data_58A
#
_chem_comp.id 58A
_chem_comp.name "5'-O-[(R)-{[(S)-{(2R)-2,3-bis[(9E)-octadec-9-enoyloxy]propoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C48 H85 N3 O15 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "cytidinediphosphate-dioleoylglycerol; CDP-1,2-dioleoyl-sn-glycerol"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-08-19
_chem_comp.pdbx_modified_date 2024-09-27
_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 1006.147
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 58A
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 5D92
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_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
58A OAA O1 O 0 1 N N N N N N 0.999 -19.094 -60.222 -6.012 4.937 0.103 OAA 58A 1
58A CAB C1 C 0 1 N N N N N N -0.113 -18.862 -59.886 -6.484 4.286 -0.815 CAB 58A 2
58A NAC N1 N 0 1 N N N N N N -0.912 -19.886 -59.638 -7.778 3.970 -0.797 NAC 58A 3
58A CAD C2 C 0 1 N N N N N N -2.165 -19.691 -59.264 -8.316 3.263 -1.781 CAD 58A 4
58A NAE N2 N 0 1 N N N N N N -3.041 -20.813 -58.991 -9.654 2.943 -1.752 NAE 58A 5
58A CAF C3 C 0 1 N N N N N N -2.616 -18.381 -59.140 -7.510 2.840 -2.858 CAF 58A 6
58A CAG C4 C 0 1 N N N N N N -1.745 -17.332 -59.411 -6.196 3.169 -2.862 CAG 58A 7
58A NAH N3 N 0 1 N N N N N N -0.502 -17.601 -59.785 -5.690 3.902 -1.831 NAH 58A 8
58A "C1'" C5 C 0 1 N N R N N N 0.403 -16.546 -60.059 -4.272 4.270 -1.826 "C1'" 58A 9
58A "O4'" O2 O 0 1 N N N N N N -0.190 -15.108 -59.509 -3.649 3.856 -0.590 "O4'" 58A 10
58A "C2'" C6 C 0 1 N N R N N N 0.596 -16.380 -61.370 -4.114 5.806 -1.852 "C2'" 58A 11
58A "O2'" O3 O 0 1 N N N N N N 1.879 -17.014 -61.768 -3.858 6.261 -3.182 "O2'" 58A 12
58A "C3'" C7 C 0 1 N N S N N N 0.677 -14.845 -61.592 -2.896 6.075 -0.941 "C3'" 58A 13
58A "O3'" O4 O 0 1 N N N N N N 1.856 -14.512 -62.114 -1.847 6.703 -1.680 "O3'" 58A 14
58A "C4'" C8 C 0 1 N N R N N N 0.524 -14.222 -60.142 -2.461 4.668 -0.472 "C4'" 58A 15
58A "C5'" C9 C 0 1 N N N N N N -0.207 -12.867 -60.199 -1.989 4.714 0.983 "C5'" 58A 16
58A "O5'" O5 O 0 1 N N N N N N -1.526 -13.059 -59.723 -1.483 3.432 1.360 "O5'" 58A 17
58A PAR P1 P 0 1 N N N N N N -2.095 -12.045 -58.534 -0.900 3.116 2.827 PAR 58A 18
58A OAT O6 O 0 1 N N N N N N -3.133 -12.790 -57.715 0.172 4.083 3.150 OAT 58A 19
58A OAS O7 O 0 1 N N N N N N -0.957 -11.579 -57.655 -2.082 3.243 3.913 OAS 58A 20
58A OAU O8 O 0 1 N N N N N N -2.802 -10.729 -59.244 -0.302 1.621 2.857 OAU 58A 21
