data_YB9
# 
_chem_comp.id                                    YB9 
_chem_comp.name                                  1-carbamamido-1,2-dideoxy-5-O-phosphono-L-threo-pentitol 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C6 H15 N2 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-01-22 
_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                        258.166 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YB9 
_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        8FTJ 
_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 
YB9 C2    C1  C 0 1 N N N N N N 13.080 26.800 18.022 -5.808 -0.092 -0.192 C2    YB9 1  
YB9 N1    N1  N 0 1 N N N N N N 14.476 27.069 17.781 -4.587 0.478  -0.221 N1    YB9 2  
YB9 N2    N2  N 0 1 N N N N N N 12.775 25.651 18.477 -6.912 0.674  -0.302 N2    YB9 3  
YB9 "C1'" C2  C 0 1 N N N N N N 14.864 28.393 17.284 -3.387 -0.354 -0.101 "C1'" YB9 4  
YB9 "C2'" C3  C 0 1 N N N N N N 15.733 28.215 16.023 -2.143 0.534  -0.163 "C2'" YB9 5  
YB9 "C3'" C4  C 0 1 N N S N N N 17.081 28.894 16.137 -0.890 -0.335 -0.038 "C3'" YB9 6  
YB9 "C4'" C5  C 0 1 N N S N N N 18.034 27.798 16.592 0.355  0.535  -0.225 "C4'" YB9 7  
YB9 "C5'" C6  C 0 1 N N N N N N 19.475 28.181 16.355 1.608  -0.307 0.023  "C5'" YB9 8  
YB9 O2    O1  O 0 1 N N N N N N 12.225 27.619 17.787 -5.913 -1.297 -0.072 O2    YB9 9  
YB9 "O3'" O2  O 0 1 N N N N N N 17.345 29.183 14.799 -0.857 -0.942 1.255  "O3'" YB9 10 
YB9 "O4'" O3  O 0 1 N N N N N N 17.729 26.618 15.882 0.320  1.621  0.703  "O4'" YB9 11 
YB9 "O5'" O4  O 0 1 N N N N N N 20.085 28.262 17.585 2.771  0.472  -0.264 "O5'" YB9 12 
YB9 OP1   O5  O 0 1 N N N N N N 22.283 29.709 17.316 5.324  1.085  -0.390 OP1   YB9 13 
YB9 OP2   O6  O 0 1 N N N N N N 22.384 27.223 16.984 4.462  -0.619 1.260  OP2   YB9 14 
YB9 P     P1  P 0 1 N N N N N N 21.725 28.363 17.692 4.268  -0.098 -0.112 P     YB9 15 
YB9 O1    O7  O 0 1 N Y N N N N 21.631 28.394 19.279 4.501  -1.286 -1.174 O1    YB9 16 
YB9 H1    H1  H 0 1 N N N N N N 15.167 26.366 17.950 -4.503 1.440  -0.320 H1    YB9 17 
YB9 H2    H2  H 0 1 N N N N N N 11.817 25.418 18.644 -6.827 1.635  -0.401 H2    YB9 18 
YB9 H3    H3  H 0 1 N N N N N N 13.493 24.982 18.667 -7.791 0.264  -0.281 H3    YB9 19 
YB9 H4    H4  H 0 1 N N N N N N 15.439 28.924 18.057 -3.407 -0.886 0.850  H4    YB9 20 
YB9 H5    H5  H 0 1 N N N N N N 13.963 28.972 17.033 -3.361 -1.073 -0.919 H5    YB9 21 
YB9 H6    H6  H 0 1 N N N N N N 15.196 28.642 15.163 -2.123 1.066  -1.114 H6    YB9 22 
YB9 H7    H7  H 0 1 N N N N N N 15.894 27.140 15.857 -2.169 1.254  0.655  H7    YB9 23 
YB9 H8    H8  H 0 1 N N N N N N 17.072 29.763 16.812 -0.908 -1.111 -0.803 H8    YB9 24 
YB9 H9    H9  H 0 1 N N N N N N 17.887 27.635 17.670 0.376  0.927  -1.242 H9    YB9 25 
YB9 H10   H10 H 0 1 N N N N N N 19.971 27.417 15.739 1.632  -0.625 1.066  H10   YB9 26 
YB9 H11   H11 H 0 1 N N N N N N 19.527 29.154 15.845 1.590  -1.184 -0.624 H11   YB9 27 
YB9 H12   H12 H 0 1 N N N N N N 18.185 29.622 14.729 -0.840 -0.309 1.986  H12   YB9 28 
YB9 H13   H13 H 0 1 N N N N N N 18.316 25.923 16.155 0.301  1.346  1.630  H13   YB9 29 
