data_II3
#
_chem_comp.id II3
_chem_comp.name
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C40 H54 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms Monadoxanthin
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-07-01
_chem_comp.pdbx_modified_date 2023-04-19
_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 566.856
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code II3
_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 7Y7B
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
II3 C03 C1 C 0 1 N N N N N N 219.487 163.013 149.395 -12.139 0.143 -1.190 C03 II3 1
II3 C04 C2 C 0 1 N N R N N N 218.368 163.284 148.430 -11.370 -0.238 0.077 C04 II3 2
II3 C05 C3 C 0 1 N N N N N N 220.701 163.780 148.939 -13.598 -0.302 -1.029 C05 II3 3
II3 C06 C4 C 0 1 N N R N N N 220.454 165.268 149.083 -14.243 0.544 0.071 C06 II3 4
II3 C07 C5 C 0 1 N N N N N N 218.086 164.741 148.531 -12.117 0.222 1.294 C07 II3 5
II3 C08 C6 C 0 1 N N N N N N 219.064 163.507 150.763 -12.082 1.659 -1.389 C08 II3 6
II3 C09 C7 C 0 1 N N N N N N 219.810 161.537 149.425 -11.518 -0.558 -2.399 C09 II3 7
II3 C10 C8 C 0 1 N N N N N N 219.090 165.615 148.546 -13.371 0.556 1.292 C10 II3 8
II3 C11 C9 C 0 1 N N N N N N 201.692 151.696 159.363 11.584 1.702 -0.103 C11 II3 9
II3 C12 C10 C 0 1 N N N N N N 217.177 162.415 148.767 -10.010 0.411 0.050 C12 II3 10
II3 C13 C11 C 0 1 N N N N N N 200.386 151.580 158.621 12.976 2.153 -0.549 C13 II3 11
II3 C14 C12 C 0 1 N N R N N N 199.266 151.515 159.637 14.021 1.418 0.299 C14 II3 12
II3 C15 C13 C 0 1 N N N N N N 216.688 165.242 148.603 -11.365 0.301 2.598 C15 II3 13
II3 C16 C14 C 0 1 N N N N N N 201.712 153.071 159.916 11.516 0.204 -0.058 C16 II3 14
II3 C17 C15 C 0 1 N N N N N N 199.466 152.539 160.747 13.992 -0.066 -0.071 C17 II3 15
II3 C18 C16 C 0 1 N N N N N N 200.584 153.508 160.452 12.582 -0.579 -0.040 C18 II3 16
II3 C19 C17 C 0 1 N N N N N N 202.891 151.507 158.452 10.543 2.228 -1.094 C19 II3 17
II3 C20 C18 C 0 1 N N N N N N 201.723 150.726 160.528 11.289 2.266 1.289 C20 II3 18
II3 C21 C19 C 0 1 N N N N N N 216.304 162.652 149.739 -8.908 -0.345 0.067 C21 II3 19
II3 C22 C20 C 0 1 N N N N N N 200.404 154.954 160.783 12.368 -2.070 0.016 C22 II3 20
II3 C23 C21 C 0 1 N N N N N N 202.764 153.759 159.852 10.224 -0.414 -0.033 C23 II3 21
II3 C24 C22 C 0 1 N N N N N N 215.193 161.698 149.931 -7.629 0.267 0.042 C24 II3 22
II3 C25 C23 C 0 1 N N N N N N 214.924 160.664 148.895 -7.512 1.768 -0.003 C25 II3 23
II3 C26 C24 C 0 1 N N N N N N 214.419 161.735 151.020 -6.508 -0.502 0.059 C26 II3 24
II3 C27 C25 C 0 1 N N N N N N 203.749 154.416 159.760 9.165 -0.920 -0.012 C27 II3 25