58A PAV P2 P 0 1 N N N N N N -4.442 -10.677 -59.389 0.664 0.823 3.868 PAV 58A 22
58A OAX O9 O 0 1 N N N N N N -4.843 -10.337 -60.805 1.742 1.723 4.333 OAX 58A 23
58A OAW O10 O 0 1 N N N N N N -4.934 -12.063 -59.048 -0.190 0.309 5.132 OAW 58A 24
58A OAY O11 O 0 1 N N N N N N -5.059 -9.551 -58.320 1.310 -0.440 3.107 OAY 58A 25
58A CAZ C10 C 0 1 N N N N N N -5.564 -8.341 -58.848 2.293 -1.289 3.704 CAZ 58A 26
58A CBA C11 C 0 1 N N R N N N -6.322 -7.554 -57.765 2.689 -2.385 2.714 CBA 58A 27
58A OBB O12 O 0 1 N N N N N N -5.510 -7.323 -56.650 3.345 -1.786 1.565 OBB 58A 28
58A CBU C12 C 0 1 N N N N N N -5.790 -6.094 -55.994 4.678 -1.645 1.629 CBU 58A 29
58A OCK O13 O 0 1 N N N N N N -5.677 -5.065 -56.587 5.278 -2.011 2.613 OCK 58A 30
58A CBV C13 C 0 1 N N N N N N -6.252 -6.084 -54.505 5.428 -1.031 0.475 CBV 58A 31
58A CBW C14 C 0 1 N N N N N N -7.163 -4.856 -54.157 6.922 -0.988 0.802 CBW 58A 32
58A CBX C15 C 0 1 N N N N N N -7.394 -4.699 -52.612 7.683 -0.365 -0.370 CBX 58A 33
58A CBY C16 C 0 1 N N N N N N -8.885 -4.861 -52.195 9.177 -0.322 -0.043 CBY 58A 34
58A CBZ C17 C 0 1 N N N N N N -9.045 -4.969 -50.647 9.938 0.301 -1.215 CBZ 58A 35
58A CCA C18 C 0 1 N N N N N N -10.164 -4.048 -50.070 11.432 0.344 -0.888 CCA 58A 36
58A CCB C19 C 0 1 N N N N N N -10.453 -4.362 -48.572 12.193 0.967 -2.060 CCB 58A 37
58A CCC C20 C 0 1 N N N N N N -11.567 -3.457 -47.963 13.664 1.010 -1.737 CCC 58A 38
58A CCD C21 C 0 1 N N N N N N -12.411 -4.205 -46.889 14.530 0.461 -2.553 CCD 58A 39
58A CCE C22 C 0 1 N N N N N N -13.943 -4.065 -47.127 16.001 0.503 -2.231 CCE 58A 40
58A CCF C23 C 0 1 N N N N N N -14.770 -4.987 -46.188 16.565 -0.919 -2.236 CCF 58A 41
58A CCG C24 C 0 1 N N N N N N -16.174 -4.404 -45.868 18.059 -0.876 -1.909 CCG 58A 42
58A CCH C25 C 0 1 N N N N N N -16.800 -5.033 -44.590 18.624 -2.298 -1.913 CCH 58A 43
58A CCI C26 C 0 1 N N N N N N -17.689 -4.032 -43.809 20.118 -2.255 -1.586 CCI 58A 44
58A CCJ C27 C 0 1 N N N N N N -18.864 -4.729 -43.092 20.682 -3.677 -1.590 CCJ 58A 45
58A CBC C28 C 0 1 N N N N N N -7.595 -8.317 -57.324 1.437 -3.133 2.253 CBC 58A 46
58A OBD O14 O 0 1 N N N N N N -8.469 -7.374 -56.732 0.478 -2.186 1.714 OBD 58A 47
58A CBE C29 C 0 1 N N N N N N -9.524 -7.935 -55.953 -0.684 -2.684 1.263 CBE 58A 48
58A OCL O15 O 0 1 N N N N N N -9.845 -9.070 -56.107 -0.892 -3.873 1.316 OCL 58A 49
58A CBF C30 C 0 1 N N N N N N -10.243 -7.058 -54.907 -1.728 -1.761 0.689 CBF 58A 50
