data_SOP
#
_chem_comp.id SOP
_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-2,2-DIMETHYL-4-OXO-4-{[3-OXO-3-({2-[(2-OXOPROPYL)THIO]ETHYL}AMINO)PROPYL]AMINO}BUTYL DIHYDROGEN
DIPHOSPHATE
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C24 H40 N7 O17 P3 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "S-(2-OXOPROPYL)-COENZYME A"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2006-03-24
_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 823.597
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SOP
_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 2FY5
_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
SOP N6 N6 N 0 1 N N N 27.821 -6.200 79.272 -11.812 -0.822 -4.663 N6 SOP 1
SOP C6 C6 C 0 1 Y N N 28.405 -6.066 78.092 -11.270 0.185 -3.884 C6 SOP 2
SOP N1 N1 N 0 1 Y N N 29.754 -5.900 77.999 -11.849 1.379 -3.817 N1 SOP 3
SOP C2 C2 C 0 1 Y N N 30.366 -5.759 76.817 -11.339 2.346 -3.077 C2 SOP 4
SOP N3 N3 N 0 1 Y N N 29.638 -5.789 75.672 -10.240 2.189 -2.369 N3 SOP 5
SOP C4 C4 C 0 1 Y N N 28.292 -5.947 75.694 -9.594 1.028 -2.369 C4 SOP 6
SOP C5 C5 C 0 1 Y N N 27.638 -6.099 76.924 -10.094 -0.031 -3.146 C5 SOP 7
SOP N7 N7 N 0 1 Y N N 26.352 -6.243 76.686 -9.256 -1.082 -2.975 N7 SOP 8
SOP C8 C8 C 0 1 Y N N 26.178 -6.190 75.361 -8.295 -0.742 -2.166 C8 SOP 9
SOP N9 N9 N 0 1 Y N N 27.344 -6.016 74.738 -8.457 0.552 -1.768 N9 SOP 10
SOP "C1'" C1* C 0 1 N N R 27.548 -5.900 73.264 -7.581 1.295 -0.859 "C1'" SOP 11
SOP "O4'" O4* O 0 1 N N N 26.904 -4.736 72.695 -6.255 0.723 -0.849 "O4'" SOP 12
SOP "C2'" C2* C 0 1 N N R 27.003 -7.048 72.388 -8.053 1.138 0.609 "C2'" SOP 13
SOP "O2'" O2* O 0 1 N N N 27.838 -8.205 72.469 -9.049 2.111 0.931 "O2'" SOP 14
SOP "C3'" C3* C 0 1 N N S 27.021 -6.399 71.015 -6.745 1.403 1.401 "C3'" SOP 15
SOP "O3'" O3* O 0 1 N N N 28.320 -6.446 70.424 -6.704 2.756 1.860 "O3'" SOP 16
SOP P3 P3 P 0 1 N N N 28.459 -6.262 68.829 -6.576 2.700 3.464 P3 SOP 17
SOP O32 O32 O 0 1 N N N 28.452 -4.670 68.516 -5.167 2.035 3.867 O32 SOP 18
SOP O33 O33 O 0 1 N N N 29.906 -6.853 68.459 -6.656 4.193 4.061 O33 SOP 19
SOP O31 O31 O 0 1 N N N 27.360 -6.977 68.116 -7.682 1.887 4.018 O31 SOP 20
SOP "C4'" C4* C 0 1 N N R 26.557 -4.982 71.299 -5.627 1.140 0.374 "C4'" SOP 21
SOP "C5'" C5* C 0 1 N N N 25.038 -4.919 71.120 -4.700 0.036 0.886 "C5'" SOP 22