II3 C28 C26 C 0 1 N N N N N N 204.752 155.166 159.640 7.873 -1.537 0.013 C28 II3 26
II3 C29 C27 C 0 1 N N N N N N 213.328 160.779 151.213 -5.240 0.104 0.034 C29 II3 27
II3 C30 C28 C 0 1 N N N N N N 205.161 156.027 160.788 7.756 -3.039 0.059 C30 II3 28
II3 C31 C29 C 0 1 N N N N N N 205.449 155.223 158.495 6.747 -0.765 -0.004 C31 II3 29
II3 C32 C30 C 0 1 N N N N N N 212.740 160.702 152.407 -4.114 -0.668 0.051 C32 II3 30
II3 C33 C31 C 0 1 N N N N N N 211.642 159.763 152.699 -2.850 -0.064 0.026 C33 II3 31
II3 C34 C32 C 0 1 N N N N N N 206.595 156.120 158.347 5.483 -1.369 0.021 C34 II3 32
II3 C35 C33 C 0 1 N N N N N N 211.161 158.814 151.655 -2.733 1.438 -0.019 C35 II3 33
II3 C36 C34 C 0 1 N N N N N N 211.081 159.745 153.912 -1.714 -0.842 0.044 C36 II3 34
II3 C37 C35 C 0 1 N N N N N N 207.150 156.284 157.149 4.347 -0.591 0.004 C37 II3 35
II3 C38 C36 C 0 1 N N N N N N 208.286 157.198 156.930 3.084 -1.194 0.029 C38 II3 36
II3 C39 C37 C 0 1 N N N N N N 209.997 158.822 154.236 -0.451 -0.239 0.019 C39 II3 37
II3 C40 C38 C 0 1 N N N N N N 208.821 157.310 155.705 1.948 -0.415 0.011 C40 II3 38
II3 C41 C39 C 0 1 N N N N N N 209.932 158.216 155.421 0.685 -1.018 0.036 C41 II3 39
II3 C42 C40 C 0 1 N N N N N N 208.814 158.019 158.061 2.967 -2.696 0.074 C42 II3 40
II3 O01 O1 O 0 1 N N N N N N 221.445 165.962 148.321 -15.517 -0.010 0.408 O01 II3 41
II3 O02 O2 O 0 1 N N N N N N 198.043 151.786 158.959 15.319 1.954 0.034 O02 II3 42
II3 H1 H1 H 0 1 N N N N N N 218.706 163.048 147.410 -11.250 -1.321 0.115 H1 II3 43
II3 H2 H2 H 0 1 N N N N N N 220.906 163.545 147.884 -14.132 -0.152 -1.967 H2 II3 44
II3 H3 H3 H 0 1 N N N N N N 221.566 163.493 149.554 -13.631 -1.355 -0.749 H3 II3 45
II3 H4 H4 H 0 1 N N N N N N 220.514 165.548 150.145 -14.376 1.564 -0.288 H4 II3 46
II3 H6 H6 H 0 1 N N N N N N 219.870 163.318 151.487 -12.637 1.928 -2.288 H6 II3 47
II3 H7 H7 H 0 1 N N N N N N 218.859 164.587 150.716 -12.525 2.156 -0.526 H7 II3 48
II3 H8 H8 H 0 1 N N N N N N 218.155 162.975 151.080 -11.044 1.973 -1.496 H8 II3 49
II3 H9 H9 H 0 1 N N N N N N 220.630 161.355 150.135 -10.479 -0.246 -2.506 H9 II3 50
II3 H10 H10 H 0 1 N N N N N N 218.920 160.973 149.741 -11.559 -1.638 -2.254 H10 II3 51
II3 H11 H11 H 0 1 N N N N N N 220.115 161.208 148.421 -12.072 -0.291 -3.299 H11 II3 52
II3 H12 H12 H 0 1 N N N N N N 218.920 166.609 148.159 -13.814 0.867 2.227 H12 II3 53
II3 H14 H14 H 0 1 N N N N N N 217.024 161.529 148.168 -9.926 1.488 0.018 H14 II3 54
II3 H15 H15 H 0 1 N N N N N N 200.248 152.457 157.971 13.121 1.909 -1.601 H15 II3 55
II3 H16 H16 H 0 1 N N N N N N 200.386 150.666 158.009 13.077 3.228 -0.402 H16 II3 56
II3 H17 H17 H 0 1 N N N N N N 199.241 150.509 160.080 13.783 1.535 1.357 H17 II3 57