58A CBG C31 C 0 1 N N N N N N -11.749 -7.388 -54.764 -2.946 -2.578 0.252 CBG 58A 51
58A CBH C32 C 0 1 N N N N N N -12.546 -6.234 -54.066 -4.006 -1.641 -0.330 CBH 58A 52
58A CBI C33 C 0 1 N N N N N N -13.399 -6.742 -52.843 -5.224 -2.457 -0.767 CBI 58A 53
58A CBJ C34 C 0 1 N N N N N N -13.875 -5.583 -51.891 -6.284 -1.520 -1.349 CBJ 58A 54
58A CBK C35 C 0 1 N N N N N N -15.431 -5.401 -51.917 -7.502 -2.336 -1.787 CBK 58A 55
58A CBL C36 C 0 1 N N N N N N -16.005 -4.953 -50.552 -8.562 -1.399 -2.369 CBL 58A 56
58A CBM C37 C 0 1 N N N N N N -17.509 -5.302 -50.410 -9.761 -2.203 -2.799 CBM 58A 57
58A CBN C38 C 0 1 N N N N N N -18.005 -5.228 -48.944 -10.950 -1.904 -2.338 CBN 58A 58
58A CBO C39 C 0 1 N N N N N N -19.538 -5.493 -48.831 -12.150 -2.708 -2.769 CBO 58A 59
58A CBP C40 C 0 1 N N N N N N -20.068 -5.383 -47.360 -12.876 -3.243 -1.533 CBP 58A 60
58A CBQ C41 C 0 1 N N N N N N -21.546 -4.877 -47.305 -14.094 -4.060 -1.970 CBQ 58A 61
58A CBR C42 C 0 1 N N N N N N -21.692 -3.554 -46.505 -14.819 -4.595 -0.734 CBR 58A 62
58A CBS C43 C 0 1 N N N N N N -22.897 -3.584 -45.545 -16.037 -5.411 -1.171 CBS 58A 63
58A CBT C44 C 0 1 N N N N N N -22.488 -3.459 -44.072 -16.763 -5.946 0.065 CBT 58A 64
58A H1 H1 H 0 1 N N N N N N -2.700 -21.748 -59.085 -10.206 3.235 -1.010 H1 58A 65
58A H2 H2 H 0 1 N N N N N N -3.987 -20.652 -58.709 -10.045 2.425 -2.473 H2 58A 66
58A H3 H3 H 0 1 N N N N N N -3.633 -18.181 -58.836 -7.933 2.263 -3.667 H3 58A 67
58A H4 H4 H 0 1 N N N N N N -2.077 -16.309 -59.318 -5.558 2.857 -3.675 H4 58A 68
58A H5 H5 H 0 1 N N N N N N 1.354 -16.723 -59.536 -3.761 3.820 -2.677 H5 58A 69
58A H6 H6 H 0 1 N N N N N N -0.230 -16.789 -61.971 -5.005 6.288 -1.450 H6 58A 70
58A H7 H7 H 0 1 N N N N N N 1.945 -17.874 -61.370 -3.751 7.219 -3.257 H7 58A 71
58A H8 H8 H 0 1 N N N N N N -0.171 -14.520 -62.213 -3.184 6.689 -0.088 H8 58A 72
58A H9 H9 H 0 1 N N N N N N 1.891 -13.572 -62.244 -2.086 7.564 -2.049 H9 58A 73
58A H10 H10 H 0 1 N N N N N N 1.525 -14.081 -59.708 -1.671 4.281 -1.116 H10 58A 74
58A H11 H11 H 0 1 N N N N N N 0.315 -12.135 -59.566 -1.201 5.460 1.086 H11 58A 75
58A H12 H12 H 0 1 N N N N N N -0.234 -12.501 -61.236 -2.827 4.978 1.628 H12 58A 76
58A H13 H13 H 0 1 N N N N N N -1.119 -11.847 -56.758 -2.821 2.637 3.763 H13 58A 77
58A H14 H14 H 0 1 N N N N N N -4.296 -12.499 -58.496 -0.916 -0.286 4.901 H14 58A 78
58A H15 H15 H 0 1 N N N N N N -4.727 -7.731 -59.219 3.172 -0.699 3.964 H15 58A 79
58A H16 H16 H 0 1 N N N N N N -6.250 -8.567 -59.678 1.881 -1.744 4.605 H16 58A 80
