data_ZKK # _chem_comp.id ZKK _chem_comp.name "(2S)-Methylsuccinyl-CoA" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C26 H42 N7 O19 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(3S)-4-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-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]ethylsulfanyl]-3-methyl-4-oxidanylidene-butanoic acid" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-06-28 _chem_comp.pdbx_modified_date 2023-07-07 _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 881.633 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ZKK _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 8CIW _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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 ZKK C01 C1 C 0 1 N N N 52.267 61.525 72.051 -10.320 3.595 2.619 C01 ZKK 1 ZKK C02 C2 C 0 1 N N S 51.289 60.343 72.053 -10.819 3.155 1.241 C02 ZKK 2 ZKK C03 C3 C 0 1 N N N 51.981 59.050 72.464 -11.067 4.388 0.370 C03 ZKK 3 ZKK C04 C4 C 0 1 N N N 53.164 58.760 71.558 -12.190 5.202 0.960 C04 ZKK 4 ZKK C07 C5 C 0 1 N N N 50.143 60.577 73.031 -9.783 2.278 0.587 C07 ZKK 5 ZKK C2P C6 C 0 1 N N N 48.269 62.130 74.624 -8.085 0.230 0.132 C2P ZKK 6 ZKK C3P C7 C 0 1 N N N 47.102 61.944 73.662 -7.500 -1.102 0.604 C3P ZKK 7 ZKK C5P C8 C 0 1 N N N 44.611 62.337 73.646 -5.869 -2.741 -0.164 C5P ZKK 8 ZKK C6P C9 C 0 1 N N N 43.393 62.880 74.381 -4.858 -3.230 -1.169 C6P ZKK 9 ZKK C7P C10 C 0 1 N N N 42.108 62.190 73.954 -4.273 -4.562 -0.697 C7P ZKK 10 ZKK C9P C11 C 0 1 N N N 40.621 64.189 73.631 -2.641 -6.201 -1.465 C9P ZKK 11 ZKK CAP C12 C 0 1 N N R 39.461 65.053 74.112 -1.559 -6.641 -2.417 CAP ZKK 12 ZKK CBP C13 C 0 1 N N N 38.132 64.404 73.738 -0.356 -5.705 -2.290 CBP ZKK 13 ZKK CDP C14 C 0 1 N N N 38.234 63.768 72.356 0.794 -6.233 -3.150 CDP ZKK 14 ZKK CEP C15 C 0 1 N N N 37.755 63.340 74.761 -0.748 -4.304 -2.767 CEP ZKK 15 ZKK CCP C16 C 0 1 N N N 37.024 65.447 73.719 0.088 -5.640 -0.828 CCP ZKK 16 ZKK C5B C17 C 0 1 N N N 35.855 71.327 73.847 5.219 -0.067 1.268 C5B ZKK 17 ZKK C4B C18 C 0 1 N N R 36.214 72.619 73.188 5.634 0.952 0.205 C4B ZKK 18 ZKK C1B C19 C 0 1 N N R 37.020 72.618 70.979 4.971 2.842 -0.916 C1B ZKK 19 ZKK C8A C20 C 0 1 Y N N 37.314 70.429 70.046 2.729 3.847 -0.340 C8A ZKK 20 ZKK C5A C21 C 0 1 Y N N 38.950 70.851 68.618 2.623 5.515 -1.721 C5A ZKK 21 ZKK C6A C22 C 0 1 Y N N 39.949 70.945 67.691 2.318 6.642 -2.504 C6A ZKK 22 ZKK C2A C23 C 0 1 