II3 H18 H18 H 0 1 N N N N N N 216.695 166.340 148.673 -10.924 1.292 2.703 H18 II3 58
II3 H19 H19 H 0 1 N N N N N N 216.142 164.935 147.699 -12.052 0.119 3.424 H19 II3 59
II3 H20 H20 H 0 1 N N N N N N 216.193 164.821 149.491 -10.576 -0.451 2.608 H20 II3 60
II3 H21 H21 H 0 1 N N N N N N 198.533 153.107 160.874 14.401 -0.197 -1.073 H21 II3 61
II3 H22 H22 H 0 1 N N N N N N 199.700 152.005 161.680 14.595 -0.629 0.642 H22 II3 62
II3 H23 H23 H 0 1 N N N N N N 203.817 151.601 159.039 9.548 1.918 -0.774 H23 II3 63
II3 H24 H24 H 0 1 N N N N N N 202.848 150.509 157.992 10.590 3.316 -1.128 H24 II3 64
II3 H25 H25 H 0 1 N N N N N N 202.877 152.275 157.664 10.748 1.824 -2.085 H25 II3 65
II3 H26 H26 H 0 1 N N N N N N 200.842 150.890 161.166 12.027 1.889 1.997 H26 II3 66
II3 H27 H27 H 0 1 N N N N N N 201.712 149.694 160.146 11.338 3.354 1.258 H27 II3 67
II3 H28 H28 H 0 1 N N N N N N 202.638 150.889 161.117 10.293 1.955 1.603 H28 II3 68
II3 H29 H29 H 0 1 N N N N N N 216.404 163.520 150.373 -8.991 -1.421 0.100 H29 II3 69
II3 H30 H30 H 0 1 N N N N N N 199.405 155.110 161.216 12.307 -2.466 -0.998 H30 II3 70
II3 H31 H31 H 0 1 N N N N N N 201.171 155.262 161.509 13.203 -2.537 0.539 H31 II3 71
II3 H32 H32 H 0 1 N N N N N N 200.504 155.555 159.867 11.441 -2.285 0.546 H32 II3 72
II3 H33 H33 H 0 1 N N N N N N 214.067 160.048 149.205 -7.478 2.161 1.013 H33 II3 73
II3 H34 H34 H 0 1 N N N N N N 214.695 161.155 147.938 -6.599 2.046 -0.531 H34 II3 74
II3 H35 H35 H 0 1 N N N N N N 215.811 160.025 148.776 -8.374 2.184 -0.525 H35 II3 75
II3 H36 H36 H 0 1 N N N N N N 214.603 162.486 151.774 -6.592 -1.578 0.092 H36 II3 76
II3 H37 H37 H 0 1 N N N N N N 213.004 160.145 150.401 -5.156 1.180 0.002 H37 II3 77
II3 H38 H38 H 0 1 N N N N N N 204.484 155.852 161.637 7.733 -3.370 1.097 H38 II3 78
II3 H39 H39 H 0 1 N N N N N N 206.191 155.779 161.083 6.838 -3.347 -0.441 H39 II3 79
II3 H40 H40 H 0 1 N N N N N N 205.109 157.085 160.490 8.613 -3.485 -0.447 H40 II3 80
II3 H41 H41 H 0 1 N N N N N N 205.158 154.594 157.666 6.831 0.311 -0.036 H41 II3 81
II3 H42 H42 H 0 1 N N N N N N 213.083 161.356 153.195 -4.198 -1.744 0.084 H42 II3 82
II3 H43 H43 H 0 1 N N N N N N 206.988 156.646 159.205 5.399 -2.445 0.054 H43 II3 83
II3 H44 H44 H 0 1 N N N N N N 210.343 158.202 152.064 -2.699 1.831 0.997 H44 II3 84
II3 H45 H45 H 0 1 N N N N N N 210.796 159.380 150.785 -1.820 1.716 -0.546 H45 II3 85
II3 H46 H46 H 0 1 N N N N N N 211.989 158.159 151.345 -3.595 1.854 -0.541 H46 II3 86
II3 H47 H47 H 0 1 N N N N N N 211.437 160.428 154.669 -1.798 -1.919 0.076 H47 II3 87
II3 H48 H48 H 0 1 N N N N N N 206.756 155.730 156.310 4.431 0.486 -0.029 H48 II3 88