58A H17 H17 H 0 1 N N N N N N -6.638 -6.595 -58.201 3.372 -3.083 3.198 H17 58A 81
58A H18 H18 H 0 1 N N N N N N -6.816 -7.007 -54.306 5.269 -1.631 -0.421 H18 58A 82
58A H19 H19 H 0 1 N N N N N N -5.361 -6.053 -53.861 5.064 -0.018 0.303 H19 58A 83
58A H20 H20 H 0 1 N N N N N N -6.683 -3.942 -54.537 7.081 -0.389 1.698 H20 58A 84
58A H21 H21 H 0 1 N N N N N N -8.138 -4.990 -54.648 7.286 -2.001 0.974 H21 58A 85
58A H22 H22 H 0 1 N N N N N N -6.800 -5.464 -52.090 7.524 -0.965 -1.266 H22 58A 86
58A H23 H23 H 0 1 N N N N N N -7.053 -3.699 -52.307 7.319 0.648 -0.542 H23 58A 87
58A H24 H24 H 0 1 N N N N N N -9.451 -3.988 -52.551 9.335 0.278 0.854 H24 58A 88
58A H25 H25 H 0 1 N N N N N N -9.287 -5.774 -52.659 9.541 -1.335 0.129 H25 58A 89
58A H26 H26 H 0 1 N N N N N N -9.288 -6.012 -50.394 9.779 -0.299 -2.111 H26 58A 90
58A H27 H27 H 0 1 N N N N N N -8.089 -4.691 -50.178 9.574 1.314 -1.387 H27 58A 91
58A H28 H28 H 0 1 N N N N N N -9.844 -2.999 -50.159 11.590 0.944 0.009 H28 58A 92
58A H29 H29 H 0 1 N N N N N N -11.086 -4.201 -50.650 11.795 -0.669 -0.716 H29 58A 93
58A H30 H30 H 0 1 N N N N N N -10.770 -5.412 -48.489 12.034 0.367 -2.956 H30 58A 94
58A H31 H31 H 0 1 N N N N N N -9.527 -4.212 -47.998 11.829 1.980 -2.231 H31 58A 95
58A H32 H32 H 0 1 N N N N N N -11.734 -2.430 -48.253 14.006 1.493 -0.834 H32 58A 96
58A H34 H34 H 0 1 N N N N N N -11.980 -4.760 -46.069 14.188 -0.022 -3.457 H34 58A 97
58A H36 H36 H 0 1 N N N N N N -14.236 -3.020 -46.945 16.520 1.102 -2.980 H36 58A 98
58A H37 H37 H 0 1 N N N N N N -14.165 -4.332 -48.171 16.145 0.948 -1.247 H37 58A 99
58A H38 H38 H 0 1 N N N N N N -14.897 -5.965 -46.676 16.047 -1.518 -1.487 H38 58A 100
58A H39 H39 H 0 1 N N N N N N -14.218 -5.116 -45.245 16.422 -1.364 -3.220 H39 58A 101
58A H40 H40 H 0 1 N N N N N N -16.080 -3.318 -45.718 18.578 -0.277 -2.657 H40 58A 102
58A H41 H41 H 0 1 N N N N N N -16.841 -4.600 -46.721 18.203 -0.431 -0.924 H41 58A 103
58A H42 H42 H 0 1 N N N N N N -17.416 -5.895 -44.887 18.105 -2.897 -1.165 H42 58A 104
58A H43 H43 H 0 1 N N N N N N -15.988 -5.373 -43.930 18.480 -2.743 -2.898 H43 58A 105
58A H44 H44 H 0 1 N N N N N N -17.070 -3.520 -43.058 20.636 -1.656 -2.334 H44 58A 106
58A H45 H45 H 0 1 N N N N N N -18.094 -3.293 -44.516 20.261 -1.811 -0.601 H45 58A 107
58A H46 H46 H 0 1 N N N N N N -19.818 -4.194 -43.207 20.163 -4.277 -0.842 H46 58A 108
58A H47 H47 H 0 1 N N N N N N -18.993 -5.779 -43.394 20.538 -4.122 -2.575 H47 58A 109