Y N N 40.146 73.104 68.159 4.340 6.392 -3.589 C2A ZKK 23 ZKK C4A C24 C 0 1 Y N N 38.596 72.037 69.313 3.851 4.868 -1.940 C4A ZKK 24 ZKK C2B C25 C 0 1 N N R 35.542 72.460 70.968 6.032 3.352 0.088 C2B ZKK 25 ZKK C3B C26 C 0 1 N N S 35.139 73.051 72.248 6.478 2.079 0.841 C3B ZKK 26 ZKK N4P N1 N 0 1 N N N 45.898 62.428 74.294 -6.517 -1.578 -0.372 N4P ZKK 27 ZKK N8P N2 N 0 1 N N N 41.005 63.015 74.393 -3.290 -5.038 -1.673 N8P ZKK 28 ZKK N9A N3 N 0 1 Y N N 37.645 71.686 70.115 3.887 3.817 -1.059 N9A ZKK 29 ZKK N7A N4 N 0 1 Y N N 38.065 69.766 69.134 1.989 4.844 -0.730 N7A ZKK 30 ZKK N6A N5 N 0 1 N N N 40.350 69.762 66.954 1.127 7.324 -2.329 N6A ZKK 31 ZKK N1A N6 N 0 1 Y N N 40.569 72.071 67.442 3.201 7.037 -3.416 N1A ZKK 32 ZKK N3A N7 N 0 1 Y N N 39.196 73.194 69.089 4.671 5.338 -2.874 N3A ZKK 33 ZKK O05 O1 O 0 1 N N N 54.282 58.513 72.054 -12.583 6.337 0.360 O05 ZKK 34 ZKK O06 O2 O 0 1 N N N 53.017 58.760 70.319 -12.736 4.834 1.973 O06 ZKK 35 ZKK O08 O3 O 0 1 N N N 49.467 59.675 73.375 -9.290 2.608 -0.471 O08 ZKK 36 ZKK O5P O4 O 0 1 N N N 44.515 61.873 72.569 -6.099 -3.394 0.831 O5P ZKK 37 ZKK O9P O5 O 0 1 N N N 41.196 64.479 72.643 -2.928 -6.893 -0.512 O9P ZKK 38 ZKK OAP O6 O 0 1 N N N 39.562 65.220 75.493 -1.159 -7.976 -2.100 OAP ZKK 39 ZKK O6A O7 O 0 1 N N N 37.076 66.208 74.881 1.212 -4.765 -0.710 O6A ZKK 40 ZKK O4A O8 O 0 1 N N N 34.520 66.341 74.962 0.945 -3.970 1.671 O4A ZKK 41 ZKK O5A O9 O 0 1 N N N 35.638 67.241 76.705 2.621 -5.809 1.249 O5A ZKK 42 ZKK O3A O10 O 0 1 N N N 35.822 68.495 74.515 3.076 -3.338 0.474 O3A ZKK 43 ZKK O1A O11 O 0 1 N N N 34.977 68.118 72.145 3.042 -1.906 2.552 O1A ZKK 44 ZKK O2A O12 O 0 1 N N N 33.430 68.790 73.619 5.138 -3.238 2.102 O2A ZKK 45 ZKK O5B O13 O 0 1 N N N 35.173 70.520 72.941 4.509 -1.141 0.646 O5B ZKK 46 ZKK O4B O14 O 0 1 N N N 37.421 72.440 72.379 4.472 1.617 -0.336 O4B ZKK 47 ZKK O2B O15 O 0 1 N N N 34.940 73.150 69.870 7.136 3.938 -0.605 O2B ZKK 48 ZKK O3B O16 O 0 1 N N N 35.232 74.475 72.114 7.871 1.838 0.637 O3B ZKK 49 ZKK O9A O17 O 0 1 N N N 34.671 75.675 74.329 8.595 0.473 2.764 O7A ZKK 50 ZKK O8A O18 O 0 1 N N N 32.858 74.996 73.072 10.418 1.602 1.243 O8A ZKK 51 ZKK O7A O19 O 0 1 N N N 34.133 76.793 72.431 8.852 2.982 2.662 O1 ZKK 52 ZKK P2A P1 P 0 1 N N N 35.736 67.053 75.278 1.941 -4.460 0.693 P2A ZKK 53 ZKK P1A P2 P 0 1 N N N 34.830 68.968 73.305 3.922 -2.395 1.468 P1A ZKK 54 ZKK P3B P3 P 0 1 N N N 34.229 75.452 72.970 8.932 