II3 H49 H49 H 0 1 N N N N N N 209.232 158.626 153.500 -0.368 0.837 -0.014 H49 II3 89
II3 H50 H50 H 0 1 N N N N N N 208.417 156.711 154.902 2.032 0.661 -0.021 H50 II3 90
II3 H51 H51 H 0 1 N N N N N N 210.694 158.393 156.165 0.601 -2.094 0.069 H51 II3 91
II3 H52 H52 H 0 1 N N N N N N 208.251 157.788 158.977 2.945 -3.027 1.112 H52 II3 92
II3 H53 H53 H 0 1 N N N N N N 209.878 157.787 158.217 2.049 -3.004 -0.426 H53 II3 93
II3 H54 H54 H 0 1 N N N N N N 208.702 159.087 157.822 3.824 -3.142 -0.431 H54 II3 94
II3 H55 H55 H 0 1 N N N N N N 222.309 165.748 148.654 -15.986 0.476 1.101 H55 II3 95
II3 H56 H56 H 0 1 N N N N N N 197.323 151.751 159.578 16.029 1.533 0.538 H56 II3 96
#
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
II3 O01 C06 SING N N 1
II3 C04 C07 SING N N 2
II3 C04 C12 SING N N 3
II3 C04 C03 SING N N 4
II3 C07 C10 DOUB N N 5
II3 C07 C15 SING N N 6
II3 C10 C06 SING N N 7
II3 C12 C21 DOUB N E 8
II3 C25 C24 SING N N 9
II3 C05 C06 SING N N 10
II3 C05 C03 SING N N 11
II3 C03 C09 SING N N 12
II3 C03 C08 SING N N 13
II3 C21 C24 SING N N 14
II3 C24 C26 DOUB N E 15
II3 C26 C29 SING N N 16
II3 C29 C32 DOUB N E 17
II3 C35 C33 SING N N 18
II3 C32 C33 SING N N 19
II3 C33 C36 DOUB N E 20
II3 C36 C39 SING N N 21
II3 C39 C41 DOUB N E 22
II3 C41 C40 SING N N 23
II3 C40 C38 DOUB N E 24
II3 C38 C37 SING N N 25
II3 C38 C42 SING N N 26
II3 C37 C34 DOUB N E 27
II3 C34 C31 SING N N 28
II3 C19 C11 SING N N 29
II3 C31 C28 DOUB N E 30
II3 C13 C11 SING N N 31
II3 C13 C14 SING N N 32
II3 O02 C14 SING N N 33
II3 C11 C16 SING N N 34
II3 C11 C20 SING N N 35
II3 C14 C17 SING N N 36
II3 C28 C27 SING N N 37
II3 C28 C30 SING N N 38
II3 C27 C23 TRIP N N 39
II3 C23 C16 SING N N 40
II3 C16 C18 DOUB N N 41
II3 C18 C17 SING N N 42
II3 C18 C22 SING N N 43
II3 C04 H1 SING N N 44
II3 C05 H2 SING N N 45
II3 C05 H3 SING N N 46
II3 C06 H4 SING N N 47
II3 C08 H6 SING N N 48
II3 C08 H7 SING N N 49
II3 C08 H8 SING N N 50
II3 C09 H9 SING N N 51
II3 C09 H10 SING N N 52
II3 C09 H11 SING N N 53
II3 C10 H12 SING N N 54
II3 C12 H14 SING N N 55
II3 C13 H15 SING N N 56
II3 C13 H16 SING N N 57
II3 C14 H17 SING N N 58
II3 C15 H18 SING N N 59
II3 C15 H19 SING N N 60
II3 C15 H20 SING N N 61
II3 C17 H21 SING N N 62
II3 C17 H22 SING N N 63
II3 C19 H23 SING N N 64
II3 C19 H24 SING N N 65
II3 C19 H25 SING N N 66
II3 C20 H26 SING N N 67
II3 C20 H27 SING N N 68
II3 C20 H28 SING N N 69
II3 C21 H29 SING N N 70
II3 C22 H30 SING N N 71
II3 C22 H31 SING N N 72
II3 C22 H32 SING N N 73
II3 C25 H33 SING N N 74
II3 C25 H34 SING N N 75
II3 C25 H35 SING N N 76
II3 C26 H36 SING N N 77
II3 C29 H37 SING N N 78
II3 C30 H38 SING N N 79
II3 C30 H39 SING N N 80
