data_A1AT1
# 
_chem_comp.id                                    A1AT1 
_chem_comp.name                                  "(1aR,7aS)-1a-methyl-7a-[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl]-1a,7a-dihydronaphtho[2,3-b]oxirene-2,7-dione" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C31 H40 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "menaquinone-4 epoxide" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-06-02 
_chem_comp.pdbx_modified_date                    2025-01-24 
_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                        460.648 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1AT1 
_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        9BUX 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_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 
A1AT1 C01 C1  C 0 1 N N N N N N 97.546  121.077 100.587 -9.847  0.924  1.200  C01 A1AT1 1  
A1AT1 C02 C2  C 0 1 N N N N N N 96.974  119.792 101.188 -10.451 -0.040 0.212  C02 A1AT1 2  
A1AT1 C03 C3  C 0 1 N N N N N N 97.370  119.238 102.361 -9.691  -0.627 -0.679 C03 A1AT1 3  
A1AT1 C04 C4  C 0 1 N N N N N N 96.933  117.906 103.108 -8.213  -0.339 -0.716 C04 A1AT1 4  
A1AT1 C05 C5  C 0 1 N N N N N N 97.507  117.380 104.510 -7.434  -1.652 -0.615 C05 A1AT1 5  
A1AT1 C06 C6  C 0 1 N N N N N N 99.022  117.283 104.999 -5.955  -1.363 -0.652 C06 A1AT1 6  
A1AT1 C07 C7  C 0 1 N N N N N N 100.008 116.648 104.368 -5.284  -1.242 0.466  C07 A1AT1 7  
A1AT1 C08 C8  C 0 1 N N N N N N 101.476 116.539 104.860 -3.836  -0.826 0.433  C08 A1AT1 8  
A1AT1 C09 C9  C 0 1 N N N N N N 101.939 115.155 104.353 -3.633  0.388  1.343  C09 A1AT1 9  
A1AT1 C10 C10 C 0 1 N N N N N N 103.351 114.605 104.611 -2.185  0.804  1.310  C10 A1AT1 10 
A1AT1 C11 C11 C 0 1 N N N N N N 104.384 115.054 103.998 -1.793  1.747  0.489  C11 A1AT1 11 
A1AT1 C12 C12 C 0 1 N N N N N N 105.781 114.476 104.276 -0.327  2.073  0.362  C12 A1AT1 12 
A1AT1 C13 C13 C 0 1 N N N N N N 106.808 115.249 103.407 0.087   1.998  -1.109 C13 A1AT1 13 
A1AT1 C14 C14 C 0 1 N N N N N N 107.968 115.946 104.073 1.553   2.325  -1.236 C14 A1AT1 14 
A1AT1 C15 C15 C 0 1 N N N N N N 108.930 115.407 104.804 2.439   1.361  -1.262 C15 A1AT1 15 
A1AT1 C16 C16 C 0 1 N N N N N N 110.158 116.057 105.536 3.909   1.687  -1.227 C16 A1AT1 16 
A1AT1 C17 C17 C 0 1 N N S N N N 110.424 116.241 107.103 4.567   0.955  -0.055 C17 A1AT1 17 
A1AT1 C18 C18 C 0 1 N N N N N N 110.204 117.646 107.411 4.042   -0.438 0.252  C18 A1AT1 18 
A1AT1 O19 O1  O 0 1 N N N N N N 110.135 118.449 106.593 2.926   -0.610 0.693  O19 A1AT1 19 
A1AT1 C20 C19 C 0 1 Y N N N N N 110.187 118.159 108.844 4.951   -1.573 -0.012 C20 A1AT1 20 
A1AT1 C21 C20 C 0 1 Y N N N N N 110.219 119.546 109.021 4.480   -2.794 -0.474 C21 A1AT1 21 
A1AT1 C22 C21 C 0 1 Y N N N N N 110.236 119.983 110.298 5.373   -3.827 -0.704 C22 A1AT1 22 
A1AT1 C23 C22 C 0 1 Y N N N N N 110.249 119.149 111.363 6.727   -3.653 -0.478 C23 A1AT1 23 
A1AT1 C24 C23 C 0 1 Y N N N N N 110.228 117.818 111.202 7.215   -2.441 -0.017 C24 A1AT1 24 
A1AT1 C25 C24 C 0 1 Y N N N N N 110.198 117.314 109.931 6.336   -1.394 0.219  C25 A1AT1 25 
