data_QPJ
# 
_chem_comp.id                                    QPJ 
_chem_comp.name                                  2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C5 H14 O10 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2019-12-05 
_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                        296.106 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     QPJ 
_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        6V5Y 
_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 
QPJ P     P1  P 0 1 N N N N N N 9.608  10.872 44.023 -3.694 -0.012 -0.063 P     QPJ 1  
QPJ "O5'" O1  O 0 1 N N N N N N 10.708 9.789  43.562 -2.347 0.836  -0.307 "O5'" QPJ 2  
QPJ "C2'" C1  C 0 1 N N N N N N 11.043 6.227  40.956 2.443  1.928  -0.324 "C2'" QPJ 3  
QPJ "C5'" C2  C 0 1 N N N N N N 10.409 8.644  42.775 -1.057 0.385  0.111  "C5'" QPJ 4  
QPJ "C4'" C3  C 0 1 N N R N N N 11.459 8.613  41.685 -0.003 1.425  -0.274 "C4'" QPJ 5  
QPJ "O4'" O2  O 0 1 N N N N N N 12.717 8.256  42.277 -0.236 2.632  0.456  "O4'" QPJ 6  
QPJ "C1'" C4  C 0 1 N N S N N N 11.053 7.683  40.549 1.390  0.888  0.061  "C1'" QPJ 7  
QPJ "C3'" C5  C 0 1 N N N N N N 10.344 5.406  39.897 3.824  1.445  0.123  "C3'" QPJ 8  
QPJ OP3   O3  O 0 1 N N N N N N 9.352  11.769 42.837 -3.535 -1.366 -0.639 OP3   QPJ 9  
QPJ OP1   O4  O 0 1 N N N N N N 10.392 11.526 45.147 -3.975 -0.130 1.517  OP1   QPJ 10 
QPJ OP2   O5  O 0 1 N N N N N N 8.420  9.997  44.405 -4.932 0.732  -0.775 OP2   QPJ 11 
QPJ O32   O6  O 0 1 N N N N N N 12.861 10.571 38.634 3.330  -1.642 0.829  O32   QPJ 12 
QPJ P2    P2  P 0 1 N N N N N N 11.598 9.336  38.674 1.928  -1.729 0.044  P2    QPJ 13 
QPJ O22   O7  O 0 1 N N N N N N 9.906  9.703  38.326 0.844  -2.042 1.003  O22   QPJ 14 
QPJ OPP   O8  O 0 1 N N N N N N 11.905 7.833  39.406 1.623  -0.319 -0.669 OPP   QPJ 15 
QPJ H1    H1  H 0 1 N N N N N N 10.511 6.119  41.913 2.440  2.066  -1.406 H1    QPJ 16 
QPJ H2    H2  H 0 1 N N N N N N 12.078 5.872  41.070 2.214  2.875  0.164  H2    QPJ 17 
QPJ H3    H3  H 0 1 N N N N N N 9.404  8.731  42.337 -1.053 0.247  1.192  H3    QPJ 18 
QPJ H4    H4  H 0 1 N N N N N N 10.465 7.732  43.388 -0.828 -0.562 -0.377 H4    QPJ 19 
QPJ H5    H5  H 0 1 N N N N N N 11.540 9.629  41.270 -0.067 1.629  -1.343 H5    QPJ 20 
QPJ H6    H6  H 0 1 N N N N N N 12.922 8.865  42.977 -0.195 2.525  1.416  H6    QPJ 21 
QPJ H7    H7  H 0 1 N N N N N N 10.027 7.951  40.256 1.454  0.684  1.130  H7    QPJ 22 
QPJ H8    H8  H 0 1 N N N N N N 9.464  5.949  39.523 3.828  1.307  1.204  H8    QPJ 23 
QPJ H9    H9  H 0 1 N N N N N N 11.033 5.206  39.063 4.054  0.498  -0.365 H9    QPJ 24 
QPJ H11   H11 H 0 1 N N N N N N 10.599 12.422 44.910 -4.090 0.722  1.961  H11   QPJ 25 
QPJ H12   H12 H 0 1 N N N N N N 7.696  10.169 43.814 -5.778 0.276  -0.669 H12   QPJ 26 
QPJ H13   H13 H 0 1 N N N N N N 13.698 10.176 38.849 4.087  -1.440 0.262  H13   QPJ 27 
QPJ O2    O9  O 0 1 N Y N N N N 9.931  4.159  40.505 4.809  2.417  -0.236 O2    QPJ 28 
QPJ O1    O10 O 0 1 N Y N N N N 12.008 8.810  37.313 2.008  -2.888 -1.071 O1    QPJ 29 
