data_COK
#
_chem_comp.id COK
_chem_comp.name
;[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL
(3R)-3-HYDROXY-4-{[3-({2-[(2-HYDROXYETHYL)DITHIO]ETHYL}AMINO)-3-OXOPROPYL]AMINO}-2,2-DIMETHYL-4-OXOBUTYL DIHYDROGEN
DIPHOSPHATE
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAC
_chem_comp.formula "C23 H40 N7 O17 P3 S2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "S-(THIOETHYLHYDROXY)COENZYME A"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2006-03-22
_chem_comp.pdbx_modified_date 2020-06-17
_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 843.652
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code COK
_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 2GES
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
# #
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
COK N6A AN6 N 0 1 N N N 37.568 38.917 -7.766 2.434 7.059 -2.700 N6A COK 1
COK C6A AC6 C 0 1 Y N N 38.357 37.854 -7.916 3.409 6.083 -2.809 C6A COK 2
COK N1A AN1 N 0 1 Y N N 37.962 36.816 -8.665 4.394 6.201 -3.693 N1A COK 3
COK C2A AC2 C 0 1 Y N N 38.730 35.747 -8.822 5.328 5.275 -3.804 C2A COK 4
COK N3A AN3 N 0 1 Y N N 39.916 35.670 -8.244 5.342 4.192 -3.055 N3A COK 5
COK C4A AC4 C 0 1 Y N N 40.376 36.670 -7.481 4.398 3.988 -2.143 C4A COK 6
COK C5A AC5 C 0 1 Y N N 39.597 37.808 -7.294 3.384 4.947 -1.982 C5A COK 7
COK N7A AN7 N 0 1 Y N N 40.273 38.628 -6.495 2.568 4.504 -0.996 N7A COK 8
COK C8A AC8 C 0 1 Y N N 41.426 38.038 -6.190 3.008 3.364 -0.548 C8A COK 9
COK N9A AN9 N 0 1 Y N N 41.495 36.848 -6.784 4.131 2.998 -1.230 N9A COK 10
COK C1B AC1* C 0 1 N N R 42.591 35.859 -6.656 4.917 1.781 -1.016 C1B COK 11
COK O4B AO4* O 0 1 N N N 42.701 35.348 -5.315 4.098 0.752 -0.420 O4B COK 12
COK C2B AC2* C 0 1 N N R 43.981 36.413 -6.967 6.038 2.039 0.015 C2B COK 13
COK O2B AO2* O 0 1 N N N 44.157 36.527 -8.382 7.279 2.290 -0.647 O2B COK 14
COK C3B AC3* C 0 1 N N S 44.807 35.262 -6.398 6.113 0.726 0.825 C3B COK 15
COK O3B AO3* O 0 1 N N N 44.722 34.133 -7.271 7.403 0.126 0.688 O3B COK 16
COK P3B AP3* P 0 1 N N N 46.050 33.569 -7.981 8.363 -0.184 1.942 P3B COK 17
COK O8A AO8 O 0 1 N N N 45.536 32.371 -8.925 7.636 -1.013 2.928 O8A COK 18
COK O9A AO9 O 0 1 N N N 46.946 32.897 -6.826 9.670 -0.975 1.435 O9A COK 19
COK O7A AO7 O 0 1 N N N 46.772 34.624 -8.727 8.809 1.202 2.632 O7A COK 20
COK C4B AC4* C 0 1 N N R 44.079 34.998 -5.079 5.028 -0.171 0.188 C4B COK 21
COK C5B AC5* C 0 1 N N N 44.619 35.903 -3.969 4.327 -1.004 1.263 C5B COK 22
COK O5B AO5* O 0 1 N N N 44.619 37.280 -4.357 3.358 -1.856 0.648 O5B COK 23
COK P1A AP1 P 0 1 N N S 45.314 38.384 -3.412 2.431 -2.874 1.482 P1A COK 24
COK O1A AO1 O 0 1 N N N 45.764 39.499 -4.275 1.702 -2.129 2.533 O1A COK 25
COK O2A AO2 O 0 1 N N N 46.335 37.700 -2.583 3.353 -4.003 2.165 O2A COK 26
COK O3A AO3 O 0 1 N N N 44.094 38.872 -2.475 1.373 -3.573 0.489 O3A COK 27
COK P2A AP2 P 0 1 N N R 43.805 38.246 -1.015 -0.032 -4.329 0.704 P2A COK 28
COK O4A AO4 O 0 1 N N N 44.979 38.440 -0.134 -0.870 -3.554 1.647 O4A COK 29