A1AT1 C26 C25 C 0 1 N N N N N N 110.178 115.810 109.719 6.803   -0.081 0.710  C26 A1AT1 26 
A1AT1 O27 O2  O 0 1 N N N N N N 109.943 115.145 110.696 7.727   0.011  1.489  O27 A1AT1 27 
A1AT1 C28 C26 C 0 1 N N R N N N 110.453 115.336 108.286 6.068   1.175  0.214  C28 A1AT1 28 
A1AT1 O29 O3  O 0 1 N N N N N N 111.352 115.138 107.214 5.047   1.719  1.053  O29 A1AT1 29 
A1AT1 C30 C27 C 0 1 N N N N N N 109.364 114.260 108.062 6.859   2.104  -0.710 C30 A1AT1 30 
A1AT1 C31 C28 C 0 1 N N N N N N 107.908 117.362 103.778 1.999   3.761  -1.333 C31 A1AT1 31 
A1AT1 C32 C29 C 0 1 N N N N N N 103.674 113.451 105.485 -1.188  0.136  2.222  C32 A1AT1 32 
A1AT1 C33 C30 C 0 1 N N N N N N 99.492  117.904 106.307 -5.250  -1.215 -1.975 C33 A1AT1 33 
A1AT1 C34 C31 C 0 1 N N N N N N 95.885  119.211 100.305 -11.930 -0.329 0.249  C34 A1AT1 34 
A1AT1 H1  H1  H 0 1 N N N N N N 98.331  121.474 101.248 -9.383  1.752  0.663  H1  A1AT1 35 
A1AT1 H2  H2  H 0 1 N N N N N N 97.975  120.860 99.598  -10.627 1.309  1.856  H2  A1AT1 36 
A1AT1 H3  H3  H 0 1 N N N N N N 96.743  121.822 100.483 -9.093  0.409  1.795  H3  A1AT1 37 
A1AT1 H4  H4  H 0 1 N N N N N N 98.123  119.809 102.885 -10.125 -1.319 -1.387 H4  A1AT1 38 
A1AT1 H5  H5  H 0 1 N N N N N N 95.848  118.003 103.259 -7.963  0.160  -1.653 H5  A1AT1 39 
A1AT1 H6  H6  H 0 1 N N N N N N 97.133  117.095 102.392 -7.947  0.306  0.121  H6  A1AT1 40 
A1AT1 H7  H7  H 0 1 N N N N N N 97.016  118.015 105.262 -7.683  -2.151 0.322  H7  A1AT1 41 
A1AT1 H8  H8  H 0 1 N N N N N N 97.126  116.352 104.593 -7.700  -2.297 -1.452 H8  A1AT1 42 
A1AT1 H9  H9  H 0 1 N N N N N N 99.765  116.167 103.432 -5.767  -1.440 1.411  H9  A1AT1 43 
A1AT1 H10 H10 H 0 1 N N N N N N 101.525 116.590 105.958 -3.213  -1.649 0.783  H10 A1AT1 44 
A1AT1 H11 H11 H 0 1 N N N N N N 102.094 117.340 104.428 -3.555  -0.566 -0.587 H11 A1AT1 45 
A1AT1 H12 H12 H 0 1 N N N N N N 101.815 115.174 103.260 -4.256  1.212  0.993  H12 A1AT1 46 
A1AT1 H13 H13 H 0 1 N N N N N N 101.243 114.423 104.788 -3.914  0.128  2.363  H13 A1AT1 47 
A1AT1 H14 H14 H 0 1 N N N N N N 104.271 115.849 103.276 -2.519  2.289  -0.097 H14 A1AT1 48 
A1AT1 H15 H15 H 0 1 N N N N N N 105.801 113.408 104.014 -0.145  3.079  0.740  H15 A1AT1 49 
A1AT1 H16 H16 H 0 1 N N N N N N 106.029 114.597 105.341 0.256   1.356  0.940  H16 A1AT1 50 
A1AT1 H17 H17 H 0 1 N N N N N N 106.247 116.018 102.856 -0.095  0.993  -1.487 H17 A1AT1 51 
A1AT1 H18 H18 H 0 1 N N N N N N 107.234 114.526 102.696 -0.496  2.715  -1.687 H18 A1AT1 52 
A1AT1 H19 H19 H 0 1 N N N N N N 108.858 114.335 104.917 2.115   0.331  -1.308 H19 A1AT1 53 
A1AT1 H20 H20 H 0 1 N N N N N N 111.024 115.479 105.179 4.374   1.371  -2.160 H20 A1AT1 54 
A1AT1 H21 H21 H 0 1 N N N N N N 110.207 117.078 105.130 4.040   2.762  -1.102 H21 A1AT1 55 
A1AT1 H22 H22 H 0 1 N N N N N N 110.230 120.228 108.184 3.424   -2.937 -0.652 H22 A1AT1 56 
A1AT1 H23 H23 H 0 1 N N N N N N 110.239 121.048 110.478 5.009   -4.778 -1.064 H23 A1AT1 57 
A1AT1 H24 H24 H 0 1 N N N N N N 110.277 119.562 112.360 7.409   -4.469 -0.663 H24 A1AT1 58 
