data_XN8
# 
_chem_comp.id                                    XN8 
_chem_comp.name                                  
; 3',4'-demethoxy-nogalose-1-hydroxy-nogalamycinone
;
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C29 H32 O13" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "methyl (1R,2S,4S)-4-[(2R,3R,4R,5S,6S)-3-methoxy-4,6-dimethyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-methyl-2,5,7,10-tetrakis(oxidanyl)-6,11-bis(oxidanylidene)-3,4-dihydro-1H-tetracene-1-carboxylate" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-11-06 
_chem_comp.pdbx_modified_date                    2024-08-02 
_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                        588.557 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     XN8 
_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        8R2E 
_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 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
XN8 CBP C1  C 0 1 N N N 28.698 19.948 36.052 2.104  -2.796 -1.642 CBP XN8 1  N N N 
XN8 OBO O1  O 0 1 N N N 29.880 20.699 36.314 3.034  -2.734 -0.559 OBO XN8 2  N N N 
XN8 CAD C2  C 0 1 N N R 29.956 21.843 35.454 3.964  -1.653 -0.653 CAD XN8 3  N N N 
XN8 CAC C3  C 0 1 N N R 31.207 21.740 34.627 5.278  -2.049 0.028  CAC XN8 4  N N N 
XN8 CAK C4  C 0 1 N N N 31.124 22.709 33.447 5.902  -3.233 -0.713 CAK XN8 5  N N N 
XN8 OAJ O2  O 0 1 N N N 31.299 20.442 34.097 5.022  -2.413 1.386  OAJ XN8 6  N N N 
XN8 CAB C5  C 0 1 N N S 32.409 21.971 35.477 6.239  -0.856 -0.011 CAB XN8 7  N N N 
XN8 OAG O3  O 0 1 N N N 33.547 22.010 34.678 6.545  -0.533 -1.369 OAG XN8 8  N N N 
XN8 CAA C6  C 0 1 N N S 32.302 23.281 36.176 5.574  0.347  0.664  CAA XN8 9  N N N 
XN8 CAL C7  C 0 1 N N N 33.499 23.427 37.087 5.298  0.020  2.133  CAL XN8 10 N N N 
XN8 OAF O4  O 0 1 N N N 31.130 23.242 36.980 4.343  0.642  0.002  OAF XN8 11 N N N 
XN8 CAE C8  C 0 1 N N R 29.912 23.068 36.319 3.387  -0.420 0.046  CAE XN8 12 N N N 
XN8 OAH O5  O 0 1 N N N 29.486 24.182 35.532 2.190  -0.012 -0.618 OAH XN8 13 N N N 
XN8 CBD C9  C 0 1 N N S 29.059 25.236 36.263 1.513  1.075  0.017  CBD XN8 14 N N N 
XN8 CBE C10 C 0 1 N N N 30.170 26.054 36.625 1.921  2.384  -0.655 CBE XN8 15 N N N 
XN8 CBF C11 C 0 1 N N S 29.923 27.559 36.415 1.030  3.505  -0.108 CBF XN8 16 N N N 
XN8 CBM C12 C 0 1 N N N 31.279 28.342 36.456 1.562  4.861  -0.575 CBM XN8 17 N N N 
XN8 OBL O6  O 0 1 N N N 29.117 27.885 37.544 1.018  3.458  1.321  OBL XN8 18 N N N 
XN8 CAY C13 C 0 1 Y N N 27.868 25.764 35.793 0.025  0.864  -0.089 CAY XN8 19 N N N 
XN8 CAX C14 C 0 1 Y N N 26.660 25.075 35.806 -0.460 -0.429 0.130  CAX XN8 20 N N N 
XN8 OBN O7  O 0 1 N N N 26.614 23.885 36.415 0.404  -1.434 0.419  OBN XN8 21 N N N 
XN8 CAT C15 C 0 1 Y N N 25.480 25.584 35.272 -1.828 -0.692 0.053  CAT XN8 22 N N N 
XN8 CAS C16 C 0 1 N N N 24.288 24.867 35.359 -2.345 -2.053 0.283  CAS XN8 23 N N N 
XN8 OBC O8  O 0 1 N N N 24.286 23.769 35.932 -1.577 -2.960 0.542  OBC XN8 24 N N N 