COK O5A AO5 O 0 1 N N N 43.301 36.865 -1.196 0.236 -5.798 1.307 O5A COK 30
COK O6A AO6 O 0 1 N N N 42.613 39.196 -0.493 -0.793 -4.459 -0.708 O6A COK 31
COK CCP PC12 C 0 1 N N N 41.258 38.842 -0.787 -2.113 -4.991 -0.835 CCP COK 32
COK CBP PC11 C 0 1 N N N 40.290 40.024 -0.692 -2.532 -4.971 -2.306 CBP COK 33
COK CDP PC13 C 0 1 N N N 40.332 40.596 0.728 -2.510 -3.531 -2.824 CDP COK 34
COK CEP PC14 C 0 1 N N N 38.881 39.503 -0.988 -1.559 -5.822 -3.125 CEP COK 35
COK CAP PC10 C 0 1 N N R 40.689 41.117 -1.692 -3.945 -5.540 -2.442 CAP COK 36
COK OAP PO10 O 0 1 N N N 41.023 40.528 -2.951 -3.938 -6.924 -2.085 OAP COK 37
COK C9P PC9 C 0 1 N N N 39.558 42.134 -1.889 -4.879 -4.791 -1.527 C9P COK 38
COK O9P PO9 O 0 1 N N N 38.650 41.911 -2.688 -5.364 -5.349 -0.566 O9P COK 39
COK N8P PN8 N 0 1 N N N 39.644 43.242 -1.158 -5.175 -3.500 -1.777 N8P COK 40
COK C7P PC7 C 0 1 N N N 38.620 44.297 -1.223 -6.004 -2.743 -0.836 C7P COK 41
COK C6P PC6 C 0 1 N N N 39.111 45.513 -2.011 -6.187 -1.314 -1.352 C6P COK 42
COK C5P PC5 C 0 1 N N N 39.295 45.211 -3.500 -7.040 -0.535 -0.384 C5P COK 43
COK O5P PO5 O 0 1 N N N 40.404 44.926 -3.951 -7.460 -1.070 0.620 O5P COK 44
COK N4P PN4 N 0 1 N N N 38.188 45.284 -4.234 -7.335 0.756 -0.634 N4P COK 45
COK C3P PC3 C 0 1 N N N 38.192 45.040 -5.684 -8.165 1.513 0.307 C3P COK 46
COK C2P PC2 C 0 1 N N N 37.717 43.621 -6.002 -8.347 2.941 -0.209 C2P COK 47
COK S1P PS1 S 0 1 N N N 37.878 43.220 -7.781 -9.374 3.878 0.956 S1P COK 48
COK S49 S49 S 0 1 N N N 39.847 43.546 -8.155 -8.144 4.098 2.581 S49 COK 49
COK C50 C50 C 0 1 N N N 40.854 42.044 -7.874 -7.173 5.571 2.162 C50 COK 50
COK C51 C51 C 0 1 N N N 42.108 42.310 -7.039 -8.072 6.807 2.214 C51 COK 51
COK O52 O52 O 0 1 N N N 41.734 42.800 -5.748 -7.307 7.968 1.884 O52 COK 52
COK HN61 1HN6 H 0 0 N N N 38.029 39.728 -8.128 2.464 7.841 -3.274 HN61 COK 53
COK HN62 2HN6 H 0 0 N N N 37.370 39.052 -6.795 1.718 6.960 -2.053 HN62 COK 54
COK H2 H2 H 0 1 N N N 38.381 34.927 -9.432 6.111 5.410 -4.536 H2 COK 55
COK H8 H8 H 0 1 N N N 42.191 38.461 -5.556 2.547 2.788 0.240 H8 COK 56
COK "H1'" H1* H 0 1 N N N 42.310 35.088 -7.389 5.339 1.432 -1.959 "H1'" COK 57
COK "H2'" H2* H 0 1 N N N 44.217 37.411 -6.569 5.776 2.876 0.663 "H2'" COK 58
COK H3 H3 H 0 1 N N N 43.307 36.552 -8.806 7.270 3.071 -1.218 H3 COK 59
COK "H3'" H3* H 0 1 N N N 45.880 35.470 -6.277 5.889 0.912 1.876 "H3'" COK 60
COK HO9 HO9 H 0 1 N N N 47.830 32.765 -7.147 10.295 -1.195 2.139 HO9 COK 61
COK HO7 HO7 H 0 1 N N N 46.927 35.367 -8.156 9.292 1.797 2.042 HO7 COK 62
COK "H4'" H4* H 0 1 N N N 44.211 33.952 -4.766 5.469 -0.820 -0.569 "H4'" COK 63
COK "H5'1" 1H5* H 0 0 N N N 45.657 35.606 -3.760 5.063 -1.611 1.789 "H5'1" COK 64
COK "H5'2" 2H5* H 0 0 N N N 43.982 35.788 -3.079 3.830 -0.340 1.970 "H5'2" COK 65
COK HO2 HO2 H 0 1 N N N 47.118 37.554 -3.101 3.860 -4.531 1.534 HO2 COK 66
COK HO5 HO5 H 0 1 N N N 43.193 36.686 -2.123 0.780 -6.362 0.741 HO5 COK 67
COK H121 1H12 H 0 0 N N N 40.943 38.099 -0.039 -2.128 -6.016 -0.467 H121 COK 68
