data_A1D9E
#
_chem_comp.id A1D9E
_chem_comp.name "[(2~{R})-2-oxidanyl-3-[oxidanyl-[(2~{S},3~{R},5~{R},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C25 H49 O12 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2024-06-19
_chem_comp.pdbx_modified_date 2024-11-08
_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 572.623
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code A1D9E
_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 8ZX4
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBC
_chem_comp.pdbx_pcm ?
#
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_n_terminal_atom_flag
_chem_comp_atom.pdbx_backbone_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
A1D9E C10 C1 C 0 1 N N N N N N 115.838 113.299 81.513 -8.786 0.333 0.124 C10 A1D9E 1
A1D9E C15 C2 C 0 1 N N N N N N 113.217 111.057 76.530 -2.533 -0.307 -0.413 C15 A1D9E 2
A1D9E C19 C3 C 0 1 N N N N N N 110.639 110.893 75.119 1.037 0.897 -0.034 C19 A1D9E 3
A1D9E C28 C4 C 0 1 N N S N N N 107.783 112.396 69.328 9.135 -1.110 1.229 C28 A1D9E 4
A1D9E C27 C5 C 0 1 N N N N N N 109.277 112.096 68.840 8.698 -0.036 0.231 C27 A1D9E 5
A1D9E C01 C6 C 0 1 N N N N N N 122.267 111.565 88.662 -20.009 -0.782 0.099 C01 A1D9E 6
A1D9E C02 C7 C 0 1 N N N N N N 120.738 111.528 88.484 -18.772 0.062 0.416 C02 A1D9E 7
A1D9E C03 C8 C 0 1 N N N N N N 120.239 111.063 87.089 -17.513 -0.714 0.026 C03 A1D9E 8
A1D9E C04 C9 C 0 1 N N N N N N 118.741 111.366 86.770 -16.276 0.130 0.343 C04 A1D9E 9
A1D9E C05 C10 C 0 1 N N N N N N 118.219 112.765 87.198 -15.016 -0.646 -0.047 C05 A1D9E 10
A1D9E C06 C11 C 0 1 N N N N N N 116.803 113.154 86.668 -13.779 0.197 0.270 C06 A1D9E 11
A1D9E C07 C12 C 0 1 N N N N N N 116.775 113.945 85.327 -12.519 -0.578 -0.120 C07 A1D9E 12
A1D9E C08 C13 C 0 1 N N N N N N 116.223 113.164 84.106 -11.283 0.265 0.197 C08 A1D9E 13
A1D9E C09 C14 C 0 1 N N N N N N 116.797 113.544 82.721 -10.023 -0.510 -0.194 C09 A1D9E 14
A1D9E C11 C15 C 0 1 N N N N N N 116.509 112.853 80.189 -7.527 -0.442 -0.267 C11 A1D9E 15
A1D9E C12 C16 C 0 1 N N N N N N 115.626 112.969 78.912 -6.290 0.401 0.051 C12 A1D9E 16
A1D9E C13 C17 C 0 1 N N N N N N 114.855 111.681 78.506 -5.030 -0.375 -0.340 C13 A1D9E 17
A1D9E C14 C18 C 0 1 N N N N N N 114.643 111.473 76.973 -3.793 0.469 -0.023 C14 A1D9E 18
A1D9E C16 C19 C 0 1 N N N N N N 112.103 112.103 76.624 -1.316 0.524 -0.101 C16 A1D9E 19
A1D9E C20 C20 C 0 1 N N R N N N 109.957 111.359 73.766 2.341 0.184 -0.399 C20 A1D9E 20
A1D9E C21 C21 C 0 1 N N N N N N 110.907 112.193 72.826 3.530 1.030 0.058 C21 A1D9E 21
A1D9E C29 C22 C 0 1 N N R N N N 106.795 113.037 68.230 10.613 -0.915 1.574 C29 A1D9E 22
A1D9E C30 C23 C 0 1 N N N N N N 106.937 112.439 66.762 11.453 -1.029 0.300 C30 A1D9E 23
A1D9E C31 C24 C 0 1 N N R N N N 108.069 111.386 66.655 11.016 0.046 -0.697 C31 A1D9E 24
A1D9E C32 C25 C 0 1 N N R N N N 109.379 111.960 67.265 9.538 -0.149 -1.042 C32 A1D9E 25
A1D9E O17 O1 O 0 1 N N N N N N 112.313 113.173 77.215 -1.442 1.623 0.384 O17 A1D9E 26