II3 C30 H40 SING N N 81
II3 C31 H41 SING N N 82
II3 C32 H42 SING N N 83
II3 C34 H43 SING N N 84
II3 C35 H44 SING N N 85
II3 C35 H45 SING N N 86
II3 C35 H46 SING N N 87
II3 C36 H47 SING N N 88
II3 C37 H48 SING N N 89
II3 C39 H49 SING N N 90
II3 C40 H50 SING N N 91
II3 C41 H51 SING N N 92
II3 C42 H52 SING N N 93
II3 C42 H53 SING N N 94
II3 C42 H54 SING N N 95
II3 O01 H55 SING N N 96
II3 O02 H56 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
II3 InChI InChI 1.06 InChI=1S/C40H54O2/c1-29(17-13-19-31(3)21-23-37-33(5)25-35(41)27-39(37,7)8)15-11-12-16-30(2)18-14-20-32(4)22-24-38-34(6)26-36(42)28-40(38,9)10/h11-21,23,25,35-37,41-42H,26-28H2,1-10H3/b12-11+,17-13+,18-14+,23-21+,29-15+,30-16+,31-19+,32-20+/t35-,36+,37-/m0/s1
II3 InChIKey InChI 1.06 VAGYSFRRYPPSFX-RLVOMNFVSA-N
II3 SMILES_CANONICAL CACTVS 3.385 "CC(=C\C=C\C=C(C)\C=C\C=C(C)\C#CC1=C(C)C[C@@H](O)CC1(C)C)/C=C/C=C(C)/C=C/[C@H]2C(=C[C@H](O)CC2(C)C)C"
II3 SMILES CACTVS 3.385 "CC(=CC=CC=C(C)C=CC=C(C)C#CC1=C(C)C[CH](O)CC1(C)C)C=CC=C(C)C=C[CH]2C(=C[CH](O)CC2(C)C)C"
II3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=C(C(C[C@@H](C1)O)(C)C)C#C/C(=C/C=C/C(=C/C=C/C=C(\C)/C=C/C=C(\C)/C=C/[C@H]2C(=C[C@@H](CC2(C)C)O)C)/C)/C"
II3 SMILES "OpenEye OEToolkits" 2.0.7 "CC1=C(C(CC(C1)O)(C)C)C#CC(=CC=CC(=CC=CC=C(C)C=CC=C(C)C=CC2C(=CC(CC2(C)C)O)C)C)C"
#
_pdbx_chem_comp_identifier.comp_id II3
_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
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
II3 'Create component' 2022-07-01 PDBJ
II3 'Initial release' 2023-04-12 RCSB
II3 'Modify synonyms' 2023-04-19 PDBJ
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id II3
_pdbx_chem_comp_synonyms.name Monadoxanthin
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id II3
_pdbe_chem_comp_synonyms.name Monadoxanthin
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
II3 C03 C 4.500 -12.000 1
II3 C04 C 5.799 -11.250 2
II3 C05 C 4.500 -13.500 3
II3 C06 C 5.799 -14.250 4
II3 C07 C 7.098 -12.000 5
II3 C08 C 3.750 -10.701 6
II3 C09 C 3.000 -12.000 7
II3 C10 C 7.098 -13.500 8
II3 C11 C 14.892 12.000 9
II3 C12 C 5.799 -9.750 10
II3 C13 C 14.892 13.500 11
II3 C14 C 16.191 14.250 12
II3 C15 C 8.397 -11.250 13
II3 C16 C 16.191 11.250 14
II3 C17 C 17.490 13.500 15
II3 C18 C 17.490 12.000 16
II3 C19 C 13.392 12.000 17
II3 C20 C 14.142 10.701 18
II3 C21 C 7.098 -9.000 19
II3 C22 C 18.790 11.250 20
II3 C23 C 16.191 9.750 21
II3 C24 C 7.098 -7.500 22
II3 C25 C 5.799 -6.750 23
II3 C26 C 8.397 -6.750 24
II3 C27 C 16.191 8.250 25
II3 C28 C 16.191 6.750 26
II3 C29 C 8.397 -5.250 27
II3 C30 C 17.490 6.000 28
II3 C31 C 14.892 6.000 29
II3 C32 C 9.696 -4.500 30
II3 C33 C 9.696 -3.000 31
