data_P9Q
# 
_chem_comp.id                                    P9Q 
_chem_comp.name                                  "(1~{S},2~{R},3~{R},4~{R},5~{R})-5-(8-azanyloctylamino)-4-(hydroxymethyl)cyclohexane-1,2,3-triol" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C15 H32 N2 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2020-04-20 
_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                        304.426 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     P9Q 
_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        6YQA 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_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 
P9Q C7     C1  C 0 1 N N N N N N -15.653 -21.394 -11.069 -0.216  -0.128 -0.180 C7     P9Q 1  
P9Q O1     O1  O 0 1 N N N N N N -12.805 -20.298 -14.453 5.661   1.423  -0.103 O1     P9Q 2  
P9Q C10    C2  C 0 1 N N N N N N -16.894 -22.285 -10.991 -1.499  0.353  0.500  C10    P9Q 3  
P9Q "C1'"  C3  C 0 1 N N N N N N -13.226 -19.668 -10.138 2.579   -1.425 0.451  "C1'"  P9Q 4  
P9Q "C2'"  C4  C 0 1 N N S N N N -13.055 -18.516 -11.143 3.884   -1.886 -0.201 "C2'"  P9Q 5  
P9Q "C3'"  C5  C 0 1 N N R N N N -13.452 -18.957 -12.567 4.998   -0.890 0.127  "C3'"  P9Q 6  
P9Q "C4'"  C6  C 0 1 N N R N N N -12.493 -20.028 -13.058 4.621   0.492  -0.410 "C4'"  P9Q 7  
P9Q "C5'"  C7  C 0 1 N N R N N N -12.700 -21.279 -12.219 3.316   0.953  0.243  "C5'"  P9Q 8  
P9Q "C6'"  C8  C 0 1 N N N N N N -11.471 -22.139 -12.347 2.938   2.336  -0.293 "C6'"  P9Q 9  
P9Q "O2'"  O2  O 0 1 N N N N N N -13.817 -17.393 -10.681 4.237   -3.177 0.299  "O2'"  P9Q 10 
P9Q "O3'"  O3  O 0 1 N N N N N N -13.548 -17.932 -13.555 6.217   -1.321 -0.483 "O3'"  P9Q 11 
P9Q "O6'"  O4  O 0 1 N N N N N N -11.507 -23.330 -11.497 3.922   3.289  0.113  "O6'"  P9Q 12 
P9Q "C7'"  C9  C 0 1 N N R N N N -13.127 -21.115 -10.714 2.202   -0.043 -0.085 "C7'"  P9Q 13 
P9Q N1     N1  N 0 1 N N N N N N -14.393 -21.895 -10.423 0.949   0.400  0.542  N1     P9Q 14 
P9Q C11    C10 C 0 1 N N N N N N -17.970 -21.773 -11.987 -2.713  -0.197 -0.251 C11    P9Q 15 
P9Q C12    C11 C 0 1 N N N N N N -19.425 -22.233 -11.748 -3.996  0.284  0.429  C12    P9Q 16 
P9Q C13    C12 C 0 1 N N N N N N -20.400 -21.912 -12.894 -5.209  -0.266 -0.322 C13    P9Q 17 
P9Q C14    C13 C 0 1 N N N N N N -21.879 -22.101 -12.507 -6.492  0.215  0.358  C14    P9Q 18 
P9Q H71    H1  H 0 1 N N N N N N -15.433 -21.229 -12.134 -0.186  -1.218 -0.170 H71    P9Q 19 
P9Q H7     H2  H 0 1 N N N N N N -15.907 -20.435 -10.594 -0.197  0.226  -1.211 H7     P9Q 20 
P9Q H1     H3  H 0 1 N N N N N N -12.218 -20.967 -14.786 6.519   1.193  -0.485 H1     P9Q 21 
P9Q H101   H4  H 0 0 N N N N N N -17.300 -22.258 -9.969  -1.519  -0.001 1.531  H101   P9Q 22 
P9Q H10    H5  H 0 1 N N N N N N -16.619 -23.318 -11.249 -1.529  1.443  0.490  H10    P9Q 23 
P9Q "H1'1" H6  H 0 0 N N N N N N -12.446 -19.560 -9.370  1.786   -2.134 0.218  "H1'1" P9Q 24 
P9Q "H2'"  H7  H 0 1 N N N N N N -11.989 -18.244 -11.162 3.751   -1.939 -1.282 "H2'"  P9Q 25 