1.751 1.844 P3B ZKK 55 ZKK S1P S1 S 0 1 N N N 49.801 62.234 73.671 -9.300 0.818 1.339 S1P ZKK 56 ZKK H1 H1 H 0 1 N N N 51.736 62.440 71.751 -9.391 4.154 2.507 H1 ZKK 57 ZKK H2 H2 H 0 1 N N N 52.684 61.658 73.060 -11.070 4.229 3.092 H2 ZKK 58 ZKK H3 H3 H 0 1 N N N 53.083 61.325 71.341 -10.143 2.717 3.239 H3 ZKK 59 ZKK H9 H4 H 0 1 N N N 50.876 60.222 71.041 -11.749 2.596 1.353 H4 ZKK 60 ZKK H4 H5 H 0 1 N N N 51.263 58.219 72.396 -10.161 4.993 0.331 H5 ZKK 61 ZKK H11 H6 H 0 1 N N N 52.336 59.145 73.501 -11.338 4.073 -0.637 H6 ZKK 62 ZKK H51A H7 H 0 1 N N N 48.129 63.056 75.200 -7.285 0.964 0.035 H7 ZKK 63 ZKK H122 H8 H 0 1 N N N 48.320 61.274 75.313 -8.570 0.092 -0.834 H8 ZKK 64 ZKK HN8 H9 H 0 1 N N N 46.989 60.877 73.419 -7.015 -0.964 1.571 H9 ZKK 65 ZKK H61A H10 H 0 1 N N N 47.289 62.512 72.739 -8.300 -1.836 0.701 H10 ZKK 66 ZKK H61 H11 H 0 1 N N N 43.534 62.728 75.461 -5.343 -3.368 -2.135 H11 ZKK 67 ZKK H62 H12 H 0 1 N N N 43.304 63.956 74.171 -4.057 -2.496 -1.266 H12 ZKK 68 ZKK H71 H13 H 0 1 N N N 42.085 62.083 72.859 -3.787 -4.424 0.270 H13 ZKK 69 ZKK H72 H14 H 0 1 N N N 42.043 61.196 74.421 -5.073 -5.296 -0.600 H14 ZKK 70 ZKK H10 H15 H 0 1 N N N 39.524 66.028 73.607 -1.939 -6.609 -3.438 H15 ZKK 71 ZKK H131 H16 H 0 1 N N N 39.033 63.012 72.358 0.499 -6.222 -4.199 H16 ZKK 72 ZKK H132 H17 H 0 1 N N N 37.277 63.290 72.101 1.671 -5.600 -3.013 H17 ZKK 73 ZKK H133 H18 H 0 1 N N N 38.466 64.544 71.612 1.033 -7.253 -2.850 H18 ZKK 74 ZKK H141 H19 H 0 1 N N N 37.681 63.799 75.758 -1.487 -3.882 -2.086 H19 ZKK 75 ZKK H142 H20 H 0 1 N N N 36.786 62.897 74.489 0.136 -3.666 -2.785 H20 ZKK 76 ZKK H143 H21 H 0 1 N N N 38.526 62.555 74.775 -1.171 -4.367 -3.770 H21 ZKK 77 ZKK H5 H22 H 0 1 N N N 37.155 66.103 72.846 -0.732 -5.263 -0.216 H22 ZKK 78 ZKK H121 H23 H 0 1 N N N 36.048 64.943 73.656 0.367 -6.637 -0.488 H23 ZKK 79 ZKK H6 H24 H 0 1 N N N 35.213 71.525 74.718 6.107 -0.457 1.764 H24 ZKK 80 ZKK H52A H25 H 0 1 N N N 36.772 70.816 74.176 4.575 0.417 2.002 H25 ZKK 81 ZKK H4B H26 H 0 1 N N N 36.378 73.394 73.951 6.195 0.461 -0.591 H26 ZKK 82 ZKK H1B H27 H 0 1 N N N 37.268 73.642 70.663 5.431 2.643 -1.884 H27 ZKK 83 ZKK H8A H28 H 0 1 N N N 36.538 69.972 70.641 2.463 3.145 0.436 H28 ZKK 84 ZKK H2A H29 H 0 1 N N N 40.660 74.031 67.954 5.030 6.748 -4.340 H29 ZKK 85 ZKK H2B H30 H 0 1 N N N 35.281 71.392 70.945 5.589 4.070 0.779 H30 ZKK 86 ZKK H3B H31 H 0 1 N N N 34.144 72.713 72.573 6.256 2.167 