58A H49 H49 H 0 1 N N N N N N -8.077 -8.780 -58.197 1.707 -3.855 1.482 H49 58A 110
58A H50 H50 H 0 1 N N N N N N -7.332 -9.097 -56.594 0.994 -3.657 3.100 H50 58A 111
58A H51 H51 H 0 1 N N N N N N -9.758 -7.209 -53.931 -2.029 -1.038 1.447 H51 58A 112
58A H52 H52 H 0 1 N N N N N N -10.143 -6.004 -55.207 -1.315 -1.236 -0.172 H52 58A 113
58A H53 H53 H 0 1 N N N N N N -12.172 -7.554 -55.766 -2.645 -3.301 -0.506 H53 58A 114
58A H54 H54 H 0 1 N N N N N N -11.855 -8.304 -54.165 -3.359 -3.103 1.113 H54 58A 115
58A H55 H55 H 0 1 N N N N N N -11.831 -5.479 -53.708 -4.307 -0.917 0.428 H55 58A 116
58A H56 H56 H 0 1 N N N N N N -13.223 -5.778 -54.803 -3.593 -1.115 -1.191 H56 58A 117
58A H57 H57 H 0 1 N N N N N N -14.287 -7.263 -53.229 -4.923 -3.181 -1.525 H57 58A 118
58A H58 H58 H 0 1 N N N N N N -12.787 -7.445 -52.258 -5.637 -2.983 0.094 H58 58A 119
58A H59 H59 H 0 1 N N N N N N -13.562 -5.818 -50.863 -6.585 -0.796 -0.592 H59 58A 120
58A H60 H60 H 0 1 N N N N N N -13.402 -4.643 -52.213 -5.871 -0.994 -2.210 H60 58A 121
58A H61 H61 H 0 1 N N N N N N -15.683 -4.641 -52.671 -7.201 -3.060 -2.544 H61 58A 122
58A H62 H62 H 0 1 N N N N N N -15.892 -6.360 -52.195 -7.915 -2.862 -0.926 H62 58A 123
58A H63 H63 H 0 1 N N N N N N -15.446 -5.457 -49.750 -8.863 -0.676 -1.611 H63 58A 124
58A H64 H64 H 0 1 N N N N N N -15.883 -3.864 -50.456 -8.149 -0.873 -3.230 H64 58A 125
58A H65 H65 H 0 1 N N N N N N -18.143 -5.568 -51.243 -9.641 -3.027 -3.488 H65 58A 126
58A H67 H67 H 0 1 N N N N N N -17.365 -5.018 -48.100 -11.071 -1.081 -1.650 H67 58A 127
58A H69 H69 H 0 1 N N N N N N -20.069 -4.756 -49.452 -12.827 -2.074 -3.341 H69 58A 128
58A H70 H70 H 0 1 N N N N N N -19.748 -6.506 -49.205 -11.824 -3.543 -3.389 H70 58A 129
58A H71 H71 H 0 1 N N N N N N -20.015 -6.375 -46.888 -12.199 -3.878 -0.961 H71 58A 130
58A H72 H72 H 0 1 N N N N N N -19.431 -4.679 -46.805 -13.202 -2.408 -0.913 H72 58A 131
58A H73 H73 H 0 1 N N N N N N -21.900 -4.709 -48.333 -14.770 -3.425 -2.542 H73 58A 132
58A H74 H74 H 0 1 N N N N N N -22.166 -5.649 -46.826 -13.767 -4.895 -2.590 H74 58A 133
58A H75 H75 H 0 1 N N N N N N -20.776 -3.392 -45.918 -14.143 -5.230 -0.162 H75 58A 134
58A H76 H76 H 0 1 N N N N N N -21.825 -2.724 -47.214 -15.145 -3.760 -0.114 H76 58A 135
58A H77 H77 H 0 1 N N N N N N -23.567 -2.748 -45.796 -16.714 -4.777 -1.743 H77 58A 136
58A H78 H78 H 0 1 N N N N N N -23.431 -4.536 -45.682 -15.711 -6.247 -1.791 H78 58A 137