SOP "O5'" O5* O 0 1 N N N 24.530 -3.861 71.915 -3.606 -0.125 -0.019 "O5'" SOP 23
SOP P1 P1 P 0 1 N N R 23.170 -4.017 72.752 -2.676 -1.296 0.578 P1 SOP 24
SOP O11 O11 O 0 1 N N N 23.144 -2.887 73.708 -3.490 -2.686 0.567 O11 SOP 25
SOP O12 O12 O 0 1 N N N 23.132 -5.361 73.355 -2.292 -0.961 1.967 O12 SOP 26
SOP O6 O6 O 0 1 N N N 22.070 -3.778 71.604 -1.351 -1.443 -0.325 O6 SOP 27
SOP P2 P2 P 0 1 N N S 21.120 -4.910 70.997 -0.303 -2.320 0.526 P2 SOP 28
SOP O21 O21 O 0 1 N N N 21.078 -6.104 71.838 -0.681 -3.880 0.400 O21 SOP 29
SOP O22 O22 O 0 1 N N N 21.606 -5.081 69.610 -0.359 -1.913 1.948 O22 SOP 30
SOP O7 O7 O 0 1 N N N 19.709 -4.186 71.027 1.184 -2.080 -0.042 O7 SOP 31
SOP CP9 CP9 C 0 1 N N N 18.775 -4.401 72.093 2.076 -2.786 0.822 CP9 SOP 32
SOP CP8 CP8 C 0 1 N N N 17.361 -4.318 71.501 3.514 -2.598 0.335 CP8 SOP 33
SOP CPB CPB C 0 1 N N N 17.173 -2.904 70.900 3.645 -3.143 -1.089 CPB SOP 34
SOP CPA CPA C 0 1 N N N 16.328 -4.539 72.616 3.866 -1.109 0.346 CPA SOP 35
SOP CP7 CP7 C 0 1 N N R 17.277 -5.424 70.408 4.469 -3.355 1.260 CP7 SOP 36
SOP OP3 OP3 O 0 1 N N N 17.247 -6.736 70.986 4.056 -4.720 1.358 OP3 SOP 37
SOP CP6 CP6 C 0 1 N N N 16.059 -5.280 69.499 5.867 -3.292 0.700 CP6 SOP 38
SOP OP2 OP2 O 0 1 N N N 14.994 -5.879 69.726 6.358 -4.273 0.184 OP2 SOP 39
SOP NP2 NP2 N 0 1 N N N 16.303 -4.448 68.469 6.570 -2.144 0.773 NP2 SOP 40
SOP CP5 CP5 C 0 1 N N N 15.293 -4.143 67.457 7.913 -2.070 0.191 CP5 SOP 41
SOP CP4 CP4 C 0 1 N N N 14.658 -2.806 67.822 8.487 -0.669 0.409 CP4 SOP 42
SOP CP3 CP3 C 0 1 N N N 13.557 -2.482 66.821 9.868 -0.593 -0.190 CP3 SOP 43
SOP OP1 OP1 O 0 1 N N N 12.565 -3.217 66.751 10.346 -1.564 -0.737 OP1 SOP 44
SOP NP1 NP1 N 0 1 N N N 13.737 -1.391 66.074 10.571 0.554 -0.117 NP1 SOP 45
SOP CP2 CP2 C 0 1 N N N 12.741 -0.949 65.063 11.914 0.628 -0.699 CP2 SOP 46
SOP CP1 CP1 C 0 1 N N N 11.454 -0.490 65.787 12.488 2.030 -0.481 CP1 SOP 47
SOP S S S 0 1 N N N 10.141 0.048 64.671 14.150 2.121 -1.202 S SOP 48
SOP CA1 CA1 C 0 1 N N N 10.262 1.787 64.401 14.570 3.841 -0.806 CA1 SOP 49
SOP CA2 CA2 C 0 1 N N N 10.535 2.304 63.011 15.951 4.152 -1.324 CA2 SOP 50
SOP OA1 OA1 O 0 1 N N N 11.666 2.601 62.688 16.585 3.302 -1.901 OA1 SOP 51
SOP CA3 CA3 C 0 1 N N N 9.283 2.383 62.172 16.539 5.525 -1.122 CA3 SOP 52
SOP HN61 1HN6 H 0 0 N N N 27.215 -5.421 79.434 -11.381 -1.690 -4.703 HN61 SOP 53
SOP HN62 2HN6 H 0 0 N N N 28.519 -6.234 79.988 -12.625 -0.661 -5.168 HN62 SOP 54