COK H122 2H12 H 0 0 N N N 41.220 38.448 -1.813 -2.806 -4.385 -0.252 H122 COK 69
COK H131 1H13 H 0 0 N N N 39.444 41.223 0.897 -1.484 -3.164 -2.834 H131 COK 70
COK H132 2H13 H 0 0 N N N 41.240 41.205 0.851 -2.916 -3.502 -3.835 H132 COK 71
COK H133 3H13 H 0 0 N N N 40.342 39.771 1.456 -3.115 -2.902 -2.171 H133 COK 72
COK H141 1H14 H 0 0 N N N 38.950 38.534 -1.503 -1.618 -6.860 -2.797 H141 COK 73
COK H142 2H14 H 0 0 N N N 38.351 40.223 -1.629 -1.821 -5.759 -4.181 H142 COK 74
COK H143 3H14 H 0 0 N N N 38.330 39.378 -0.044 -0.543 -5.453 -2.980 H143 COK 75
COK H10 H10 H 0 1 N N N 41.563 41.645 -1.283 -4.283 -5.433 -3.473 H10 COK 76
COK H1 H1 H 0 1 N N N 41.097 41.208 -3.610 -3.647 -7.095 -1.179 H1 COK 77
COK HN8 HN8 H 0 1 N N N 40.427 43.361 -0.547 -4.839 -3.072 -2.580 HN8 COK 78
COK H71 1H7 H 0 1 N N N 38.393 44.620 -0.196 -6.978 -3.223 -0.743 H71 COK 79
COK H72 2H7 H 0 1 N N N 37.726 43.892 -1.719 -5.516 -2.717 0.139 H72 COK 80
COK H61 1H6 H 0 1 N N N 40.090 45.804 -1.604 -5.213 -0.834 -1.446 H61 COK 81
COK H62 2H6 H 0 1 N N N 38.369 46.318 -1.908 -6.674 -1.339 -2.327 H62 COK 82
COK HN4 HN4 H 0 1 N N N 37.324 45.512 -3.785 -6.999 1.184 -1.437 HN4 COK 83
COK H31 1H3 H 0 1 N N N 39.220 45.159 -6.057 -9.139 1.033 0.400 H31 COK 84
COK H32 2H3 H 0 1 N N N 37.517 45.760 -6.170 -7.677 1.538 1.282 H32 COK 85
COK H21 1H2 H 0 1 N N N 36.652 43.552 -5.734 -7.373 3.421 -0.303 H21 COK 86
COK H22 2H2 H 0 1 N N N 38.327 42.910 -5.426 -8.835 2.916 -1.184 H22 COK 87
COK H501 1H50 H 0 0 N N N 41.184 41.679 -8.858 -6.357 5.685 2.876 H501 COK 88
COK H502 2H50 H 0 0 N N N 40.234 41.308 -7.341 -6.763 5.462 1.158 H502 COK 89
COK H511 1H51 H 0 0 N N N 42.731 43.061 -7.547 -8.887 6.694 1.500 H511 COK 90
COK H512 2H51 H 0 0 N N N 42.675 41.375 -6.924 -8.482 6.916 3.218 H512 COK 91
COK H52 H52 H 0 1 N N N 41.651 42.071 -5.144 -7.815 8.791 1.897 H52 COK 92
# #
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
COK N6A C6A SING N N 1
COK N6A HN61 SING N N 2
COK N6A HN62 SING N N 3
COK C6A N1A SING Y N 4
COK C6A C5A DOUB Y N 5
COK N1A C2A DOUB Y N 6
COK C2A N3A SING Y N 7
COK C2A H2 SING N N 8
COK N3A C4A DOUB Y N 9
COK C4A C5A SING Y N 10
COK C4A N9A SING Y N 11
COK C5A N7A SING Y N 12
COK N7A C8A DOUB Y N 13
COK C8A N9A SING Y N 14
COK C8A H8 SING N N 15
COK N9A C1B SING N N 16
COK C1B O4B SING N N 17
COK C1B C2B SING N N 18
COK C1B "H1'" SING N N 19
COK O4B C4B SING N N 20
COK C2B O2B SING N N 21
COK C2B C3B SING N N 22
COK C2B "H2'" SING N N 23
COK O2B H3 SING N N 24
COK C3B O3B SING N N 25
COK C3B C4B SING N N 26
COK C3B "H3'" SING N N 27
COK O3B P3B SING N N 28
COK P3B O8A DOUB N N 29
COK P3B O9A SING N N 30
COK P3B O7A SING N N 31
COK O9A HO9 SING N N 32
COK O7A HO7 SING N N 33
COK C4B C5B SING N N 34
COK C4B "H4'" SING N N 35
COK C5B O5B SING N N 36
COK C5B "H5'1" SING N N 37
COK C5B "H5'2" SING N N 38
COK O5B P1A SING N N 39
COK P1A O1A DOUB N N 40
COK P1A O2A SING N N 41
COK P1A O3A SING N N 42
COK O2A HO2 SING N N 43
COK O3A P2A SING N N 44
COK P2A O4A DOUB N N 45
COK P2A O5A SING N N 46
