data_HD4 # _chem_comp.id HD4 _chem_comp.name 4-O-[2-acetamido-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol _chem_comp.type D-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C13 H26 N O13 P" _chem_comp.mon_nstd_parent_comp_id NAG _chem_comp.pdbx_synonyms ;4-O-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol; 4-O-[2-acetamido-2-deoxy-beta-D-glucosyl]-1-O-phosphono-D-ribitol; 4-O-[2-acetamido-2-deoxy-D-glucosyl]-1-O-phosphono-D-ribitol; 4-O-[2-acetamido-2-deoxy-glucosyl]-1-O-phosphono-D-ribitol ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-06-26 _chem_comp.pdbx_modified_date 2020-07-17 _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 435.318 _chem_comp.one_letter_code ? _chem_comp.three_letter_code HD4 _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 6DW2 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 HD4 "4-O-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol" PDB ? 2 HD4 4-O-[2-acetamido-2-deoxy-beta-D-glucosyl]-1-O-phosphono-D-ribitol PDB ? 3 HD4 4-O-[2-acetamido-2-deoxy-D-glucosyl]-1-O-phosphono-D-ribitol PDB ? 4 HD4 4-O-[2-acetamido-2-deoxy-glucosyl]-1-O-phosphono-D-ribitol PDB ? # # 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 HD4 C1 C14 C 0 1 N N S -2.695 46.590 38.627 2.170 -0.120 0.485 C1 HD4 1 HD4 C2 C5 C 0 1 N N R -3.731 46.975 37.567 2.907 -0.265 -0.849 C2 HD4 2 HD4 C5 C11 C 0 1 N N R -2.579 44.279 37.931 2.808 2.184 0.673 C5 HD4 3 HD4 C3 C7 C 0 1 N N R -4.507 45.706 37.135 4.090 0.707 -0.878 C3 HD4 4 HD4 C4 C9 C 0 1 N N S -3.575 44.520 36.775 3.571 2.131 -0.653 C4 HD4 5 HD4 C8 C1 C 0 1 N N N -5.809 50.030 38.683 3.095 -4.009 -1.625 C8 HD4 6 HD4 C7 C2 C 0 1 N N N -4.783 49.225 37.930 2.589 -2.597 -1.480 C7 HD4 7 HD4 O7 O3 O 0 1 N N N -4.051 49.798 37.146 1.453 -2.324 -1.806 O7 HD4 8 HD4 N2 N4 N 0 1 N N N -4.702 47.897 38.186 3.399 -1.638 -0.989 N2 HD4 9 HD4 O5 O13 O 0 1 N N N -1.875 45.496 38.170 1.741 1.234 0.646 O5 HD4 10 HD4 O1 O16 O 0 1 N N N -1.802 47.683 38.904 1.032 -0.984 0.497 O1 HD4 11 HD4 C17 C17 C 0 1 N N R -1.053 47.592 40.132 0.335 -1.009 1.744 C17 HD4 12 HD4 C19 C19 C 0 1 N N N -0.919 49.000 40.721 0.919 -2.109 2.634 C19 HD4 13 HD4 O20 O20 O 0 1 N N N -2.231 49.529 40.916 0.674 -3.384 2.038 O20 HD4 14 HD4 C21 C21 C 0 1 N N S 0.307 46.864 40.008 -1.148 -1.291 1.494 C21 HD4 15 HD4 C23 C23 C 0 1 N N S 0.993 47.061 38.647 -1.733 -0.191 0.604 C23 HD4 16 HD4 C25 C25 C 0 1 N N N 2.300 46.275 38.585 -3.216 -0.472 0.354 