A1D9E O18 O2 O 0 1 N N N N N N 110.881 111.920 76.068 -0.090 0.042 -0.361 O18 A1D9E 27
A1D9E O22 O3 O 0 1 N N N N N N 110.859 111.753 71.527 4.744 0.313 -0.177 O22 A1D9E 28
A1D9E O24 O4 O 0 1 N N N N N N 112.154 113.921 70.882 6.494 2.196 -0.729 O24 A1D9E 29
A1D9E O25 O5 O 0 1 N N N N N N 112.350 111.825 69.389 6.229 1.293 1.613 O25 A1D9E 30
A1D9E O26 O6 O 0 1 N N N N N N 110.153 113.054 69.272 7.317 -0.218 -0.091 O26 A1D9E 31
A1D9E O33 O7 O 0 1 N N N N N N 109.646 113.214 66.711 9.351 -1.442 -1.622 O33 A1D9E 32
A1D9E O34 O8 O 0 1 N N N N N N 108.309 111.122 65.293 11.800 -0.060 -1.887 O34 A1D9E 33
A1D9E O35 O9 O 0 1 N N N N N N 105.705 111.831 66.452 12.833 -0.846 0.622 O35 A1D9E 34
A1D9E O36 O10 O 0 1 N N N N N N 105.479 112.870 68.669 10.800 0.377 2.154 O36 A1D9E 35
A1D9E O37 O11 O 0 1 N N N N N N 107.834 113.293 70.403 8.948 -2.403 0.648 O37 A1D9E 36
A1D9E O38 O12 O 0 1 N N N N N N 108.859 112.141 74.112 2.403 0.001 -1.815 O38 A1D9E 37
A1D9E P23 P1 P 0 1 N N N N N N 111.545 112.713 70.265 6.197 0.904 0.186 P23 A1D9E 38
A1D9E H1 H1 H 0 1 N N N N N N 115.298 114.237 81.317 -8.828 1.265 -0.440 H1 A1D9E 39
A1D9E H2 H2 H 0 1 N N N N N N 112.917 110.202 77.154 -2.492 -1.239 0.150 H2 A1D9E 40
A1D9E H3 H3 H 0 1 N N N N N N 113.280 110.740 75.479 -2.559 -0.528 -1.480 H3 A1D9E 41
A1D9E H4 H4 H 0 1 N N N N N N 109.983 110.145 75.589 1.030 1.117 1.033 H4 A1D9E 42
A1D9E H5 H5 H 0 1 N N N N N N 111.604 110.428 74.869 0.963 1.828 -0.597 H5 A1D9E 43
A1D9E H6 H6 H 0 1 N N N N N N 107.342 111.442 69.651 8.536 -1.030 2.136 H6 A1D9E 44
A1D9E H7 H7 H 0 1 N N N N N N 109.558 111.120 69.263 8.840 0.950 0.674 H7 A1D9E 45
A1D9E H8 H8 H 0 1 N N N N N N 122.510 111.906 89.679 -20.034 -1.003 -0.968 H8 A1D9E 46
A1D9E H9 H9 H 0 1 N N N N N N 122.679 110.557 88.505 -19.967 -1.714 0.662 H9 A1D9E 47
A1D9E H10 H10 H 0 1 N N N N N N 122.705 112.258 87.929 -20.906 -0.229 0.377 H10 A1D9E 48
A1D9E H11 H11 H 0 1 N N N N N N 120.351 112.542 88.662 -18.814 0.994 -0.147 H11 A1D9E 49
A1D9E H12 H12 H 0 1 N N N N N N 120.385 109.975 87.023 -17.471 -1.646 0.589 H12 A1D9E 50
A1D9E H13 H13 H 0 1 N N N N N N 118.604 111.275 85.682 -16.318 1.062 -0.220 H13 A1D9E 51
A1D9E H14 H14 H 0 1 N N N N N N 118.934 113.518 86.834 -14.974 -1.578 0.516 H14 A1D9E 52
A1D9E H15 H15 H 0 1 N N N N N N 116.314 113.772 87.435 -13.821 1.130 -0.293 H15 A1D9E 53
A1D9E H16 H16 H 0 1 N N N N N N 116.230 112.226 86.525 -13.754 0.418 1.337 H16 A1D9E 54
A1D9E H17 H17 H 0 1 N N N N N N 117.804 114.255 85.094 -12.478 -1.510 0.443 H17 A1D9E 55
A1D9E H18 H18 H 0 1 N N N N N N 116.147 114.837 85.472 -12.545 -0.799 -1.188 H18 A1D9E 56
A1D9E H19 H19 H 0 1 N N N N N N 115.135 113.325 84.072 -11.325 1.197 -0.366 H19 A1D9E 57
A1D9E H20 H20 H 0 1 N N N N N N 116.431 112.097 84.271 -11.258 0.486 1.264 H20 A1D9E 58
A1D9E H21 H21 H 0 1 N N N N N N 117.709 112.952 82.557 -10.048 -0.731 -1.261 H21 A1D9E 59