58A H79 H79 H 0 1 N N N N N N -23.055 -2.528 -43.927 -16.086 -6.581 0.637 H79 58A 138
58A H80 H80 H 0 1 N N N N N N -23.104 -4.316 -43.762 -17.089 -5.111 0.685 H80 58A 139
58A C1 C45 C 0 1 N N N N N N ? ? ? 22.176 -3.634 -1.263 C1 58A 140
58A C2 C46 C 0 1 N N N N N N ? ? ? 22.740 -5.056 -1.268 C2 58A 141
58A C3 C47 C 0 1 N N N N N N ? ? ? -17.981 -6.763 -0.373 C3 58A 142
58A C4 C48 C 0 1 N N N N N N ? ? ? -18.706 -7.298 0.864 C4 58A 143
58A H33 H33 H 0 1 N N N N N N ? ? ? 22.695 -3.035 -2.012 H33 58A 144
58A H35 H35 H 0 1 N N N N N N ? ? ? 22.320 -3.190 -0.279 H35 58A 145
58A H48 H48 H 0 1 N N N N N N ? ? ? 22.597 -5.501 -2.253 H48 58A 146
58A H66 H66 H 0 1 N N N N N N ? ? ? 23.805 -5.026 -1.035 H66 58A 147
58A H68 H68 H 0 1 N N N N N N ? ? ? 22.222 -5.656 -0.520 H68 58A 148
58A H81 H81 H 0 1 N N N N N N ? ? ? -18.657 -6.128 -0.945 H81 58A 149
58A H82 H82 H 0 1 N N N N N N ? ? ? -17.655 -7.598 -0.992 H82 58A 150
58A H83 H83 H 0 1 N N N N N N ? ? ? -19.033 -6.463 1.484 H83 58A 151
58A H84 H84 H 0 1 N N N N N N ? ? ? -19.574 -7.880 0.552 H84 58A 152
58A H85 H85 H 0 1 N N N N N N ? ? ? -18.030 -7.933 1.436 H85 58A 153
#
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
58A "O3'" "C3'" SING N N 1
58A "O2'" "C2'" SING N N 2
58A "C3'" "C2'" SING N N 3
58A "C3'" "C4'" SING N N 4
58A "C2'" "C1'" SING N N 5
58A OAX PAV DOUB N N 6
58A OAA CAB DOUB N N 7
58A "C5'" "C4'" SING N N 8
58A "C5'" "O5'" SING N N 9
58A "C4'" "O4'" SING N N 10
58A "C1'" NAH SING N N 11
58A "C1'" "O4'" SING N N 12
58A CAB NAH SING N N 13
58A CAB NAC SING N N 14
58A NAH CAG SING N N 15
58A "O5'" PAR SING N N 16
58A NAC CAD DOUB N N 17
58A CAG CAF DOUB N N 18
58A PAV OAU SING N N 19
58A PAV OAW SING N N 20
58A PAV OAY SING N N 21
58A CAD CAF SING N N 22
58A CAD NAE SING N N 23
58A OAU PAR SING N N 24
58A CAZ OAY SING N N 25
58A CAZ CBA SING N N 26
58A PAR OAT DOUB N N 27
58A PAR OAS SING N N 28
58A CBA CBC SING N N 29
58A CBA OBB SING N N 30
58A CBC OBD SING N N 31
58A OBD CBE SING N N 32
58A OBB CBU SING N N 33
58A OCK CBU DOUB N N 34
58A OCL CBE DOUB N N 35
58A CBU CBV SING N N 36
58A CBE CBF SING N N 37
58A CBF CBG SING N N 38
58A CBG CBH SING N N 39
58A CBV CBW SING N N 40
58A CBW CBX SING N N 41
58A CBH CBI SING N N 42
58A CBI CBJ SING N N 43
58A CBX CBY SING N N 44
58A CBY CBZ SING N N 45
58A CBK CBJ SING N N 46
58A CBK CBL SING N N 47
58A CBZ CCA SING N N 48
58A CBL CBM SING N N 49
58A CBM CBN DOUB N E 50
58A CCA CCB SING N N 51
58A CBN CBO SING N N 52
