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 ? #