 H 0 0 N N N N N N 9.923  29.197 33.184 6.391  0.599  7.255   H431 COD 77 
COD H432 2H43 H 0 0 N N N N N N 11.215 28.904 32.171 6.003  0.737  8.986   H432 COD 78 
COD HS44 HS44 H 0 0 N N N N N N 11.417 31.318 33.102 8.519  -0.185 8.709   HS44 COD 79 
# 
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 
COD N1  C2   SING Y N 1  
COD N1  C6   DOUB Y N 2  
COD C2  N3   DOUB Y N 3  
COD C2  HC2  SING N N 4  
COD N3  C4   SING Y N 5  
COD C4  C5   DOUB Y N 6  
COD C4  N10  SING Y N 7  
COD C5  C6   SING Y N 8  
COD C5  N8   SING Y N 9  
COD C6  N7   SING N N 10 
COD N7  HN71 SING N N 11 
COD N7  HN72 SING N N 12 
COD N8  C9   DOUB Y N 13 
COD C9  N10  SING Y N 14 
COD C9  HC9  SING N N 15 
COD N10 C11  SING N N 16 
COD C11 C12  SING N N 17 
COD C11 O17  SING N N 18 
COD C11 HC11 SING N N 19 
COD C12 O13  SING N N 20 
COD C12 C14  SING N N 21 
COD C12 HC12 SING N N 22 
COD O13 HO13 SING N N 23 
COD C14 O15  SING N N 24 
COD C14 C16  SING N N 25 
COD C14 HC14 SING N N 26 
COD O15 HO15 SING N N 27 
COD C16 O17  SING N N 28 
COD C16 C18  SING N N 29 
COD C16 HC16 SING N N 30 
COD C18 O19  SING N N 31 
COD C18 H181 SING N N 32 
COD C18 H182 SING N N 33 
COD O19 P20  SING N N 34 
COD P20 O21  SING N N 35 
COD P20 O22  DOUB N N 36 
COD P20 O23  SING N N 37 
COD O21 HO21 SING N N 38 
COD O23 P24  SING N N 39 
COD P24 O25  SING N N 40 
COD P24 O26  DOUB N N 41 
COD P24 O27  SING N N 42 
COD O25 HO25 SING N N 43 
COD O27 C28  SING N N 44 
COD C28 C29  SING N N 45 
COD C28 H281 SING N N 46 
COD C28 H282 SING N N 47 
COD C29 C30  SING N N 48 
COD C29 C31  SING N N 49 
COD C29 C32  SING N N 50 
COD C30 H301 SING N N 51 
COD C30 H302 SING N N 52 
COD C30 H303 SING N N 53 
COD C31 H311 SING N N 54 
COD C31 H312 SING N N 55 
COD C31 H313 SING N N 56 
COD C32 O33  SING N N 57 
COD C32 C34  SING N N 58 
COD C32 HC32 SING N N 59 
COD O33 HO33 SING N N 60 
COD C34 O35  DOUB N N 61 
COD C34 N36  SING N N 62 
COD N36 C37  SING N N 63 
COD N36 HN36 SING N N 64 
COD C37 C38  SING N N 65 
COD C37 H371 SING N N 66 
COD C37 H372 SING N N 67 
COD C38 C39  SING N N 68 
COD C38 H381 SING N N 69 
COD C38 H382 SING N N 70 
COD C39 O40  DOUB N N 71 
COD C39 N41  SING N N 72 
COD N41 C42  SING N N 73 
COD N41 HN41 SING N N 74 
COD C42 C43  SING N N 75 
COD C42 H421 SING N N 76 
COD C42 H422 SING N N 77 
COD C43 S44  SING N N 78 
COD C43 H431 SING N N 79 
COD C43 H432 SING N N 80 
COD S44 HS44 SING N N 81 
# 
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 
COD SMILES           ACDLabs              10.04 "O=C(NCCS)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O"                                                                                                                                                                                                 
COD SMILES_CANONICAL CACTVS               3.341 "CC(C)(CO[P@](O)(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCS"                                                                                                                                                                     
COD SMILES           CACTVS               3.341 "CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCS"                                                                                                                                                                              
COD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC(C)(CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)[C@H](C(=O)NCCC(=O)NCCS)O"                                                                                                                                                                   
COD SMILES           "OpenEye OEToolkits" 1.5.0 "CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)C(C(=O)NCCC(=O)NCCS)O"                                                                                                                                                                                                 
COD InChI            InChI                1.03  "InChI=1S/C21H35N7O13P2S/c1-21(2,16(32)19(33)24-4-3-12(29)23-5-6-44)8-39-43(36,37)41-42(34,35)38-7-11-14(30)15(31)20(40-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-32,44H,3-8H2,1-2H3,(H,23,29)(H,24,33)(H,34,35)(H,36,37)(H2,22,25,26)/t11-,14-,15-,16+,20-/m1/s1" 
COD InChIKey         InChI                1.03  KDTSHFARGAKYJN-IBOSZNHHSA-N                                                                                                                                                                                                                                                      
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
COD "SYSTEMATIC NAME" ACDLabs              10.04 "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)butyl dihydrogen diphosphate (non-preferred name)" 
COD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[(3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-[[3-oxo-3-(2-sulfanylethylamino)propyl]amino]butoxy]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 
COD "Create component"  1999-07-29 EBI  
COD "Modify descriptor" 2011-06-04 RCSB 
COD "Modify PCM"        2024-10-29 RCSB 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            COD 
_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               S44 
_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      ? 
# 