A1D9E H22 H22 H 0 1 N N N N N N 117.053 114.614 82.741 -9.981 -1.443 0.370 H22 A1D9E 60
A1D9E H23 H23 H 0 1 N N N N N N 116.807 111.800 80.299 -7.485 -1.375 0.296 H23 A1D9E 61
A1D9E H24 H24 H 0 1 N N N N N N 116.280 113.250 78.073 -6.332 1.333 -0.513 H24 A1D9E 62
A1D9E H25 H25 H 0 1 N N N N N N 114.887 113.765 79.083 -6.265 0.622 1.117 H25 A1D9E 63
A1D9E H26 H26 H 0 1 N N N N N N 113.864 111.716 78.982 -4.988 -1.307 0.223 H26 A1D9E 64
A1D9E H27 H27 H 0 1 N N N N N N 115.416 110.816 78.890 -5.055 -0.595 -1.407 H27 A1D9E 65
A1D9E H28 H28 H 0 1 N N N N N N 115.340 110.689 76.641 -3.768 0.690 1.044 H28 A1D9E 66
A1D9E H29 H29 H 0 1 N N N N N N 114.889 112.419 76.469 -3.835 1.401 -0.586 H29 A1D9E 67
A1D9E H30 H30 H 0 1 N N N N N N 109.636 110.460 73.219 2.374 -0.787 0.095 H30 A1D9E 68
A1D9E H31 H31 H 0 1 N N N N N N 111.940 112.102 73.194 3.547 1.966 -0.501 H31 A1D9E 69
A1D9E H32 H32 H 0 1 N N N N N N 110.599 113.248 72.855 3.436 1.245 1.123 H32 A1D9E 70
A1D9E H33 H33 H 0 1 N N N N N N 107.033 114.109 68.170 10.924 -1.681 2.284 H33 A1D9E 71
A1D9E H34 H34 H 0 1 N N N N N N 107.152 113.266 66.069 11.310 -2.015 -0.143 H34 A1D9E 72
A1D9E H35 H35 H 0 1 N N N N N N 107.778 110.476 67.200 11.158 1.032 -0.255 H35 A1D9E 73
A1D9E H36 H36 H 0 1 N N N N N N 110.198 111.261 67.040 9.226 0.617 -1.752 H36 A1D9E 74
A1D9E H37 H37 H 0 1 N N N N N N 113.065 113.986 70.619 6.488 2.015 -1.679 H37 A1D9E 75
A1D9E H38 H38 H 0 1 N N N N N N 110.447 113.562 67.085 9.855 -1.584 -2.435 H38 A1D9E 76
A1D9E H39 H39 H 0 1 N N N N N N 109.002 110.477 65.212 12.750 0.054 -1.743 H39 A1D9E 77
A1D9E H40 H40 H 0 1 N N N N N N 105.009 112.474 66.517 13.426 -0.906 -0.140 H40 A1D9E 78
A1D9E H41 H41 H 0 1 N N N N N N 105.389 113.226 69.545 11.715 0.570 2.398 H41 A1D9E 79
A1D9E H42 H42 H 0 1 N N N N N N 108.410 112.949 71.076 9.205 -3.134 1.226 H42 A1D9E 80
A1D9E H43 H43 H 0 1 N N N N N N 108.282 111.644 74.679 2.378 0.825 -2.320 H43 A1D9E 81
A1D9E H44 H44 H 0 1 N N N N N N 115.121 112.518 81.806 -8.761 0.554 1.191 H44 A1D9E 82
A1D9E H45 H45 H 0 1 N N N N N N 120.325 110.841 89.238 -18.747 0.282 1.483 H45 A1D9E 83
A1D9E H46 H46 H 0 1 N N N N N N 120.855 111.562 86.326 -17.538 -0.935 -1.041 H46 A1D9E 84
A1D9E H47 H47 H 0 1 N N N N N N 118.129 110.608 87.281 -16.251 0.350 1.410 H47 A1D9E 85
A1D9E H48 H48 H 0 1 N N N N N N 118.187 112.791 88.297 -15.041 -0.867 -1.114 H48 A1D9E 86
A1D9E H49 H49 H 0 1 N N N N N N 117.405 113.474 80.038 -7.552 -0.663 -1.334 H49 A1D9E 87
#
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
A1D9E O34 C31 SING N N 1
A1D9E O35 C30 SING N N 2
A1D9E C31 C30 SING N N 3
A1D9E C31 C32 SING N N 4
A1D9E O33 C32 SING N N 5
A1D9E C30 C29 SING N N 6
A1D9E C32 C27 SING N N 7
A1D9E C29 O36 SING N N 8
A1D9E C29 C28 SING N N 9
A1D9E C27 O26 SING N N 10
A1D9E C27 C28 SING N N 11
A1D9E O26 P23 SING N N 12
A1D9E C28 O37 SING N N 13
A1D9E O25 P23 DOUB N N 14
A1D9E P23 O24 SING N N 15
A1D9E P23 O22 SING N N 16
A1D9E O22 C21 SING N N 17