1.905 H31 ZKK 87 ZKK HN4 H32 H 0 1 N N N 45.957 62.837 75.205 -6.333 -1.056 -1.169 H32 ZKK 88 ZKK H7 H33 H 0 1 N N N 40.505 62.776 75.225 -3.105 -4.516 -2.469 H33 ZKK 89 ZKK H8 H34 H 0 1 N N N 41.089 69.997 66.323 0.491 7.026 -1.660 H34 ZKK 90 ZKK H62A H35 H 0 1 N N N 40.667 69.062 67.594 0.928 8.100 -2.876 H35 ZKK 91 ZKK H34 H36 H 0 1 N N N 54.908 58.348 71.359 -13.307 6.825 0.775 H36 ZKK 92 ZKK HO1 H37 H 0 1 N N N 38.842 65.758 75.801 -0.810 -8.079 -1.204 H37 ZKK 93 ZKK HOA5 H38 H 0 1 N N N 34.829 66.856 77.021 3.286 -6.187 0.658 H38 ZKK 94 ZKK HOA2 H39 H 0 1 N N N 33.039 68.191 72.994 5.756 -3.590 1.448 H39 ZKK 95 ZKK HO2A H40 H 0 1 N N N 33.998 73.027 69.896 6.900 4.706 -1.143 H40 ZKK 96 ZKK HOA9 H41 H 0 1 N N N 34.771 76.607 74.481 8.628 -0.371 2.292 H41 ZKK 97 ZKK HOA8 H42 H 0 1 N N N 32.273 75.679 72.766 11.111 1.543 1.915 H42 ZKK 98 # 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 ZKK N6A C6A SING N N 1 ZKK N1A C6A DOUB Y N 2 ZKK N1A C2A SING Y N 3 ZKK C6A C5A SING Y N 4 ZKK C2A N3A DOUB Y N 5 ZKK C5A N7A SING Y N 6 ZKK C5A C4A DOUB Y N 7 ZKK N3A C4A SING Y N 8 ZKK N7A C8A DOUB Y N 9 ZKK C4A N9A SING Y N 10 ZKK O2B C2B SING N N 11 ZKK C8A N9A SING Y N 12 ZKK N9A C1B SING N N 13 ZKK O06 C04 DOUB N N 14 ZKK C2B C1B SING N N 15 ZKK C2B C3B SING N N 16 ZKK C1B O4B SING N N 17 ZKK C04 O05 SING N N 18 ZKK C04 C03 SING N N 19 ZKK C01 C02 SING N N 20 ZKK C02 C03 SING N N 21 ZKK C02 C07 SING N N 22 ZKK O3B C3B SING N N 23 ZKK O3B P3B SING N N 24 ZKK O1A P1A DOUB N N 25 ZKK C3B C4B SING N N 26 ZKK CDP CBP SING N N 27 ZKK O4B C4B SING N N 28 ZKK O7A P3B DOUB N N 29 ZKK O5P C5P DOUB N N 30 ZKK O9P C9P DOUB N N 31 ZKK O5B P1A SING N N 32 ZKK O5B C5B SING N N 33 ZKK P3B O8A SING N N 34 ZKK P3B O9A SING N N 35 ZKK C07 O08 DOUB N N 36 ZKK C07 S1P SING N N 37 ZKK C4B C5B SING N N 38 ZKK P1A O2A SING N N 39 ZKK P1A O3A SING N N 40 ZKK C9P CAP SING N N 41 ZKK C9P N8P SING N N 42 ZKK C5P N4P SING N N 43 ZKK C5P C6P SING N N 44 ZKK C3P N4P SING N N 45 ZKK C3P C2P SING N N 46 ZKK S1P C2P SING N N 47 ZKK CCP CBP SING N N 48 ZKK CCP O6A SING N N 49 ZKK CBP CAP SING N N 50 ZKK CBP CEP SING N N 51 ZKK C7P C6P SING N N 52 ZKK C7P N8P SING N N 53 ZKK CAP OAP SING N N 54 ZKK O3A P2A SING N N 55 ZKK O6A P2A SING N N 56 ZKK O4A P2A DOUB N N 57 ZKK P2A O5A SING N N 58 ZKK C01 H1 SING N N 59 ZKK C01 H2 SING N N 60 ZKK C01 H3 SING N N 61 ZKK C02 H9 SING N N 62 ZKK C03 H4 SING N N 63 ZKK C03 H11 