SOP H2 H2 H 0 1 N N N 31.436 -5.622 76.775 -11.842 3.302 -3.051 H2 SOP 55
SOP H8 H8 H 0 1 N N N 25.223 -6.276 74.864 -7.488 -1.389 -1.857 H8 SOP 56
SOP "H1'" H1* H 0 1 N N N 28.647 -5.880 73.233 -7.543 2.347 -1.139 "H1'" SOP 57
SOP "H2'" H2* H 0 1 N N N 26.012 -7.425 72.680 -8.423 0.130 0.794 "H2'" SOP 58
SOP "HO2'" HO2* H 0 0 N N N 28.023 -8.524 71.594 -9.798 1.949 0.342 "HO2'" SOP 59
SOP "H3'" H3* H 0 1 N N N 26.380 -6.911 70.282 -6.661 0.714 2.241 "H3'" SOP 60
SOP HO32 HO32 H 0 0 N N N 28.451 -4.186 69.334 -4.475 2.594 3.487 HO32 SOP 61
SOP HO33 HO33 H 0 0 N N N 29.970 -6.970 67.518 -6.576 4.114 5.022 HO33 SOP 62
SOP "H4'" H4* H 0 1 N N N 27.017 -4.240 70.630 -5.056 2.054 0.205 "H4'" SOP 63
SOP "H5'1" 1H5* H 0 0 N N N 24.585 -5.872 71.431 -5.254 -0.900 0.957 "H5'1" SOP 64
SOP "H5'2" 2H5* H 0 0 N N N 24.796 -4.738 70.062 -4.319 0.308 1.871 "H5'2" SOP 65
SOP HO11 HO11 H 0 0 N N N 23.138 -3.223 74.596 -3.721 -2.867 -0.354 HO11 SOP 66
SOP HO21 HO21 H 0 0 N N N 21.069 -6.879 71.288 -0.632 -4.104 -0.540 HO21 SOP 67
SOP HP91 1HP9 H 0 0 N N N 18.907 -3.642 72.878 1.825 -3.847 0.814 HP91 SOP 68
SOP HP92 2HP9 H 0 0 N N N 18.938 -5.392 72.543 1.982 -2.399 1.836 HP92 SOP 69
SOP HPB1 1HPB H 0 0 N N N 16.237 -2.873 70.323 3.395 -4.204 -1.097 HPB1 SOP 70
SOP HPB2 2HPB H 0 0 N N N 18.020 -2.672 70.238 2.965 -2.604 -1.748 HPB2 SOP 71
SOP HPB3 3HPB H 0 0 N N N 17.128 -2.163 71.712 4.670 -3.009 -1.436 HPB3 SOP 72
SOP HPA1 1HPA H 0 0 N N N 15.789 -5.481 72.435 4.838 -0.962 -0.124 HPA1 SOP 73
SOP HPA2 2HPA H 0 0 N N N 15.613 -3.703 72.624 3.108 -0.553 -0.206 HPA2 SOP 74
SOP HPA3 3HPA H 0 0 N N N 16.842 -4.592 73.587 3.901 -0.752 1.375 HPA3 SOP 75
SOP HP7 HP7 H 0 1 N N N 18.186 -5.293 69.802 4.453 -2.899 2.250 HP7 SOP 76
SOP HOP3 HOP3 H 0 0 N N N 17.240 -7.387 70.294 4.084 -5.085 0.463 HOP3 SOP 77
SOP HNP2 HNP2 H 0 0 N N N 17.206 -4.024 68.394 6.188 -1.368 1.210 HNP2 SOP 78
SOP HP51 1HP5 H 0 0 N N N 14.530 -4.935 67.426 7.857 -2.278 -0.878 HP51 SOP 79
SOP HP52 2HP5 H 0 0 N N N 15.762 -4.079 66.464 8.558 -2.806 0.671 HP52 SOP 80
SOP HP41 1HP4 H 0 0 N N N 15.423 -2.016 67.797 8.542 -0.461 1.477 HP41 SOP 81
SOP HP42 2HP4 H 0 0 N N N 14.229 -2.866 68.833 7.841 0.067 -0.072 HP42 SOP 82
SOP HNP1 HNP1 H 0 0 N N N 14.570 -0.852 66.199 10.189 1.331 0.320 HNP1 SOP 83
