data_YAS # _chem_comp.id YAS _chem_comp.name "~{S}-[2-[3-[[(2~{R})-4-[[[(2~{S},3~{R},4~{S},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] butanethioate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C25 H42 N7 O17 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms Butyryl-CoA _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-12-06 _chem_comp.pdbx_modified_date 2021-03-01 _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 837.624 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YAS _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 6NA4 _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 YAS C1B C1 C 0 1 N N R -17.529 8.515 -4.241 -7.172 0.303 -0.846 C1B YAS 1 YAS C2A C2 C 0 1 Y N N -15.473 11.540 -6.443 -9.306 -1.740 -4.225 C2A YAS 2 YAS C2B C3 C 0 1 N N S -18.785 8.840 -4.070 -8.027 -0.272 0.305 C2B YAS 3 YAS C2P C4 C 0 1 N N N -16.078 -10.760 -7.033 10.271 -1.955 -0.248 C2P YAS 4 YAS C3B C5 C 0 1 N N R -19.123 8.077 -2.809 -7.003 -0.553 1.428 C3B YAS 5 YAS C3P C6 C 0 1 N N N -16.868 -10.342 -5.787 9.702 -0.647 0.307 C3P YAS 6 YAS C4A C7 C 0 1 Y N N -16.358 9.439 -6.135 -7.581 -1.281 -2.777 C4A YAS 7 YAS C4B C8 C 0 1 N N S -18.437 6.741 -3.229 -5.652 -0.115 0.822 C4B YAS 8 YAS C5A C9 C 0 1 Y N N -15.930 9.034 -7.386 -6.803 -2.266 -3.409 C5A YAS 9 YAS C5B C10 C 0 1 N N N -18.435 5.576 -2.202 -4.777 0.542 1.893 C5B YAS 10 YAS C5P C11 C 0 1 N N N -16.039 -7.994 -5.341 7.996 0.986 -0.291 C5P YAS 11 YAS C6A C12 C 0 1 Y N N -15.243 9.986 -8.163 -7.368 -2.965 -4.490 C6A YAS 12 YAS C6P C13 C 0 1 N N N -16.317 -6.490 -5.318 6.909 1.489 -1.206 C6P YAS 13 YAS C7P C14 C 0 1 N N N -17.013 -6.052 -4.025 6.340 2.796 -0.651 C7P YAS 14 YAS C8A C15 C 0 1 Y N N -16.956 7.373 -6.420 -5.598 -1.411 -1.822 C8A YAS 15 YAS C9P C16 C 0 1 N N N -16.416 -3.665 -3.623 4.634 4.430 -1.249 C9P YAS 16 YAS CAD C17 C 0 1 N N N -18.547 -11.484 -8.472 12.027 -3.987 0.021 CAD YAS 17 YAS CAF C18 C 0 1 N N N -19.770 -11.142 -9.332 13.120 -4.865 0.571 CAF YAS 18 YAS CAI C19 C 0 1 N N N -21.779 -11.974 -10.652 14.434 -6.959 0.205 CAI YAS 19 YAS CAJ C20 C 0 1 N N N -20.804 -12.259 -9.490 13.324 -6.067 -0.354 CAJ YAS 20 YAS CAP C21 C 0 1 N N R -16.763 -2.178 -3.629 3.466 4.870 -2.095 CAP YAS 21 YAS CBP C22 C 0 1 N N N -16.130 -1.396 -4.796 2.277 3.939 -1.846 CBP YAS 22 YAS CCP C23 C 0 1 N N N -16.588 0.047 -4.662 1.969 3.895 -0.348 CCP YAS 23 YAS CDP C24 C 0 1 N N N -16.541 -1.918 -6.165 1.054 4.461 -2.603 CDP YAS 24 YAS CEP C25 C 0 1 N N N -14.601 -1.395 -4.734 2.619 2.532 -2.339 CEP YAS 25 YAS N1A N1 N 0 1 Y N N -15.046 11.200 -7.652 -8.612 -2.672 -4.853 N1A YAS 26 YAS N3A N2 N 0 1 Y N N -16.125 10.679 -5.675 -8.815 -1.054 -3.215 N3A YAS 27 YAS N4P N3 N 0 1 N N N -17.087 -8.901 -5.767 8.645 -0.159 -0.582 N4P YAS 28 YAS N6A N4 N 0 1 N N N -14.756 9.660 -9.490 -6.648 -3.943 -5.154 N6A YAS 29 YAS N7A N5 N 0 1 Y N N -16.319 7.747 -7.530 -5.605 -2.294 -2.777 N7A YAS 30 YAS N8P N6 N 0 1 N N N -17.391 -4.647 -4.070 5.283 3.285 -1.540 N8P YAS 31 YAS N9A N7 N 0 1 Y N N -16.997 8.408 -5.585 -6.795 -0.759 -1.781 N9A YAS 32 YAS O1A O1 O 0 1 N N N -19.467 2.956 -4.849 -2.803 2.802 2.765 O1A YAS 33 YAS O2A O2 O 0 1 N N N -17.322 4.169 -4.633 -1.853 0.546 3.379 O2A YAS 34 YAS O2B O3 O 0 1 N N N -19.743 8.387 -5.153 -8.667 -1.482 -0.104 O2B YAS 35 YAS O3A O4 O 0 1 N N N -17.877 2.256 -2.983 -1.058 1.825 1.224 O3A YAS 36 YAS O3B O5 O 0 1 N N N -20.465 8.021 -2.763 -6.981 -1.946 1.747 O3B YAS 37 YAS O4A O6 O 0 1 N N N -15.862 2.016 -1.392 1.362 1.975 2.241 O4A YAS 38 YAS O4B O7 O 0 1 N N N -17.252 7.153 -3.417 -5.999 0.844 -0.200 O4B YAS 39 YAS O5A O8 O 0 1 N N N -15.371 2.810 -3.671 -0.091 4.025 1.998 O5A YAS 40 YAS O5B O9 O 0 1 N N N -19.164 4.540 -2.805 -3.490 0.834 1.343 O5B YAS 41 YAS O5P O10 O 0 1 N N N -14.973 -8.408 -4.994 8.287 1.612 0.706 O5P YAS 42 YAS O6A O11 O 0 1 N N N -16.180 0.372 -3.368 0.859 3.026 -0.116 O6A YAS 43 YAS O7A O12 O 0 1 N N N -21.074 9.740 -0.873 -6.157 -2.007 4.243 O7A YAS 44 YAS O8A O13 O 0 1 N N N -22.718 8.064 -1.640 -8.615 -2.018 3.670 O8A YAS 45 YAS O9A O14 O 0 1 N N N -20.724 7.376 -0.298 -7.307 -4.122 3.186 O9A YAS 46 YAS O9P O15 O 0 1 N N N -15.361 -4.043 -3.237 4.989 5.106 -0.308 O9P YAS 47 YAS OAE O16 O 0 1 N N N -18.546 -12.456 -7.777 11.465 -4.291 -1.011 OAE YAS 48 YAS OAP O17 O 0 1 N N N -18.168 -2.070 -3.643 3.104 6.208 -1.748 OAP YAS 49 YAS P1A P1 P 0 1 N N N -18.451 3.502 -3.874 -2.312 1.530 2.190 P1A YAS 50 YAS P2A P2 P 0 1 N N N -16.278 1.922 -2.840 0.260 2.741 1.351 P2A YAS 51 YAS P3B P3 P 0 1 N N N -21.262 8.316 -1.349 -7.294 -2.512 3.221 P3B YAS 52 YAS S1P S1 S 0 1 N N N -17.089 -10.401 -8.500 11.577 -2.558 0.851 S1P YAS 53 YAS H1 H1 H 0 1 N N N -16.914 9.271 -3.731 -7.717 1.092 -1.366 H1 YAS 54 YAS H2 H2 H 0 1 N N N -15.286 12.539 -6.077 -10.313 -1.531 -4.556 H2 YAS 55 YAS H3 H3 H 0 1 N N N -18.921 9.917 -3.892 -8.765 0.459 0.635 H3 YAS 56 YAS H4 H4 H 0 1 N N N -15.857 -11.837 -6.989 9.477 -2.699 -0.311 H4 YAS 57 YAS H5 H5 H 0 1 N N N -15.136 -10.194 -7.083 10.684 -1.778 -1.241 H5 YAS 58 YAS H6 H6 H 0 1 N N N -18.644 8.513 -1.920 -7.237 0.037 2.314 H6 YAS 59 YAS H7 H7 H 0 1 N N N -17.842 -10.854 -5.790 9.289 -0.823 1.300 H7 YAS 60 YAS H8 H8 H 0 1 N N N -16.303 -10.633 -4.889 10.496 0.097 0.371 H8 YAS 61 YAS H9 H9 H 0 1 N N N -18.913 6.385 -4.154 -5.137 -0.970 0.384 H9 YAS 62 YAS H10 H10 H 0 1 N N N -17.405 5.250 -1.993 -5.246 1.466 2.229 H10 YAS 63 YAS H11 H11 H 0 1 N N N -18.917 5.890 -1.265 -4.665 -0.138 2.737 H11 YAS 64 YAS H12 H12 H 0 1 N N N -15.362 -5.951 -5.407 7.322 1.665 -2.199 H12 YAS 65 YAS H13 H13 H 0 1 N N N -16.962 -6.235 -6.172 6.115 0.745 -1.269 H13 YAS 66 YAS H14 H14 H 0 1 N N N -17.918 -6.661 -3.883 5.926 2.620 0.342 H14 YAS 67 YAS H15 H15 H 0 1 N N N -16.328 -6.210 -3.179 7.134 3.540 -0.587 H15 YAS 68 YAS H16 H16 H 0 1 N N N -17.370 6.394 -6.230 -4.767 -1.222 -1.159 H16 YAS 69 YAS H17 H17 H 0 1 N N N -19.412 -10.869 -10.335 14.047 -4.295 0.635 H17 YAS 70 YAS H18 H18 H 0 1 N N N -20.274 -10.278 -8.875 12.840 -5.215 1.565 H18 YAS 71 YAS H19 H19 H 0 1 N N N -22.504 -12.797 -10.733 14.153 -7.309 1.198 H19 YAS 72 YAS H20 H20 H 0 1 N N N -22.313 -11.032 -10.459 14.579 -7.815 -0.454 H20 YAS 73 YAS H21 H21 H 0 1 N N N -21.214 -11.889 -11.592 15.361 -6.389 0.269 H21 YAS 74 YAS H22 H22 H 0 1 N N N -21.379 -12.348 -8.556 12.397 -6.637 -0.418 H22 YAS 75 YAS H23 H23 H 0 1 N N N -20.279 -13.205 -9.689 13.604 -5.717 -1.348 H23 YAS 76 YAS H24 H24 H 0 1 N N N -16.378 -1.743 -2.695 3.745 4.830 -3.148 H24 YAS 77 YAS H25 H25 H 0 1 N N N -16.098 0.691 -5.407 2.841 3.523 0.191 H25 YAS 78 YAS H26 H26 H 0 1 N N N -17.680 0.129 -4.767 1.725 4.897 0.003 H26 YAS 79 YAS H27 H27 H 0 1 N N N -17.638 -1.930 -6.239 0.186 3.849 -2.357 H27 YAS 80 YAS H28 H28 H 0 1 N N N -16.128 -1.263 -6.946 0.863 5.495 -2.316 H28 YAS 81 YAS H29 H29 H 0 1 N N N -16.153 -2.939 -6.300 1.242 4.411 -3.676 H29 YAS 82 YAS H30 H30 H 0 1 N N N -14.274 -1.021 -3.753 1.740 1.893 -2.253 H30 YAS 83 YAS H31 H31 H 0 1 N N N -14.228 -2.419 -4.879 2.935 2.578 -3.381 H31 YAS 84 YAS H32 H32 H 0 1 N N N -14.202 -0.744 -5.526 3.427 2.121 -1.733 H32 YAS 85 YAS H33 H33 H 0 1 N N N -17.972 -8.533 -6.051 8.412 -0.659 -1.380 H33 YAS 86 YAS H34 H34 H 0 1 N N N -14.297 10.457 -9.882 -7.051 -4.424 -5.894 H34 YAS 87 YAS H35 H35 H 0 1 N N N -14.110 8.899 -9.430 -5.741 -4.148 -4.879 H35 YAS 88 YAS H36 H36 H 0 1 N N N -18.293 -4.366 -4.398 5.050 2.784 -2.338 H36 YAS 89 YAS H37 H37 H 0 1 N N N -17.487 4.106 -5.566 -1.519 -0.309 3.075 H37 YAS 90 YAS H38 H38 H 0 1 N N N -20.623 8.671 -4.936 -9.276 -1.374 -0.847 H38 YAS 91 YAS H39 H39 H 0 1 N N N -15.124 2.609 -1.312 1.640 1.124 1.876 H39 YAS 92 YAS H40 H40 H 0 1 N N N -21.915 10.182 -0.856 -5.263 -2.295 4.011 H40 YAS 93 YAS H41 H41 H 0 1 N N N -21.416 6.791 -0.012 -7.490 -4.533 4.042 H41 YAS 94 YAS H42 H42 H 0 1 N N N -18.531 -2.560 -2.915 2.844 6.318 -0.823 H42 YAS 95 # # 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 YAS CAI CAJ SING N N 1 YAS CAJ CAF SING N N 2 YAS N6A C6A SING N N 3 YAS CAF CAD SING N N 4 YAS S1P CAD SING N N 5 YAS S1P C2P SING N N 6 YAS CAD OAE DOUB N N 7 YAS C6A N1A DOUB Y N 8 YAS C6A C5A SING Y N 9 YAS N1A C2A SING Y N 10 YAS N7A C5A SING Y N 11 YAS N7A C8A DOUB Y N 12 YAS C5A C4A DOUB Y N 13 YAS C2P C3P SING N N 14 YAS C2A N3A DOUB Y N 15 YAS C8A N9A SING Y N 16 YAS CDP CBP SING N N 17 YAS C4A N3A SING Y N 18 YAS C4A N9A SING Y N 19 YAS C3P N4P SING N N 20 YAS N4P C5P SING N N 21 YAS N9A C1B SING N N 22 YAS C5P C6P SING N N 23 YAS C5P O5P DOUB N N 24 YAS C6P C7P SING N N 25 YAS O2B C2B SING N N 26 YAS O1A P1A DOUB N N 27 YAS CBP CEP SING N N 28 YAS CBP CCP SING N N 29 YAS CBP CAP SING N N 30 YAS CCP O6A SING N N 31 YAS O2A P1A SING N N 32 YAS C1B C2B SING N N 33 YAS C1B