SING N N 64 ZKK C2P H51A SING N N 65 ZKK C2P H122 SING N N 66 ZKK C3P HN8 SING N N 67 ZKK C3P H61A SING N N 68 ZKK C6P H61 SING N N 69 ZKK C6P H62 SING N N 70 ZKK C7P H71 SING N N 71 ZKK C7P H72 SING N N 72 ZKK CAP H10 SING N N 73 ZKK CDP H131 SING N N 74 ZKK CDP H132 SING N N 75 ZKK CDP H133 SING N N 76 ZKK CEP H141 SING N N 77 ZKK CEP H142 SING N N 78 ZKK CEP H143 SING N N 79 ZKK CCP H5 SING N N 80 ZKK CCP H121 SING N N 81 ZKK C5B H6 SING N N 82 ZKK C5B H52A SING N N 83 ZKK C4B H4B SING N N 84 ZKK C1B H1B SING N N 85 ZKK C8A H8A SING N N 86 ZKK C2A H2A SING N N 87 ZKK C2B H2B SING N N 88 ZKK C3B H3B SING N N 89 ZKK N4P HN4 SING N N 90 ZKK N8P H7 SING N N 91 ZKK N6A H8 SING N N 92 ZKK N6A H62A SING N N 93 ZKK O05 H34 SING N N 94 ZKK OAP HO1 SING N N 95 ZKK O5A HOA5 SING N N 96 ZKK O2A HOA2 SING N N 97 ZKK O2B HO2A SING N N 98 ZKK O9A HOA9 SING N N 99 ZKK O8A HOA8 SING N N 100 # 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 ZKK InChI InChI 1.06 "InChI=1S/C26H42N7O19P3S/c1-13(8-16(35)36)25(40)56-7-6-28-15(34)4-5-29-23(39)20(38)26(2,3)10-49-55(46,47)52-54(44,45)48-9-14-19(51-53(41,42)43)18(37)24(50-14)33-12-32-17-21(27)30-11-31-22(17)33/h11-14,18-20,24,37-38H,4-10H2,1-3H3,(H,28,34)(H,29,39)(H,35,36)(H,44,45)(H,46,47)(H2,27,30,31)(H2,41,42,43)/t13-,14+,18+,19+,20-,24+/m0/s1" ZKK InChIKey InChI 1.06 OUFHQHVVFSERRI-VKBDFPRVSA-N ZKK SMILES_CANONICAL CACTVS 3.385 "C[C@@H](CC(O)=O)C(=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" ZKK SMILES CACTVS 3.385 "C[CH](CC(O)=O)C(=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" ZKK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H](CC(=O)O)C(=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" ZKK SMILES "OpenEye OEToolkits" 2.0.7 "CC(CC(=O)O)C(=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 ZKK _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "(3~{S})-4-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},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]ethylsulfanyl]-3-methyl-4-oxidanylidene-butanoic acid" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id ZKK _pdbx_chem_comp_synonyms.name "(3S)-4-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-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]ethylsulfanyl]-3-methyl-4-oxidanylidene-butanoic acid" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site ZKK "Create component" 2023-06-28 PDBE ZKK "Initial release" 2023-07-12 RCSB #