A1AT1 H25 H25 H 0 1 N N N N N N 110.235 117.158 112.057 8.274   -2.312 0.158  H25 A1AT1 59 
A1AT1 H26 H26 H 0 1 N N N N N N 109.351 113.567 108.916 6.425   3.104  -0.676 H26 A1AT1 60 
A1AT1 H27 H27 H 0 1 N N N N N N 108.382 114.746 107.969 7.897   2.147  -0.380 H27 A1AT1 61 
A1AT1 H28 H28 H 0 1 N N N N N N 109.585 113.701 107.141 6.816   1.724  -1.730 H28 A1AT1 62 
A1AT1 H29 H29 H 0 1 N N N N N N 108.753 117.874 104.262 2.280   4.122  -0.343 H29 A1AT1 63 
A1AT1 H30 H30 H 0 1 N N N N N N 107.963 117.512 102.690 2.856   3.831  -2.002 H30 A1AT1 64 
A1AT1 H31 H31 H 0 1 N N N N N N 106.962 117.776 104.158 1.183   4.370  -1.723 H31 A1AT1 65 
A1AT1 H32 H32 H 0 1 N N N N N N 102.759 113.103 105.987 -0.691  -0.673 1.687  H32 A1AT1 66 
A1AT1 H33 H33 H 0 1 N N N N N N 104.091 112.635 104.876 -0.447  0.866  2.547  H33 A1AT1 67 
A1AT1 H34 H34 H 0 1 N N N N N N 104.412 113.759 106.240 -1.706  -0.268 3.092  H34 A1AT1 68 
A1AT1 H35 H35 H 0 1 N N N N N N 98.649  118.417 106.794 -5.191  -0.159 -2.239 H35 A1AT1 69 
A1AT1 H36 H36 H 0 1 N N N N N N 99.874  117.115 106.971 -4.243  -1.626 -1.898 H36 A1AT1 70 
A1AT1 H37 H37 H 0 1 N N N N N N 100.293 118.629 106.101 -5.804  -1.751 -2.745 H37 A1AT1 71 
A1AT1 H38 H38 H 0 1 N N N N N N 95.494  118.290 100.762 -12.454 0.377  -0.396 H38 A1AT1 72 
A1AT1 H39 H39 H 0 1 N N N N N N 95.070  119.942 100.199 -12.111 -1.345 -0.101 H39 A1AT1 73 
A1AT1 H40 H40 H 0 1 N N N N N N 96.301  118.980 99.313  -12.295 -0.227 1.271  H40 A1AT1 74 
# 
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 
A1AT1 C34 C02 SING N N 1  
A1AT1 C01 C02 SING N N 2  
A1AT1 C02 C03 DOUB N N 3  
A1AT1 C03 C04 SING N N 4  
A1AT1 C04 C05 SING N N 5  
A1AT1 C13 C14 SING N N 6  
A1AT1 C13 C12 SING N N 7  
A1AT1 C31 C14 SING N N 8  
A1AT1 C11 C12 SING N N 9  
A1AT1 C11 C10 DOUB N E 10 
A1AT1 C14 C15 DOUB N E 11 
A1AT1 C09 C10 SING N N 12 
A1AT1 C09 C08 SING N N 13 
A1AT1 C07 C08 SING N N 14 
A1AT1 C07 C06 DOUB N E 15 
A1AT1 C05 C06 SING N N 16 
A1AT1 C10 C32 SING N N 17 
A1AT1 C15 C16 SING N N 18 
A1AT1 C06 C33 SING N N 19 
A1AT1 C16 C17 SING N N 20 
A1AT1 O19 C18 DOUB N N 21 
A1AT1 C17 O29 SING N N 22 
A1AT1 C17 C18 SING N N 23 
A1AT1 C17 C28 SING N N 24 
A1AT1 O29 C28 SING N N 25 
A1AT1 C18 C20 SING N N 26 
A1AT1 C30 C28 SING N N 27 
A1AT1 C28 C26 SING N N 28 
A1AT1 C20 C21 DOUB Y N 29 
A1AT1 C20 C25 SING Y N 30 
A1AT1 C21 C22 SING Y N 31 
A1AT1 C26 C25 SING N N 32 
A1AT1 C26 O27 DOUB N N 33 
A1AT1 C25 C24 DOUB Y N 34 
A1AT1 C22 C23 DOUB Y N 35 
A1AT1 C24 C23 SING Y N 36 
A1AT1 C01 H1  SING N N 37 
A1AT1 C01 H2  SING N N 38 
A1AT1 C01 H3  SING N N 39 
A1AT1 C03 H4  SING N N 40 
A1AT1 C04 H5  SING N N 41 
A1AT1 C04 H6  SING N N 42 
A1AT1 C05 H7  SING N N 43 
A1AT1 C05 H8  SING N N 44 
A1AT1 C07 H9  SING N N 45 
A1AT1 C08 H10 SING N N 46 
A1AT1 C08 H11 SING N N 47 
A1AT1 C09 H12 SING N N 48 
A1AT1 C09 H13 SING N N 49 
A1AT1 C11 H14 SING N N 50 
A1AT1 C12 H15 SING N N 51 
A1AT1 C12 H16 SING N N 52 
A1AT1 C13 H17 SING N N 53 
A1AT1 C13 H18 SING N N 54 
A1AT1 C15 H19 SING N N 55 
A1AT1 C16 H20 SING N N 56 
A1AT1 C16 H21 SING N N 57 
A1AT1 C21 H22 SING N N 58 
A1AT1 C22 H23 SING N N 59 