O4B SING N N 34 YAS C2B C3B SING N N 35 YAS N8P C7P SING N N 36 YAS N8P C9P SING N N 37 YAS P1A O3A SING N N 38 YAS P1A O5B SING N N 39 YAS O5A P2A DOUB N N 40 YAS OAP CAP SING N N 41 YAS CAP C9P SING N N 42 YAS C9P O9P DOUB N N 43 YAS O4B C4B SING N N 44 YAS O6A P2A SING N N 45 YAS C4B C3B SING N N 46 YAS C4B C5B SING N N 47 YAS O3A P2A SING N N 48 YAS P2A O4A SING N N 49 YAS C3B O3B SING N N 50 YAS O5B C5B SING N N 51 YAS O3B P3B SING N N 52 YAS O8A P3B DOUB N N 53 YAS P3B O7A SING N N 54 YAS P3B O9A SING N N 55 YAS C1B H1 SING N N 56 YAS C2A H2 SING N N 57 YAS C2B H3 SING N N 58 YAS C2P H4 SING N N 59 YAS C2P H5 SING N N 60 YAS C3B H6 SING N N 61 YAS C3P H7 SING N N 62 YAS C3P H8 SING N N 63 YAS C4B H9 SING N N 64 YAS C5B H10 SING N N 65 YAS C5B H11 SING N N 66 YAS C6P H12 SING N N 67 YAS C6P H13 SING N N 68 YAS C7P H14 SING N N 69 YAS C7P H15 SING N N 70 YAS C8A H16 SING N N 71 YAS CAF H17 SING N N 72 YAS CAF H18 SING N N 73 YAS CAI H19 SING N N 74 YAS CAI H20 SING N N 75 YAS CAI H21 SING N N 76 YAS CAJ H22 SING N N 77 YAS CAJ H23 SING N N 78 YAS CAP H24 SING N N 79 YAS CCP H25 SING N N 80 YAS CCP H26 SING N N 81 YAS CDP H27 SING N N 82 YAS CDP H28 SING N N 83 YAS CDP H29 SING N N 84 YAS CEP H30 SING N N 85 YAS CEP H31 SING N N 86 YAS CEP H32 SING N N 87 YAS N4P H33 SING N N 88 YAS N6A H34 SING N N 89 YAS N6A H35 SING N N 90 YAS N8P H36 SING N N 91 YAS O2A H37 SING N N 92 YAS O2B H38 SING N N 93 YAS O4A H39 SING N N 94 YAS O7A H40 SING N N 95 YAS O9A H41 SING N N 96 YAS OAP H42 SING N N 97 # # 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 YAS InChI InChI 1.03 "InChI=1S/C25H42N7O17P3S/c1-4-5-16(34)53-9-8-27-15(33)6-7-28-23(37)20(36)25(2,3)11-46-52(43,44)49-51(41,42)45-10-14-19(48-50(38,39)40)18(35)24(47-14)32-13-31-17-21(26)29-12-30-22(17)32/h12-14,18-20,24,35-36H,4-11H2,1-3H3,(H,27,33)(H,28,37)(H,41,42)(H,43,44)(H2,26,29,30)(H2,38,39,40)/t14-,18-,19-,20-,24+/m0/s1" YAS InChIKey InChI 1.03 CRFNGMNYKDXRTN-JSFVJHESSA-N YAS SMILES_CANONICAL CACTVS 3.385 "CCCC(=O)SCCNC(=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" YAS SMILES CACTVS 3.385 "CCCC(=O)SCCNC(=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" YAS SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@H]1[C@@H]([C@@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O" YAS SMILES "OpenEye OEToolkits" 2.0.6 "CCCC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id YAS _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _pdbx_chem_comp_identifier.identifier "~{S}-[2-[3-[[(2~{R})-4-[[[(2~{S},3~{R},4~{S},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] butanethioate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YAS "Create component" 2018-12-06 RCSB YAS "Initial release" 2020-03-18 RCSB YAS "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id YAS _pdbx_chem_comp_synonyms.name Butyryl-CoA _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##