II3 C34 C 14.892 4.500 32
II3 C35 C 8.397 -2.250 33
II3 C36 C 10.995 -2.250 34
II3 C37 C 13.593 3.750 35
II3 C38 C 13.593 2.250 36
II3 C39 C 10.995 -0.750 37
II3 C40 C 12.294 1.500 38
II3 C41 C 12.294 0.000 39
II3 C42 C 14.892 1.500 40
II3 O01 O 5.799 -15.750 41
II3 O02 O 16.191 15.750 42
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
II3 C06 O01 SINGLE BEGINDASH 1
II3 C04 C07 SINGLE NONE 2
II3 C04 C12 SINGLE BEGINWEDGE 3
II3 C04 C03 SINGLE NONE 4
II3 C07 C10 DOUBLE NONE 5
II3 C07 C15 SINGLE NONE 6
II3 C10 C06 SINGLE NONE 7
II3 C12 C21 DOUBLE NONE 8
II3 C25 C24 SINGLE ENDDOWNRIGHT 9
II3 C05 C06 SINGLE NONE 10
II3 C05 C03 SINGLE NONE 11
II3 C03 C09 SINGLE NONE 12
II3 C03 C08 SINGLE NONE 13
II3 C21 C24 SINGLE ENDUPRIGHT 14
II3 C24 C26 DOUBLE NONE 15
II3 C26 C29 SINGLE ENDUPRIGHT 16
II3 C29 C32 DOUBLE NONE 17
II3 C35 C33 SINGLE ENDDOWNRIGHT 18
II3 C32 C33 SINGLE ENDUPRIGHT 19
II3 C33 C36 DOUBLE NONE 20
II3 C36 C39 SINGLE ENDUPRIGHT 21
II3 C39 C41 DOUBLE NONE 22
II3 C41 C40 SINGLE ENDUPRIGHT 23
II3 C40 C38 DOUBLE NONE 24
II3 C38 C37 SINGLE ENDUPRIGHT 25
II3 C38 C42 SINGLE ENDDOWNRIGHT 26
II3 C37 C34 DOUBLE NONE 27
II3 C34 C31 SINGLE ENDUPRIGHT 28
II3 C19 C11 SINGLE NONE 29
II3 C31 C28 DOUBLE NONE 30
II3 C13 C11 SINGLE NONE 31
II3 C13 C14 SINGLE NONE 32
II3 C14 O02 SINGLE BEGINDASH 33
II3 C11 C16 SINGLE NONE 34
II3 C11 C20 SINGLE NONE 35
II3 C14 C17 SINGLE NONE 36
II3 C28 C27 SINGLE ENDUPRIGHT 37
II3 C28 C30 SINGLE ENDDOWNRIGHT 38
II3 C27 C23 TRIPLE NONE 39
II3 C23 C16 SINGLE NONE 40
II3 C16 C18 DOUBLE NONE 41
II3 C18 C17 SINGLE NONE 42
II3 C18 C22 SINGLE NONE 43
#
_pdbe_chem_comp_substructure.comp_id II3
_pdbe_chem_comp_substructure.substructure_name MurckoScaffold
_pdbe_chem_comp_substructure.id S1
_pdbe_chem_comp_substructure.substructure_type scaffold
_pdbe_chem_comp_substructure.substructure_smiles 'C(#CC1=CCCCC1)/C=C/C=C/C=C/C=C/C=C/C=C/C=C/C=C/[C@H]1C=CCCC1'
_pdbe_chem_comp_substructure.substructure_inchis
InChI=1S/C30H34/c1(3-5-7-9-11-13-17-23-29-25-19-15-20-26-29)2-4-6-8-10-12-14-18-24-30-27-21-16-22-28-30/h1-14,17,19,23,25,27,29H,15-16,20-22,26,28H2/b2-1+,5-3+,6-4+,9-7+,10-8+,13-11+,14-12+,23-17+/t29-/m0/s1
_pdbe_chem_comp_substructure.substructure_inchikeys PMQCVXYHQGYQAQ-KPLWHTCHSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
II3 C03 S1 1
II3 C04 S1 1
II3 C05 S1 1
II3 C06 S1 1
II3 C07 S1 1
II3 C10 S1 1
II3 C11 S1 1
II3 C12 S1 1
II3 C13 S1 1
II3 C14 S1 1
II3 C16 S1 1
II3 C17 S1 1
II3 C18 S1 1
II3 C21 S1 1
II3 C23 S1 1
II3 C24 S1 1
II3 C26 S1 1
II3 C27 S1 1
II3 C28 S1 1
II3 C29 S1 1
II3 C31 S1 1
II3 C32 S1 1
II3 C33 S1 1
II3 C34 S1 1
II3 C36 S1 1
II3 C37 S1 1
II3 C38 S1 1
II3 C39 S1 1