58A CBO CBP SING N N 53
58A CCB CCC SING N N 54
58A CCC CCD DOUB N E 55
58A CBP CBQ SING N N 56
58A CBQ CBR SING N N 57
58A CCE CCD SING N N 58
58A CCE CCF SING N N 59
58A CBR CBS SING N N 60
58A CCF CCG SING N N 61
58A CCG CCH SING N N 62
58A CBS CBT SING N N 63
58A CCH CCI SING N N 64
58A CCI CCJ SING N N 65
58A NAE H1 SING N N 66
58A NAE H2 SING N N 67
58A CAF H3 SING N N 68
58A CAG H4 SING N N 69
58A "C1'" H5 SING N N 70
58A "C2'" H6 SING N N 71
58A "O2'" H7 SING N N 72
58A "C3'" H8 SING N N 73
58A "O3'" H9 SING N N 74
58A "C4'" H10 SING N N 75
58A "C5'" H11 SING N N 76
58A "C5'" H12 SING N N 77
58A OAS H13 SING N N 78
58A OAW H14 SING N N 79
58A CAZ H15 SING N N 80
58A CAZ H16 SING N N 81
58A CBA H17 SING N N 82
58A CBV H18 SING N N 83
58A CBV H19 SING N N 84
58A CBW H20 SING N N 85
58A CBW H21 SING N N 86
58A CBX H22 SING N N 87
58A CBX H23 SING N N 88
58A CBY H24 SING N N 89
58A CBY H25 SING N N 90
58A CBZ H26 SING N N 91
58A CBZ H27 SING N N 92
58A CCA H28 SING N N 93
58A CCA H29 SING N N 94
58A CCB H30 SING N N 95
58A CCB H31 SING N N 96
58A CCC H32 SING N N 97
58A CCD H34 SING N N 98
58A CCE H36 SING N N 99
58A CCE H37 SING N N 100
58A CCF H38 SING N N 101
58A CCF H39 SING N N 102
58A CCG H40 SING N N 103
58A CCG H41 SING N N 104
58A CCH H42 SING N N 105
58A CCH H43 SING N N 106
58A CCI H44 SING N N 107
58A CCI H45 SING N N 108
58A CCJ H46 SING N N 109
58A CCJ H47 SING N N 110
58A CBC H49 SING N N 111
58A CBC H50 SING N N 112
58A CBF H51 SING N N 113
58A CBF H52 SING N N 114
58A CBG H53 SING N N 115
58A CBG H54 SING N N 116
58A CBH H55 SING N N 117
58A CBH H56 SING N N 118
58A CBI H57 SING N N 119
58A CBI H58 SING N N 120
58A CBJ H59 SING N N 121
58A CBJ H60 SING N N 122
58A CBK H61 SING N N 123
58A CBK H62 SING N N 124
58A CBL H63 SING N N 125
58A CBL H64 SING N N 126
58A CBM H65 SING N N 127
58A CBN H67 SING N N 128
58A CBO H69 SING N N 129
58A CBO H70 SING N N 130
58A CBP H71 SING N N 131
58A CBP H72 SING N N 132
58A CBQ H73 SING N N 133
58A CBQ H74 SING N N 134
58A CBR H75 SING N N 135
58A CBR H76 SING N N 136
58A CBS H77 SING N N 137
58A CBS H78 SING N N 138
58A CBT H79 SING N N 139
58A CBT H80 SING N N 140
58A CCJ C1 SING N N 141
58A C1 C2 SING N N 142
58A CBT C3 SING N N 143
58A C3 C4 SING N N 144
58A C1 H33 SING N N 145
58A C1 H35 SING N N 146
58A C2 H48 SING N N 147
58A C2 H66 SING N N 148
58A C2 H68 SING N N 149
58A C3 H81 SING N N 150
58A C3 H82 SING N N 151
58A C4 H83 SING N N 152