YB9 H14   H14 H 0 1 N N N N N N 22.976 29.597 16.676 6.249  0.812  -0.316 H14   YB9 30 
YB9 H15   H15 H 0 1 N Y N N N N 22.041 27.615 19.636 4.390  -1.016 -2.096 H15   YB9 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 
YB9 "O3'" "C3'" SING N N 1  
YB9 "O4'" "C4'" SING N N 2  
YB9 "C2'" "C3'" SING N N 3  
YB9 "C2'" "C1'" SING N N 4  
YB9 "C3'" "C4'" SING N N 5  
YB9 "C5'" "C4'" SING N N 6  
YB9 "C5'" "O5'" SING N N 7  
YB9 OP2   P     DOUB N N 8  
YB9 "C1'" N1    SING N N 9  
YB9 OP1   P     SING N N 10 
YB9 "O5'" P     SING N N 11 
YB9 N1    C2    SING N N 12 
YB9 O2    C2    DOUB N N 13 
YB9 C2    N2    SING N N 14 
YB9 P     O1    SING N N 15 
YB9 N1    H1    SING N N 16 
YB9 N2    H2    SING N N 17 
YB9 N2    H3    SING N N 18 
YB9 "C1'" H4    SING N N 19 
YB9 "C1'" H5    SING N N 20 
YB9 "C2'" H6    SING N N 21 
YB9 "C2'" H7    SING N N 22 
YB9 "C3'" H8    SING N N 23 
YB9 "C4'" H9    SING N N 24 
YB9 "C5'" H10   SING N N 25 
YB9 "C5'" H11   SING N N 26 
YB9 "O3'" H12   SING N N 27 
YB9 "O4'" H13   SING N N 28 
YB9 OP1   H14   SING N N 29 
YB9 O1    H15   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 
YB9 SMILES           ACDLabs              12.01 "O=P(O)(O)OCC(O)C(O)CCNC(N)=O"                                                                                       
YB9 InChI            InChI                1.06  "InChI=1S/C6H15N2O7P/c7-6(11)8-2-1-4(9)5(10)3-15-16(12,13)14/h4-5,9-10H,1-3H2,(H3,7,8,11)(H2,12,13,14)/t4-,5-/m0/s1" 
YB9 InChIKey         InChI                1.06  QCWIKWZHQRZZSF-WHFBIAKZSA-N                                                                                          
YB9 SMILES_CANONICAL CACTVS               3.385 "NC(=O)NCC[C@H](O)[C@@H](O)CO[P](O)(O)=O"                                                                            
YB9 SMILES           CACTVS               3.385 "NC(=O)NCC[CH](O)[CH](O)CO[P](O)(O)=O"                                                                               
YB9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C(CNC(=O)N)[C@@H]([C@H](COP(=O)(O)O)O)O"                                                                            
YB9 SMILES           "OpenEye OEToolkits" 2.0.7 "C(CNC(=O)N)C(C(COP(=O)(O)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 
YB9 "SYSTEMATIC NAME" ACDLabs              12.01 1-carbamamido-1,2-dideoxy-5-O-phosphono-L-threo-pentitol                              
YB9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{S},3~{S})-5-(aminocarbonylamino)-2,3-bis(oxidanyl)pentyl] 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 
YB9 "Create component" 2023-01-22 RCSB 
YB9 "Initial release"  2023-04-26 RCSB 
YB9 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            YB9 
_pdbx_chem_comp_pcm.modified_residue_id                GLY 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid backbone" 
_pdbx_chem_comp_pcm.polypeptide_position               N-terminal 
_pdbx_chem_comp_pcm.comp_id_linking_atom               "C1'" 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   N 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