SOP HP21 1HP2 H 0 0 N N N 12.507 -1.783 64.385 11.858 0.420 -1.768 HP21 SOP 84
SOP HP22 2HP2 H 0 0 N N N 13.154 -0.113 64.479 12.559 -0.107 -0.219 HP22 SOP 85
SOP HP11 1HP1 H 0 0 N N N 11.725 0.377 66.408 12.543 2.237 0.588 HP11 SOP 86
SOP HP12 2HP1 H 0 0 N N N 11.074 -1.338 66.376 11.842 2.765 -0.961 HP12 SOP 87
SOP HA11 1HA1 H 0 0 N N N 11.153 2.083 64.974 14.548 3.981 0.275 HA11 SOP 88
SOP HA12 2HA1 H 0 0 N N N 9.295 2.214 64.704 13.847 4.509 -1.274 HA12 SOP 89
SOP HA31 1HA3 H 0 0 N N N 9.229 1.505 61.511 16.277 6.161 -1.968 HA31 SOP 90
SOP HA32 2HA3 H 0 0 N N N 9.307 3.299 61.564 16.143 5.959 -0.204 HA32 SOP 91
SOP HA33 3HA3 H 0 0 N N N 8.401 2.402 62.829 17.624 5.448 -1.049 HA33 SOP 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
SOP N6 C6 SING N N 1
SOP N6 HN61 SING N N 2
SOP N6 HN62 SING N N 3
SOP C6 N1 SING Y N 4
SOP C6 C5 DOUB Y N 5
SOP N1 C2 DOUB Y N 6
SOP C2 N3 SING Y N 7
SOP C2 H2 SING N N 8
SOP N3 C4 DOUB Y N 9
SOP C4 C5 SING Y N 10
SOP C4 N9 SING Y N 11
SOP C5 N7 SING Y N 12
SOP N7 C8 DOUB Y N 13
SOP C8 N9 SING Y N 14
SOP C8 H8 SING N N 15
SOP N9 "C1'" SING N N 16
SOP "C1'" "O4'" SING N N 17
SOP "C1'" "C2'" SING N N 18
SOP "C1'" "H1'" SING N N 19
SOP "O4'" "C4'" SING N N 20
SOP "C2'" "O2'" SING N N 21
SOP "C2'" "C3'" SING N N 22
SOP "C2'" "H2'" SING N N 23
SOP "O2'" "HO2'" SING N N 24
SOP "C3'" "O3'" SING N N 25
SOP "C3'" "C4'" SING N N 26
SOP "C3'" "H3'" SING N N 27
SOP "O3'" P3 SING N N 28
SOP P3 O32 SING N N 29
SOP P3 O33 SING N N 30
SOP P3 O31 DOUB N N 31
SOP O32 HO32 SING N N 32
SOP O33 HO33 SING N N 33
SOP "C4'" "C5'" SING N N 34
SOP "C4'" "H4'" SING N N 35
SOP "C5'" "O5'" SING N N 36
SOP "C5'" "H5'1" SING N N 37
SOP "C5'" "H5'2" SING N N 38
SOP "O5'" P1 SING N N 39
SOP P1 O11 SING N N 40
SOP P1 O12 DOUB N N 41
SOP P1 O6 SING N N 42
SOP O11 HO11 SING N N 43
SOP O6 P2 SING N N 44
SOP P2 O21 SING N N 45
SOP P2 O22 DOUB N N 46
SOP P2 O7 SING N N 47
SOP O21 HO21 SING N N 48
SOP O7 CP9 SING N N 49
SOP CP9 CP8 SING N N 50
SOP CP9 HP91 SING N N 51
SOP CP9 HP92 SING N N 52
SOP CP8 CPB SING N N 53
SOP CP8 CPA SING N N 54
SOP CP8 CP7 SING N N 55
SOP CPB HPB1 SING N N 56
SOP CPB HPB2 SING N N 57
SOP CPB HPB3 SING N N 58
SOP CPA HPA1 SING N N 59
SOP CPA HPA2 SING N N 60
SOP CPA HPA3 SING N N 61
SOP CP7 OP3 SING N N 62
SOP CP7 CP6 SING N N 63
SOP CP7 HP7 SING N N 64
SOP OP3 HOP3 SING N N 65
SOP CP6 OP2 DOUB N N 66