QPJ H10   H10 H 0 1 N N N N N N 9.488  3.623  39.858 5.710  2.176  0.017  H10   QPJ 30 
QPJ H14   H14 H 0 1 N N N N N N 11.263 8.840  36.724 2.189  -3.767 -0.712 H14   QPJ 31 
# 
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 
QPJ O22   P2    DOUB N N 1  
QPJ O32   P2    SING N N 2  
QPJ P2    OPP   SING N N 3  
QPJ OPP   "C1'" SING N N 4  
QPJ "C3'" "C2'" SING N N 5  
QPJ "C1'" "C2'" SING N N 6  
QPJ "C1'" "C4'" SING N N 7  
QPJ "C4'" "O4'" SING N N 8  
QPJ "C4'" "C5'" SING N N 9  
QPJ "C5'" "O5'" SING N N 10 
QPJ OP3   P     DOUB N N 11 
QPJ "O5'" P     SING N N 12 
QPJ P     OP2   SING N N 13 
QPJ P     OP1   SING N N 14 
QPJ "C2'" H1    SING N N 15 
QPJ "C2'" H2    SING N N 16 
QPJ "C5'" H3    SING N N 17 
QPJ "C5'" H4    SING N N 18 
QPJ "C4'" H5    SING N N 19 
QPJ "O4'" H6    SING N N 20 
QPJ "C1'" H7    SING N N 21 
QPJ "C3'" H8    SING N N 22 
QPJ "C3'" H9    SING N N 23 
QPJ OP1   H11   SING N N 24 
QPJ OP2   H12   SING N N 25 
QPJ O32   H13   SING N N 26 
QPJ "C3'" O2    SING N N 27 
QPJ P2    O1    SING N N 28 
QPJ O2    H10   SING N N 29 
QPJ O1    H14   SING N N 30 
# 
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 
QPJ SMILES           ACDLabs              12.01 "P(O)(O)(OCC(O)C(CCO)OP(O)(O)=O)=O"                                                                                
QPJ InChI            InChI                1.03  "InChI=1S/C5H14O10P2/c6-2-1-5(15-17(11,12)13)4(7)3-14-16(8,9)10/h4-7H,1-3H2,(H2,8,9,10)(H2,11,12,13)/t4-,5+/m1/s1" 
QPJ InChIKey         InChI                1.03  BUWHXMOYXFBKFR-UHNVWZDZSA-N                                                                                        
QPJ SMILES_CANONICAL CACTVS               3.385 "OCC[C@H](O[P](O)(O)=O)[C@H](O)CO[P](O)(O)=O"                                                                      
QPJ SMILES           CACTVS               3.385 "OCC[CH](O[P](O)(O)=O)[CH](O)CO[P](O)(O)=O"                                                                        
QPJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C(CO)[C@@H]([C@@H](COP(=O)(O)O)O)OP(=O)(O)O"                                                                      
QPJ SMILES           "OpenEye OEToolkits" 2.0.7 "C(CO)C(C(COP(=O)(O)O)O)OP(=O)(O)O"                                                                                
# 
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 
QPJ "SYSTEMATIC NAME" ACDLabs              12.01 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol                                       
QPJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S})-2,5-bis(oxidanyl)-1-phosphonooxy-pentan-3-yl] dihydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
QPJ "Create component" 2019-12-05 RCSB 
QPJ "Initial release"  2022-03-09 RCSB 
QPJ "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            QPJ 
_pdbx_chem_comp_pcm.modified_residue_id                LYS 
_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               "C3'" 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   NZ 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
