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 ?
#