A1AT1 C23 H24 SING N N 60 
A1AT1 C24 H25 SING N N 61 
A1AT1 C30 H26 SING N N 62 
A1AT1 C30 H27 SING N N 63 
A1AT1 C30 H28 SING N N 64 
A1AT1 C31 H29 SING N N 65 
A1AT1 C31 H30 SING N N 66 
A1AT1 C31 H31 SING N N 67 
A1AT1 C32 H32 SING N N 68 
A1AT1 C32 H33 SING N N 69 
A1AT1 C32 H34 SING N N 70 
A1AT1 C33 H35 SING N N 71 
A1AT1 C33 H36 SING N N 72 
A1AT1 C33 H37 SING N N 73 
A1AT1 C34 H38 SING N N 74 
A1AT1 C34 H39 SING N N 75 
A1AT1 C34 H40 SING N N 76 
# 
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 
A1AT1 SMILES           ACDLabs              12.01 "C/C(C)=C\CCC(\C)=C\CCC(\C)=C\CCC(\C)=C\CC12OC2(C)C(=O)c2ccccc2C1=O"                                                                                                                                          
A1AT1 InChI            InChI                1.06  "InChI=1S/C31H40O3/c1-22(2)12-9-13-23(3)14-10-15-24(4)16-11-17-25(5)20-21-31-29(33)27-19-8-7-18-26(27)28(32)30(31,6)34-31/h7-8,12,14,16,18-20H,9-11,13,15,17,21H2,1-6H3/b23-14+,24-16+,25-20+/t30-,31+/m0/s1" 
A1AT1 InChIKey         InChI                1.06  TUZHANAISKEZFG-YNKDMHFFSA-N                                                                                                                                                                                   
A1AT1 SMILES_CANONICAL CACTVS               3.385 "CC(C)=CCC/C(C)=C/CC/C(C)=C/CC\C(C)=C\C[C@]12O[C@@]1(C)C(=O)c3ccccc3C2=O"                                                                                                                                     
A1AT1 SMILES           CACTVS               3.385 "CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CC[C]12O[C]1(C)C(=O)c3ccccc3C2=O"                                                                                                                                              
A1AT1 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(=CCC/C(=C/CC/C(=C/CC/C(=C/C[C@@]12C(=O)c3ccccc3C(=O)[C@@]1(O2)C)/C)/C)/C)C"                                                                                                                               
A1AT1 SMILES           "OpenEye OEToolkits" 2.0.7 "CC(=CCCC(=CCCC(=CCCC(=CCC12C(=O)c3ccccc3C(=O)C1(O2)C)C)C)C)C"                                                                                                                                                
# 
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 
A1AT1 "SYSTEMATIC NAME" ACDLabs              12.01 "(1aR,7aS)-1a-methyl-7a-[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl]-1a,7a-dihydronaphtho[2,3-b]oxirene-2,7-dione"           
A1AT1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(1~{a}~{S},7~{a}~{R})-7~{a}-methyl-1~{a}-[(2~{E},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]naphtho[2,3-b]oxirene-2,7-dione" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1AT1 "Create component" 2024-06-02 RCSB 
A1AT1 "Initial release"  2025-01-29 RCSB 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      A1AT1 
_pdbx_chem_comp_synonyms.name         "menaquinone-4 epoxide" 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