II3 C40 S1 1
II3 C41 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id II3
_pdbe_chem_comp_rdkit_properties.exactmw 566.412
_pdbe_chem_comp_rdkit_properties.amw 566.870
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 20
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 42
_pdbe_chem_comp_rdkit_properties.NumAtoms 96
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.450
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 332.694
_pdbe_chem_comp_rdkit_properties.tpsa 40.460
_pdbe_chem_comp_rdkit_properties.CrippenClogP 9.850
_pdbe_chem_comp_rdkit_properties.CrippenMR 182.738
_pdbe_chem_comp_rdkit_properties.chi0v 20.816
_pdbe_chem_comp_rdkit_properties.chi1v 10.658
_pdbe_chem_comp_rdkit_properties.chi2v 4.142
_pdbe_chem_comp_rdkit_properties.chi3v 4.142
_pdbe_chem_comp_rdkit_properties.chi4v 2.443
_pdbe_chem_comp_rdkit_properties.chi0n 74.816
_pdbe_chem_comp_rdkit_properties.chi1n 37.475
_pdbe_chem_comp_rdkit_properties.chi2n 4.142
_pdbe_chem_comp_rdkit_properties.chi3n 4.142
_pdbe_chem_comp_rdkit_properties.chi4n 2.443
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.120
_pdbe_chem_comp_rdkit_properties.kappa1 6.330
_pdbe_chem_comp_rdkit_properties.kappa2 15.925
_pdbe_chem_comp_rdkit_properties.kappa3 11.635
_pdbe_chem_comp_rdkit_properties.Phi 2.400
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
II3 UniChem ZINC ZINC000255272544
II3 UniChem PubChem 101306756
II3 UniChem NMRShiftDB 70074127
II3 UniChem LipidMaps LMPR01070902
II3 UniChem Nikkaji J17.266I
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
II3 C03 12.153 -1.433 0.080 ETKDGv3 1
II3 C04 11.121 -0.270 -0.119 ETKDGv3 2
II3 C05 13.539 -0.947 -0.408 ETKDGv3 3
II3 C06 14.026 0.286 0.373 ETKDGv3 4
II3 C07 11.631 1.084 0.379 ETKDGv3 5
II3 C08 11.744 -2.651 -0.780 ETKDGv3 6
II3 C09 12.238 -1.889 1.560 ETKDGv3 7
II3 C10 12.948 1.332 0.539 ETKDGv3 8
II3 C11 -11.787 0.085 1.383 ETKDGv3 9
II3 C12 9.789 -0.603 0.523 ETKDGv3 10
II3 C13 -12.653 0.554 2.577 ETKDGv3 11
II3 C14 -13.974 1.245 2.165 ETKDGv3 12
II3 C15 10.679 2.250 0.511 ETKDGv3 13
II3 C16 -11.541 1.282 0.465 ETKDGv3 14
II3 C17 -13.914 1.970 0.799 ETKDGv3 15
II3 C18 -12.521 2.191 0.249 ETKDGv3 16
II3 C19 -10.461 -0.477 1.954 ETKDGv3 17
II3 C20 -12.486 -1.045 0.597 ETKDGv3 18
II3 C21 8.746 -1.035 -0.197 ETKDGv3 19
II3 C22 -12.289 3.395 -0.634 ETKDGv3 20
II3 C23 -10.247 1.449 -0.170 ETKDGv3 21
II3 C24 7.435 -1.381 0.406 ETKDGv3 22
II3 C25 7.354 -1.862 1.837 ETKDGv3 23
II3 C26 6.333 -1.246 -0.357 ETKDGv3 24
II3 C27 -9.171 1.587 -0.695 ETKDGv3 25
II3 C28 -7.884 1.750 -1.323 ETKDGv3 26
II3 C29 4.955 -1.481 0.126 ETKDGv3 27
II3 C30 -7.698 2.890 -2.286 ETKDGv3 28