SOP CP6 NP2 SING N N 67
SOP NP2 CP5 SING N N 68
SOP NP2 HNP2 SING N N 69
SOP CP5 CP4 SING N N 70
SOP CP5 HP51 SING N N 71
SOP CP5 HP52 SING N N 72
SOP CP4 CP3 SING N N 73
SOP CP4 HP41 SING N N 74
SOP CP4 HP42 SING N N 75
SOP CP3 OP1 DOUB N N 76
SOP CP3 NP1 SING N N 77
SOP NP1 CP2 SING N N 78
SOP NP1 HNP1 SING N N 79
SOP CP2 CP1 SING N N 80
SOP CP2 HP21 SING N N 81
SOP CP2 HP22 SING N N 82
SOP CP1 S SING N N 83
SOP CP1 HP11 SING N N 84
SOP CP1 HP12 SING N N 85
SOP S CA1 SING N N 86
SOP CA1 CA2 SING N N 87
SOP CA1 HA11 SING N N 88
SOP CA1 HA12 SING N N 89
SOP CA2 OA1 DOUB N N 90
SOP CA2 CA3 SING N N 91
SOP CA3 HA31 SING N N 92
SOP CA3 HA32 SING N N 93
SOP CA3 HA33 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
SOP SMILES ACDLabs 10.04 "O=C(C)CSCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O"
SOP SMILES_CANONICAL CACTVS 3.341 "CC(=O)CSCCNC(=O)CCNC(=O)[C@H](O)C(C)(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"
SOP SMILES CACTVS 3.341 "CC(=O)CSCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23"
SOP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC(=O)CSCCNC(=O)CCNC(=O)[C@@H](C(C)(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)O"
SOP SMILES "OpenEye OEToolkits" 1.5.0 "CC(=O)CSCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O"
SOP InChI InChI 1.03 "InChI=1S/C24H40N7O17P3S/c1-13(32)9-52-7-6-26-15(33)4-5-27-22(36)19(35)24(2,3)10-45-51(42,43)48-50(40,41)44-8-14-18(47-49(37,38)39)17(34)23(46-14)31-12-30-16-20(25)28-11-29-21(16)31/h11-12,14,17-19,23,34-35H,4-10H2,1-3H3,(H,26,33)(H,27,36)(H,40,41)(H,42,43)(H2,25,28,29)(H2,37,38,39)/t14-,17-,18-,19+,23-/m1/s1"
SOP InChIKey InChI 1.03 GAMKENBUYYJLCQ-NDZSKPAWSA-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
SOP "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-2,2-dimethyl-4-oxo-4-{[3-oxo-3-({2-[(2-oxopropyl)sulfanyl]ethyl}amino)propyl]amino}butyl dihydrogen diphosphate (non-preferred name)"
SOP "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-2,2-dimethyl-4-oxo-4-[[3-oxo-3-[2-(2-oxopropylsulfanyl)ethylamino]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
SOP "Create component" 2006-03-24 RCSB
SOP "Modify descriptor" 2011-06-04 RCSB
SOP "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id SOP
_pdbx_chem_comp_synonyms.name "S-(2-OXOPROPYL)-COENZYME A"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##