COK P2A O6A SING N N 47
COK O5A HO5 SING N N 48
COK O6A CCP SING N N 49
COK CCP CBP SING N N 50
COK CCP H121 SING N N 51
COK CCP H122 SING N N 52
COK CBP CDP SING N N 53
COK CBP CEP SING N N 54
COK CBP CAP SING N N 55
COK CDP H131 SING N N 56
COK CDP H132 SING N N 57
COK CDP H133 SING N N 58
COK CEP H141 SING N N 59
COK CEP H142 SING N N 60
COK CEP H143 SING N N 61
COK CAP OAP SING N N 62
COK CAP C9P SING N N 63
COK CAP H10 SING N N 64
COK OAP H1 SING N N 65
COK C9P O9P DOUB N N 66
COK C9P N8P SING N N 67
COK N8P C7P SING N N 68
COK N8P HN8 SING N N 69
COK C7P C6P SING N N 70
COK C7P H71 SING N N 71
COK C7P H72 SING N N 72
COK C6P C5P SING N N 73
COK C6P H61 SING N N 74
COK C6P H62 SING N N 75
COK C5P O5P DOUB N N 76
COK C5P N4P SING N N 77
COK N4P C3P SING N N 78
COK N4P HN4 SING N N 79
COK C3P C2P SING N N 80
COK C3P H31 SING N N 81
COK C3P H32 SING N N 82
COK C2P S1P SING N N 83
COK C2P H21 SING N N 84
COK C2P H22 SING N N 85
COK S1P S49 SING N N 86
COK S49 C50 SING N N 87
COK C50 C51 SING N N 88
COK C50 H501 SING N N 89
COK C50 H502 SING N N 90
COK C51 O52 SING N N 91
COK C51 H511 SING N N 92
COK C51 H512 SING N N 93
COK O52 H52 SING N N 94
# #
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
COK SMILES ACDLabs 10.04 "O=C(NCCSSCCO)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O"
COK InChI InChI 1.03 "InChI=1S/C23H40N7O17P3S2/c1-23(2,18(34)21(35)26-4-3-14(32)25-5-7-51-52-8-6-31)10-44-50(41,42)47-49(39,40)43-9-13-17(46-48(36,37)38)16(33)22(45-13)30-12-29-15-19(24)27-11-28-20(15)30/h11-13,16-18,22,31,33-34H,3-10H2,1-2H3,(H,25,32)(H,26,35)(H,39,40)(H,41,42)(H2,24,27,28)(H2,36,37,38)/t13-,16-,17-,18+,22-/m1/s1"
COK InChIKey InChI 1.03 MQCDRNSLNTXXSJ-ZSJPKINUSA-N
COK SMILES_CANONICAL CACTVS 3.385 "CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCSSCCO"
COK SMILES CACTVS 3.385 "CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCSSCCO"
COK SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 "CC(C)(CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSSCCO)O"
COK SMILES "OpenEye OEToolkits" 1.7.5 "CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSSCCO)O"
# #
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
COK "SYSTEMATIC NAME" ACDLabs 10.04 "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-3-hydroxy-4-{[3-({2-[(2-hydroxyethyl)disulfanyl]ethyl}amino)-3-oxopropyl]amino}-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate (non-preferred name)"
COK "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxy-oxolan-2-yl]methyl [hydroxy-[(3R)-3-hydroxy-4-[[3-[2-(2-hydroxyethyldisulfanyl)ethylamino]-3-oxo-propyl]amino]-2,2-dimethyl-4-oxo-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
COK "Create component" 2006-03-22 RCSB
COK "Modify descriptor" 2011-06-04 RCSB
COK "Modify descriptor" 2012-01-05 RCSB
COK "Modify coordinates" 2012-01-05 RCSB
COK "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id COK
_pdbx_chem_comp_synonyms.name "S-(THIOETHYLHYDROXY)COENZYME A"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##