XN8 CAP C17 C 0 1 Y N N 23.132 25.371 34.809 -3.792 -2.314 0.199  CAP XN8 25 N N N 
XN8 CAO C18 C 0 1 Y N N 21.936 24.652 34.882 -4.290 -3.601 0.414  CAO XN8 26 N N N 
XN8 OAW O9  O 0 1 N N N 21.953 23.447 35.542 -3.441 -4.618 0.704  OAW XN8 27 N N N 
XN8 CAN C19 C 0 1 Y N N 20.761 25.119 34.340 -5.661 -3.838 0.330  CAN XN8 28 N N N 
XN8 CAM C20 C 0 1 Y N N 20.774 26.352 33.727 -6.531 -2.812 0.037  CAM XN8 29 N N N 
XN8 CAR C21 C 0 1 Y N N 21.943 27.068 33.673 -6.054 -1.521 -0.181 CAR XN8 30 N N N 
XN8 OAS O10 O 0 1 N N N 21.911 28.254 33.063 -6.918 -0.516 -0.468 OAS XN8 31 N N N 
XN8 CAQ C22 C 0 1 Y N N 23.154 26.600 34.195 -4.683 -1.263 -0.101 CAQ XN8 32 N N N 
XN8 CAV C23 C 0 1 N N N 24.373 27.322 34.102 -4.168 0.098  -0.328 CAV XN8 33 N N N 
XN8 OBB O11 O 0 1 N N N 24.422 28.432 33.563 -4.936 1.005  -0.584 OBB XN8 34 N N N 
XN8 CAU C24 C 0 1 Y N N 25.531 26.800 34.640 -2.716 0.359  -0.246 CAU XN8 35 N N N 
XN8 CBA C25 C 0 1 Y N N 26.727 27.540 34.614 -2.216 1.635  -0.462 CBA XN8 36 N N N 
XN8 CAZ C26 C 0 1 Y N N 27.942 27.032 35.124 -0.848 1.885  -0.385 CAZ XN8 37 N N N 
XN8 CBG C27 C 0 1 N N R 29.116 27.819 35.192 -0.386 3.297  -0.641 CBG XN8 38 N N N 
XN8 CBH C28 C 0 1 N N N 28.998 29.183 34.881 -1.322 4.258  0.046  CBH XN8 39 N N N 
XN8 OBJ O12 O 0 1 N N N 29.380 29.993 34.156 -0.900 5.013  0.890  OBJ XN8 40 N N N 
XN8 OBI O13 O 0 1 N N N 28.618 29.826 35.656 -2.624 4.275  -0.279 OBI XN8 41 N N N 
XN8 CBK C29 C 0 1 N N N 27.800 31.134 35.781 -3.467 5.226  0.423  CBK XN8 42 N N N 
XN8 H1  H1  H 0 1 N N N 28.661 19.076 36.722 2.646  -2.919 -2.580 H1  XN8 43 N N N 
XN8 H2  H2  H 0 1 N N N 27.815 20.581 36.225 1.433  -3.643 -1.497 H2  XN8 44 N N N 
XN8 H3  H3  H 0 1 N N N 28.705 19.606 35.006 1.523  -1.874 -1.676 H3  XN8 45 N N N 
XN8 H4  H4  H 0 1 N N N 29.088 21.856 34.779 4.151  -1.424 -1.702 H4  XN8 46 N N N 
XN8 H5  H5  H 0 1 N N N 31.051 23.740 33.823 6.100  -2.951 -1.747 H5  XN8 47 N N N 
XN8 H6  H6  H 0 1 N N N 32.027 22.609 32.826 6.837  -3.513 -0.228 H6  XN8 48 N N N 
XN8 H7  H7  H 0 1 N N N 30.235 22.475 32.842 5.214  -4.078 -0.692 H7  XN8 49 N N N 
XN8 H8  H8  H 0 1 N N N 31.352 19.813 34.807 5.812  -2.675 1.878  H8  XN8 50 N N N 
XN8 H9  H9  H 0 1 N N N 32.486 21.166 36.223 7.156  -1.110 0.520  H9  XN8 51 N N N 
XN8 H10 H10 H 0 1 N N N 34.312 22.157 35.222 7.150  0.214  -1.468 H10 XN8 52 N N N 
XN8 H11 H11 H 0 1 N N N 32.270 24.107 35.450 6.236  1.210  0.601  H11 XN8 53 N N N 
XN8 H12 H12 H 0 1 N N N 33.443 24.390 37.616 6.206  -0.365 2.596  H12 XN8 54 N N N 
XN8 H13 H13 H 0 1 N N N 33.505 22.606 37.819 4.980  0.924  2.652  H13 XN8 55 N N N 
XN8 H14 H14 H 0 1 N N N 34.421 23.391 36.489 4.511  -0.731 2.196  H14 XN8 56 N N N 
XN8 H15 H15 H 0 1 N N N 29.138 22.887 37.080 3.162  -0.663 1.085  H15 XN8 57 N N N 
XN8 H16 H16 H 0 1 N N N 28.770 24.782 37.222 1.796  1.108  1.069  H16 XN8 58 N N N 
XN8 H17 H17 H 0 1 N N N 30.395 25.884 37.688 2.965  2.602  -0.430 H17 XN8 59 N N N 
XN8 H18 H18 H 0 1 N N N 31.035 25.755 36.015 1.787  2.301  -1.733 H18 XN8 60 N N N 