A1D9E C21 C20 SING N N 18
A1D9E C20 O38 SING N N 19
A1D9E C20 C19 SING N N 20
A1D9E C19 O18 SING N N 21
A1D9E O18 C16 SING N N 22
A1D9E C15 C16 SING N N 23
A1D9E C15 C14 SING N N 24
A1D9E C16 O17 DOUB N N 25
A1D9E C14 C13 SING N N 26
A1D9E C13 C12 SING N N 27
A1D9E C12 C11 SING N N 28
A1D9E C11 C10 SING N N 29
A1D9E C10 C09 SING N N 30
A1D9E C09 C08 SING N N 31
A1D9E C08 C07 SING N N 32
A1D9E C07 C06 SING N N 33
A1D9E C06 C05 SING N N 34
A1D9E C04 C03 SING N N 35
A1D9E C04 C05 SING N N 36
A1D9E C03 C02 SING N N 37
A1D9E C02 C01 SING N N 38
A1D9E C10 H1 SING N N 39
A1D9E C15 H2 SING N N 40
A1D9E C15 H3 SING N N 41
A1D9E C19 H4 SING N N 42
A1D9E C19 H5 SING N N 43
A1D9E C28 H6 SING N N 44
A1D9E C27 H7 SING N N 45
A1D9E C01 H8 SING N N 46
A1D9E C01 H9 SING N N 47
A1D9E C01 H10 SING N N 48
A1D9E C02 H11 SING N N 49
A1D9E C03 H12 SING N N 50
A1D9E C04 H13 SING N N 51
A1D9E C05 H14 SING N N 52
A1D9E C06 H15 SING N N 53
A1D9E C06 H16 SING N N 54
A1D9E C07 H17 SING N N 55
A1D9E C07 H18 SING N N 56
A1D9E C08 H19 SING N N 57
A1D9E C08 H20 SING N N 58
A1D9E C09 H21 SING N N 59
A1D9E C09 H22 SING N N 60
A1D9E C11 H23 SING N N 61
A1D9E C12 H24 SING N N 62
A1D9E C12 H25 SING N N 63
A1D9E C13 H26 SING N N 64
A1D9E C13 H27 SING N N 65
A1D9E C14 H28 SING N N 66
A1D9E C14 H29 SING N N 67
A1D9E C20 H30 SING N N 68
A1D9E C21 H31 SING N N 69
A1D9E C21 H32 SING N N 70
A1D9E C29 H33 SING N N 71
A1D9E C30 H34 SING N N 72
A1D9E C31 H35 SING N N 73
A1D9E C32 H36 SING N N 74
A1D9E O24 H37 SING N N 75
A1D9E O33 H38 SING N N 76
A1D9E O34 H39 SING N N 77
A1D9E O35 H40 SING N N 78
A1D9E O36 H41 SING N N 79
A1D9E O37 H42 SING N N 80
A1D9E O38 H43 SING N N 81
A1D9E C10 H44 SING N N 82
A1D9E C02 H45 SING N N 83
A1D9E C03 H46 SING N N 84
A1D9E C04 H47 SING N N 85
A1D9E C05 H48 SING N N 86
A1D9E C11 H49 SING N N 87
#
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
A1D9E InChI InChI 1.06 "InChI=1S/C25H49O12P/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-19(27)35-16-18(26)17-36-38(33,34)37-25-23(31)21(29)20(28)22(30)24(25)32/h18,20-26,28-32H,2-17H2,1H3,(H,33,34)/t18-,20-,21-,22-,23-,24+,25-/m1/s1"
A1D9E InChIKey InChI 1.06 UOXRPRZMAROFPH-LGNGRQRGSA-N
A1D9E SMILES_CANONICAL CACTVS 3.385 "CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P](O)(=O)O[C@@H]1[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H]1O"
A1D9E SMILES CACTVS 3.385 "CCCCCCCCCCCCCCCC(=O)OC[CH](O)CO[P](O)(=O)O[CH]1[CH](O)[CH](O)[CH](O)[CH](O)[CH]1O"
A1D9E SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OC1[C@@H]([C@@H](C([C@H]([C@@H]1O)O)O)O)O)O"
A1D9E SMILES "OpenEye OEToolkits" 2.0.7 "CCCCCCCCCCCCCCCC(=O)OCC(COP(=O)(O)OC1C(C(C(C(C1O)O)O)O)O)O"
#
_pdbx_chem_comp_identifier.comp_id A1D9E
_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 "[(2~{R})-2-oxidanyl-3-[oxidanyl-[(2~{S},3~{R},5~{R},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
A1D9E "Create component" 2024-06-19 PDBC
A1D9E "Initial release" 2024-11-13 RCSB
#