58A C4 H84 SING N N 153
58A C4 H85 SING N N 154
#
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
58A SMILES ACDLabs 12.01 "O=C1N(C=CC(=N1)N)C2OC(C(C2O)O)COP(=O)(O)OP(O)(OCC(COC(CCCCCCC\C=C\CCCCCCCC)=O)OC(CCCCCCCC=[C@H]CCCCCCCC)=O)=O"
58A InChI InChI 1.03 "InChI=1S/C48H85N3O15P2/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-43(52)61-37-40(64-44(53)34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2)38-62-67(57,58)66-68(59,60)63-39-41-45(54)46(55)47(65-41)51-36-35-42(49)50-48(51)56/h17-20,35-36,40-41,45-47,54-55H,3-16,21-34,37-39H2,1-2H3,(H,57,58)(H,59,60)(H2,49,50,56)/b19-17+,20-18+/t40-,41-,45-,46-,47-/m1/s1"
58A InChIKey InChI 1.03 WVVFFOKRFKIBHD-ZIPNUMAKSA-N
58A SMILES_CANONICAL CACTVS 3.385 "CCCCCCCC/C=C/CCCCCCCC(=O)OC[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=NC2=O)N)OC(=O)CCCCCCC\C=C\CCCCCCCC"
58A SMILES CACTVS 3.385 "CCCCCCCCC=CCCCCCCCC(=O)OC[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=NC2=O)N)OC(=O)CCCCCCCC=CCCCCCCCC"
58A SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "CCCCCCCC/C=C/CCCCCCCC(=O)OC[C@H](COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=NC2=O)N)O)O)OC(=O)CCCCCCCC=CCCCCCCCC"
58A SMILES "OpenEye OEToolkits" 1.9.2 "CCCCCCCCC=CCCCCCCCC(=O)OCC(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)N2C=CC(=NC2=O)N)O)O)OC(=O)CCCCCCCC=CCCCCCCCC"
#
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
58A "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(R)-{[(S)-{(2R)-2,3-bis[(9E)-octadec-9-enoyloxy]propoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine"
58A "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(2R)-3-[[[(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-2-octadec-9-enoyloxy-propyl] (E)-octadec-9-enoate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
58A "Create component" 2015-08-19 RCSB
58A "Initial release" 2015-11-04 RCSB
58A "Modify synonyms" 2020-05-26 PDBE
58A "Modify synonyms" 2020-07-02 RCSB
58A "Modify PCM" 2024-09-27 PDBE
#
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 58A cytidinediphosphate-dioleoylglycerol PUBCHEM ?
2 58A CDP-1,2-dioleoyl-sn-glycerol CHEBI ?
#
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_pdbx_chem_comp_pcm.comp_id_linking_atom
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
1 58A LEU None Lipid/lipid-like "Amino-acid side chain" "Any position" CCD CD1 ? ?
2 58A THR None Lipid/lipid-like "Amino-acid side chain" "Any position" NAE OG1 ? ?
#