XN8 H19 H19 H 0 1 N N N 31.815 28.099 37.385 1.560  4.897  -1.664 H19 XN8 61 N N N 
XN8 H20 H20 H 0 1 N N N 31.895 28.054 35.591 0.926  5.656  -0.184 H20 XN8 62 N N N 
XN8 H21 H21 H 0 1 N N N 31.079 29.423 36.420 2.579  4.998  -0.208 H21 XN8 63 N N N 
XN8 H22 H22 H 0 1 N N N 29.609 27.728 38.341 1.889  3.575  1.725  H22 XN8 64 N N N 
XN8 H23 H23 H 0 1 N N N 25.727 23.547 36.384 0.630  -1.500 1.357  H23 XN8 65 N N N 
XN8 H24 H24 H 0 1 N N N 22.833 23.268 35.853 -3.279 -4.737 1.650  H24 XN8 66 N N N 
XN8 H25 H25 H 0 1 N N N 19.854 24.535 34.394 -6.044 -4.834 0.496  H25 XN8 67 N N N 
XN8 H26 H26 H 0 1 N N N 19.870 26.753 33.292 -7.591 -3.009 -0.025 H26 XN8 68 N N N 
XN8 H27 H27 H 0 1 N N N 22.780 28.639 33.072 -7.251 -0.049 0.311  H27 XN8 69 N N N 
XN8 H28 H28 H 0 1 N N N 26.716 28.533 34.189 -2.894 2.443  -0.692 H28 XN8 70 N N N 
XN8 H29 H29 H 0 1 N N N 29.748 27.418 34.386 -0.398 3.490  -1.714 H29 XN8 71 N N N 
XN8 H30 H30 H 0 1 N N N 27.673 31.388 36.844 -4.492 5.136  0.066  H30 XN8 72 N N N 
XN8 H31 H31 H 0 1 N N N 28.333 31.950 35.270 -3.435 5.019  1.493  H31 XN8 73 N N N 
XN8 H32 H32 H 0 1 N N N 26.812 30.994 35.317 -3.105 6.238  0.238  H32 XN8 74 N N N 
# 
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 
XN8 OAS CAR SING N N 1  
XN8 CAK CAC SING N N 2  
XN8 OBB CAV DOUB N N 3  
XN8 CAR CAM DOUB Y N 4  
XN8 CAR CAQ SING Y N 5  
XN8 CAM CAN SING Y N 6  
XN8 OAJ CAC SING N N 7  
XN8 CAV CAQ SING N N 8  
XN8 CAV CAU SING N N 9  
XN8 OBJ CBH DOUB N N 10 
XN8 CAQ CAP DOUB Y N 11 
XN8 CAN CAO DOUB Y N 12 
XN8 CBA CAU SING Y N 13 
XN8 CBA CAZ DOUB Y N 14 
XN8 CAC CAD SING N N 15 
XN8 CAC CAB SING N N 16 
XN8 CAU CAT DOUB Y N 17 
XN8 OAG CAB SING N N 18 
XN8 CAP CAO SING Y N 19 
XN8 CAP CAS SING N N 20 
XN8 CBH CBG SING N N 21 
XN8 CBH OBI SING N N 22 
XN8 CAO OAW SING N N 23 
XN8 CAZ CBG SING N N 24 
XN8 CAZ CAY SING Y N 25 
XN8 CBG CBF SING N N 26 
XN8 CAT CAS SING N N 27 
XN8 CAT CAX SING Y N 28 
XN8 CAS OBC DOUB N N 29 
XN8 CAD OBO SING N N 30 
XN8 CAD CAE SING N N 31 
XN8 CAB CAA SING N N 32 
XN8 OAH CBD SING N N 33 
XN8 OAH CAE SING N N 34 
XN8 OBI CBK SING N N 35 
XN8 CAY CAX DOUB Y N 36 
XN8 CAY CBD SING N N 37 
XN8 CAX OBN SING N N 38 
XN8 CBP OBO SING N N 39 
XN8 CAA OAF SING N N 40 
XN8 CAA CAL SING N N 41 
XN8 CBD CBE SING N N 42 
XN8 CAE OAF SING N N 43 
XN8 CBF CBM SING N N 44 
XN8 CBF CBE SING N N 45 
XN8 CBF OBL SING N N 46 
XN8 CBP H1  SING N N 47 
XN8 CBP H2  SING N N 48 
XN8 CBP H3  SING N N 49 
XN8 CAD H4  SING N N 50 
XN8 CAK H5  SING N N 51 
XN8 CAK H6  SING N N 52 
XN8 CAK H7  SING N N 53 
XN8 OAJ H8  SING N N 54 
XN8 CAB H9  SING N N 55 
XN8 OAG H10 SING N N 56 
XN8 CAA H11 SING N N 57 
XN8 CAL H12 SING N N 58 
XN8 CAL H13 SING N N 59 
XN8 CAL H14 SING N N 60 
XN8 CAE H15 SING N N 61 
XN8 CBD H16 SING N N 62 
XN8 CBE H17 SING N N 63 
XN8 CBE H18 SING N N 64 
XN8 CBM H19 SING N N 65 
XN8 CBM H20 SING N N 66 
XN8 CBM H21 SING N N 67 
XN8 OBL H22 SING N N 68 
XN8 OBN H23 SING N N 69 