II3 C31 -6.904 0.881 -1.025 ETKDGv3 29
II3 C32 3.914 -1.393 -0.710 ETKDGv3 30
II3 C33 2.507 -1.591 -0.280 ETKDGv3 31
II3 C34 -5.546 0.948 -1.606 ETKDGv3 32
II3 C35 2.185 -2.470 0.908 ETKDGv3 33
II3 C36 1.539 -0.960 -0.973 ETKDGv3 34
II3 C37 -4.611 0.056 -1.259 ETKDGv3 35
II3 C38 -3.226 0.081 -1.796 ETKDGv3 36
II3 C39 0.103 -1.001 -0.620 ETKDGv3 37
II3 C40 -2.243 -0.431 -1.030 ETKDGv3 38
II3 C41 -0.809 -0.409 -1.396 ETKDGv3 39
II3 C42 -2.942 0.674 -3.157 ETKDGv3 40
II3 O01 15.156 0.844 -0.248 ETKDGv3 41
II3 O02 -15.019 0.306 2.139 ETKDGv3 42
II3 H1 10.968 -0.133 -1.213 ETKDGv3 43
II3 H2 13.477 -0.691 -1.490 ETKDGv3 44
II3 H3 14.294 -1.758 -0.305 ETKDGv3 45
II3 H4 14.335 -0.037 1.390 ETKDGv3 46
II3 H6 12.498 -3.464 -0.689 ETKDGv3 47
II3 H7 10.764 -3.059 -0.455 ETKDGv3 48
II3 H8 11.665 -2.371 -1.852 ETKDGv3 49
II3 H9 12.360 -1.024 2.244 ETKDGv3 50
II3 H10 11.316 -2.429 1.865 ETKDGv3 51
II3 H11 13.095 -2.581 1.708 ETKDGv3 52
II3 H12 13.266 2.320 0.864 ETKDGv3 53
II3 H14 9.701 -0.484 1.596 ETKDGv3 54
II3 H15 -12.062 1.285 3.175 ETKDGv3 55
II3 H16 -12.869 -0.301 3.256 ETKDGv3 56
II3 H17 -14.203 2.015 2.941 ETKDGv3 57
II3 H18 10.627 2.569 1.573 ETKDGv3 58
II3 H19 9.657 1.991 0.166 ETKDGv3 59
II3 H20 11.033 3.103 -0.108 ETKDGv3 60
II3 H21 -14.441 2.944 0.897 ETKDGv3 61
II3 H22 -14.481 1.393 0.037 ETKDGv3 62
II3 H23 -9.819 -0.891 1.146 ETKDGv3 63
II3 H24 -10.661 -1.296 2.678 ETKDGv3 64
II3 H25 -9.891 0.320 2.480 ETKDGv3 65
II3 H26 -11.833 -1.401 -0.229 ETKDGv3 66
II3 H27 -13.440 -0.709 0.147 ETKDGv3 67
II3 H28 -12.705 -1.906 1.265 ETKDGv3 68
II3 H29 8.845 -1.096 -1.275 ETKDGv3 69
II3 H30 -13.209 4.006 -0.741 ETKDGv3 70
II3 H31 -11.978 3.067 -1.649 ETKDGv3 71
II3 H32 -11.495 4.036 -0.196 ETKDGv3 72
II3 H33 8.341 -2.211 2.203 ETKDGv3 73
II3 H34 6.673 -2.734 1.920 ETKDGv3 74
II3 H35 6.993 -1.040 2.490 ETKDGv3 75
II3 H36 6.451 -0.921 -1.386 ETKDGv3 76
II3 H37 4.781 -1.680 1.175 ETKDGv3 77
II3 H38 -8.633 3.481 -2.388 ETKDGv3 78
II3 H39 -7.426 2.499 -3.289 ETKDGv3 79
II3 H40 -6.899 3.569 -1.920 ETKDGv3 80
II3 H41 -7.115 0.082 -0.321 ETKDGv3 81
II3 H42 4.096 -1.117 -1.744 ETKDGv3 82
II3 H43 -5.300 1.743 -2.297 ETKDGv3 83
II3 H44 1.943 -1.839 1.788 ETKDGv3 84
II3 H45 3.033 -3.138 1.161 ETKDGv3 85
II3 H46 1.329 -3.139 0.679 ETKDGv3 86
II3 H47 1.822 -0.358 -1.830 ETKDGv3 87
II3 H48 -4.855 -0.693 -0.513 ETKDGv3 88
II3 H49 -0.222 -1.501 0.285 ETKDGv3 89
II3 H50 -2.504 -0.864 -0.070 ETKDGv3 90
II3 H51 -0.483 0.103 -2.292 ETKDGv3 91
II3 H52 -2.258 0.018 -3.735 ETKDGv3 92
II3 H53 -3.866 0.759 -3.765 ETKDGv3 93
II3 H54 -2.487 1.680 -3.042 ETKDGv3 94
II3 H55 14.870 1.196 -1.133 ETKDGv3 95
II3 H56 -15.266 0.119 3.082 ETKDGv3 96
#