P9Q "H3'"  H8  H 0 1 N N N N N N -14.440 -19.434 -12.481 5.131   -0.837 1.207  "H3'"  P9Q 26 
P9Q "H4'"  H9  H 0 1 N N N N N N -11.456 -19.676 -12.952 4.487   0.439  -1.490 "H4'"  P9Q 27 
P9Q "H5'"  H10 H 0 1 N N N N N N -13.518 -21.837 -12.699 3.449   1.007  1.324  "H5'"  P9Q 28 
P9Q "H6'2" H11 H 0 0 N N N N N N -11.377 -22.461 -13.395 2.892   2.303  -1.382 "H6'2" P9Q 29 
P9Q "H6'1" H12 H 0 0 N N N N N N -10.593 -21.537 -12.068 1.965   2.626  0.103  "H6'1" P9Q 30 
P9Q "HO2'" H13 H 0 0 N N N N N N -13.538 -17.160 -9.804  5.056   -3.533 -0.072 "HO2'" P9Q 31 
P9Q "HO3'" H14 H 0 0 N N N N N N -14.146 -17.258 -13.255 6.517   -2.192 -0.189 "HO3'" P9Q 32 
P9Q "HO6'" H15 H 0 0 N N N N N N -10.709 -23.831 -11.620 3.747   4.190  -0.192 "HO6'" P9Q 33 
P9Q "H7'"  H16 H 0 1 N N N N N N -12.332 -21.606 -10.133 2.069   -0.096 -1.165 "H7'"  P9Q 34 
P9Q HN1    H17 H 0 1 N N N N N N -14.535 -21.886 -9.433  0.911   1.407  0.602  HN1    P9Q 35 
P9Q H111   H19 H 0 0 N N N N N N -17.677 -22.109 -12.993 -2.693  0.157  -1.282 H111   P9Q 36 
P9Q H11    H20 H 0 1 N N N N N N -17.960 -20.674 -11.950 -2.683  -1.287 -0.241 H11    P9Q 37 
P9Q H121   H21 H 0 0 N N N N N N -19.794 -21.740 -10.837 -4.015  -0.070 1.460  H121   P9Q 38 
P9Q H12    H22 H 0 1 N N N N N N -19.419 -23.323 -11.599 -4.025  1.374  0.419  H12    P9Q 39 
P9Q H131   H23 H 0 0 N N N N N N -20.173 -22.576 -13.741 -5.190  0.088  -1.353 H131   P9Q 40 
P9Q H13    H24 H 0 1 N N N N N N -20.250 -20.865 -13.197 -5.179  -1.356 -0.312 H13    P9Q 41 
P9Q H14    H25 H 0 1 N N N N N N -22.690 -21.783 -13.179 -6.512  -0.139 1.389  H14    P9Q 42 
P9Q H141   H26 H 0 0 N N N N N N -22.209 -22.972 -11.921 -6.522  1.305  0.348  H141   P9Q 43 
P9Q H4     H33 H 0 1 N N N N N N -14.217 -19.561 -9.672  2.713   -1.372 1.532  H4     P9Q 44 
P9Q C1     C14 C 0 1 N N N N N N ?       ?       ?       -7.706  -0.335 -0.394 C1     P9Q 45 
P9Q C2     C15 C 0 1 N N N N N N ?       ?       ?       -8.989  0.146  0.287  C2     P9Q 46 
P9Q N2     N2  N 0 1 N N N N N N ?       ?       ?       -10.154 -0.382 -0.435 N2     P9Q 47 
P9Q H2     H27 H 0 1 N N N N N N ?       ?       ?       -7.686  0.019  -1.424 H2     P9Q 48 
P9Q H3     H28 H 0 1 N N N N N N ?       ?       ?       -7.676  -1.425 -0.383 H3     P9Q 49 
P9Q H5     H29 H 0 1 N N N N N N ?       ?       ?       -9.008  -0.208 1.317  H5     P9Q 50 
P9Q H6     H30 H 0 1 N N N N N N ?       ?       ?       -9.019  1.236  0.276  H6     P9Q 51 
P9Q H8     H31 H 0 1 N N N N N N ?       ?       ?       -11.014 -0.078 -0.004 H8     P9Q 52 
P9Q H9     H32 H 0 1 N N N N N N ?       ?       ?       -10.125 -0.121 -1.409 H9     P9Q 53 
# 
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 
P9Q O1    "C4'"  SING N N 1  
P9Q "O3'" "C3'"  SING N N 2  
P9Q "C4'" "C3'"  SING N N 3  
P9Q "C4'" "C5'"  SING N N 4  
P9Q C13   C14    SING N N 5  
P9Q C13   C12    SING N N 6  
P9Q "C3'" "C2'"  SING N N 7  
P9Q "C6'" "C5'"  SING N N 8  
P9Q "C6'" "O6'"  SING N N 9  
P9Q "C5'" "C7'"  SING N N 10 
P9Q C11   C12    SING N N 11 