XN8 OAW H24 SING N N 70 
XN8 CAN H25 SING N N 71 
XN8 CAM H26 SING N N 72 
XN8 OAS H27 SING N N 73 
XN8 CBA H28 SING N N 74 
XN8 CBG H29 SING N N 75 
XN8 CBK H30 SING N N 76 
XN8 CBK H31 SING N N 77 
XN8 CBK H32 SING N N 78 
# 
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 
XN8 InChI            InChI                1.06  "InChI=1S/C29H32O13/c1-10-24(35)29(3,38)25(39-4)27(41-10)42-15-9-28(2,37)20(26(36)40-5)11-8-12-17(22(33)16(11)15)23(34)19-14(31)7-6-13(30)18(19)21(12)32/h6-8,10,15,20,24-25,27,30-31,33,35,37-38H,9H2,1-5H3/t10-,15-,20-,24-,25-,27-,28-,29+/m0/s1" 
XN8 InChIKey         InChI                1.06  JMZPXXMAMHNKHM-WOAFMFBISA-N                                                                                                                                                                                                                          
XN8 SMILES_CANONICAL CACTVS               3.385 "CO[C@H]1[C@@H](O[C@@H](C)[C@H](O)[C@@]1(C)O)O[C@H]2C[C@](C)(O)[C@H](C(=O)OC)c3cc4C(=O)c5c(O)ccc(O)c5C(=O)c4c(O)c23"                                                                                                                                 
XN8 SMILES           CACTVS               3.385 "CO[CH]1[CH](O[CH](C)[CH](O)[C]1(C)O)O[CH]2C[C](C)(O)[CH](C(=O)OC)c3cc4C(=O)c5c(O)ccc(O)c5C(=O)c4c(O)c23"                                                                                                                                            
XN8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@H]1[C@@H]([C@@]([C@H]([C@@H](O1)O[C@H]2C[C@]([C@@H](c3c2c(c4c(c3)C(=O)c5c(ccc(c5C4=O)O)O)O)C(=O)OC)(C)O)OC)(C)O)O"                                                                                                                              
XN8 SMILES           "OpenEye OEToolkits" 2.0.7 "CC1C(C(C(C(O1)OC2CC(C(c3c2c(c4c(c3)C(=O)c5c(ccc(c5C4=O)O)O)O)C(=O)OC)(C)O)OC)(C)O)O"                                                                                                                                                                
# 
_pdbx_chem_comp_identifier.comp_id           XN8 
_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        "methyl (1~{R},2~{S},4~{S})-4-[(2~{R},3~{R},4~{R},5~{S},6~{S})-3-methoxy-4,6-dimethyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-methyl-2,5,7,10-tetrakis(oxidanyl)-6,11-bis(oxidanylidene)-3,4-dihydro-1~{H}-tetracene-1-carboxylate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
XN8 "Create component" 2023-11-06 PDBE 
XN8 "Modify name"      2023-11-06 PDBE 
XN8 "Initial release"  2024-08-07 RCSB 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      XN8 
_pdbx_chem_comp_synonyms.name         "methyl (1R,2S,4S)-4-[(2R,3R,4R,5S,6S)-3-methoxy-4,6-dimethyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-methyl-2,5,7,10-tetrakis(oxidanyl)-6,11-bis(oxidanylidene)-3,4-dihydro-1H-tetracene-1-carboxylate" 
_pdbx_chem_comp_synonyms.provenance   PDB 
_pdbx_chem_comp_synonyms.type         ? 
# 