P9Q C11   C10    SING N N 12 
P9Q "C2'" "O2'"  SING N N 13 
P9Q "C2'" "C1'"  SING N N 14 
P9Q C7    C10    SING N N 15 
P9Q C7    N1     SING N N 16 
P9Q "C7'" N1     SING N N 17 
P9Q "C7'" "C1'"  SING N N 18 
P9Q C7    H71    SING N N 19 
P9Q C7    H7     SING N N 20 
P9Q O1    H1     SING N N 21 
P9Q C10   H101   SING N N 22 
P9Q C10   H10    SING N N 23 
P9Q "C1'" "H1'1" SING N N 24 
P9Q "C2'" "H2'"  SING N N 25 
P9Q "C3'" "H3'"  SING N N 26 
P9Q "C4'" "H4'"  SING N N 27 
P9Q "C5'" "H5'"  SING N N 28 
P9Q "C6'" "H6'2" SING N N 29 
P9Q "C6'" "H6'1" SING N N 30 
P9Q "O2'" "HO2'" SING N N 31 
P9Q "O3'" "HO3'" SING N N 32 
P9Q "O6'" "HO6'" SING N N 33 
P9Q "C7'" "H7'"  SING N N 34 
P9Q N1    HN1    SING N N 35 
P9Q C11   H111   SING N N 36 
P9Q C11   H11    SING N N 37 
P9Q C12   H121   SING N N 38 
P9Q C12   H12    SING N N 39 
P9Q C13   H131   SING N N 40 
P9Q C13   H13    SING N N 41 
P9Q C14   H14    SING N N 42 
P9Q C14   H141   SING N N 43 
P9Q "C1'" H4     SING N N 44 
P9Q C14   C1     SING N N 45 
P9Q C1    C2     SING N N 46 
P9Q C2    N2     SING N N 47 
P9Q C1    H2     SING N N 48 
P9Q C1    H3     SING N N 49 
P9Q C2    H5     SING N N 50 
P9Q C2    H6     SING N N 51 
P9Q N2    H8     SING N N 52 
P9Q N2    H9     SING N N 53 
# 
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 
P9Q InChI            InChI                1.03  "InChI=1S/C15H32N2O4/c16-7-5-3-1-2-4-6-8-17-12-9-13(19)15(21)14(20)11(12)10-18/h11-15,17-21H,1-10,16H2/t11-,12+,13-,14+,15+/m0/s1" 
P9Q InChIKey         InChI                1.03  HEJOCOWXPPQFHY-XPABHHOTSA-N                                                                                                        
P9Q SMILES_CANONICAL CACTVS               3.385 "NCCCCCCCCN[C@@H]1C[C@H](O)[C@@H](O)[C@H](O)[C@H]1CO"                                                                              
P9Q SMILES           CACTVS               3.385 "NCCCCCCCCN[CH]1C[CH](O)[CH](O)[CH](O)[CH]1CO"                                                                                     
P9Q SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1O)O)O)CO)NCCCCCCCCN"                                                                            
P9Q SMILES           "OpenEye OEToolkits" 2.0.7 "C1C(C(C(C(C1O)O)O)CO)NCCCCCCCCN"                                                                                                  
# 
_pdbx_chem_comp_identifier.comp_id           P9Q 
_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~{S},2~{R},3~{R},4~{R},5~{R})-5-(8-azanyloctylamino)-4-(hydroxymethyl)cyclohexane-1,2,3-triol" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
P9Q "Create component" 2020-04-20 PDBE 
P9Q "Initial release"  2021-02-24 RCSB 
P9Q "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            P9Q 
_pdbx_chem_comp_pcm.modified_residue_id                ASP 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               "C1'" 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   OD1 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