C25 HD4 17 HD4 O26 O26 O 0 1 N N N 2.863 46.515 37.296 -3.789 0.612 -0.378 O26 HD4 18 HD4 P27 P27 P 0 1 N N N 4.063 45.648 36.673 -5.338 0.652 -0.817 P27 HD4 19 HD4 O28 O28 O 0 1 N N N 3.459 44.365 36.248 -5.629 -0.533 -1.867 O28 HD4 20 HD4 O29 O29 O 0 1 N N N 4.672 46.427 35.400 -6.194 0.475 0.377 O29 HD4 21 HD4 O30 O30 O 0 1 N N N 5.202 45.413 37.782 -5.664 2.071 -1.506 O30 HD4 22 HD4 O31 O31 O 0 1 N N N 1.283 48.445 38.419 -1.035 -0.166 -0.642 O31 HD4 23 HD4 O32 O32 O 0 1 N N N 0.098 45.451 40.239 -1.846 -1.316 2.741 O32 HD4 24 HD4 C6 C33 C 0 1 N N N -1.534 43.214 37.594 2.236 3.588 0.877 C6 HD4 25 HD4 O6 O34 O 0 1 N N N -0.442 43.242 38.535 1.624 3.671 2.166 O6 HD4 26 HD4 O4 O35 O 0 1 N N N -4.369 43.327 36.617 4.674 3.039 -0.607 O4 HD4 27 HD4 O3 O36 O 0 1 N N N -5.351 46.079 36.039 4.741 0.629 -2.148 O3 HD4 28 HD4 H1 H1 H 0 1 N N N -3.225 46.299 39.546 2.839 -0.389 1.302 H1 HD4 29 HD4 H2 H2 H 0 1 N N N -3.240 47.436 36.697 2.226 -0.037 -1.668 H2 HD4 30 HD4 H5 H3 H 0 1 N N N -3.137 43.969 38.827 3.487 1.946 1.492 H5 HD4 31 HD4 H3 H4 H 0 1 N N N -5.134 45.393 37.983 4.796 0.447 -0.090 H3 HD4 32 HD4 H4 H5 H 0 1 N N N -3.022 44.753 35.853 2.904 2.409 -1.469 H4 HD4 33 HD4 H81 H6 H 0 1 N N N -5.735 51.087 38.388 3.392 -4.391 -0.648 H81 HD4 34 HD4 H82 H7 H 0 1 N N N -6.815 49.654 38.447 2.305 -4.638 -2.035 H82 HD4 35 HD4 H83 H8 H 0 1 N N N -5.627 49.937 39.764 3.954 -4.021 -2.296 H83 HD4 36 HD4 HN2 H9 H 0 1 N N N -5.349 47.513 38.844 4.307 -1.857 -0.728 HN2 HD4 37 HD4 H10 H10 H 0 1 N N N -1.653 47.009 40.846 0.443 -0.045 2.240 H10 HD4 38 HD4 H11 H11 H 0 1 N N N -0.390 48.952 41.684 1.993 -1.957 2.739 H11 HD4 39 HD4 H12 H12 H 0 1 N N N -0.358 49.642 40.026 0.448 -2.070 3.616 H12 HD4 40 HD4 H13 H13 H 0 1 N N N -2.169 50.404 41.281 1.018 -4.129 2.549 H13 HD4 41 HD4 H14 H14 H 0 1 N N N 0.975 47.262 40.786 -1.257 -2.255 0.998 H14 HD4 42 HD4 H15 H15 H 0 1 N N N 0.321 46.686 37.861 -1.625 0.773 1.101 H15 HD4 43 HD4 H16 H16 H 0 1 N N N 2.103 45.201 38.719 -3.319 -1.393 -0.220 H16 HD4 44 HD4 H17 H17 H 0 1 N N N 2.988 46.622 39.370 -3.731 -0.580 1.308 H17 HD4 45 HD4 H18 H18 H 0 1 N N N 3.555 44.265 35.308 -5.101 -0.481 -2.676 H18 HD4 46 HD4 H19 H19 H 0 1 N N N 6.023 45.780 37.476 -6.581 2.165 -1.797 H19 HD4 47 HD4 H20 H20 H 0 1 N N N 0.478 48.948 38.455 -1.089 -0.994 -1.140 H20 HD4 48 HD4 H21 H21 H 0 1 N N N -0.326 45.326 41.080 -1.792 -0.488 3.238 H21 HD4 49 HD4 H61 H22 H 0 1 N N N -2.009 42.222 37.624 3.040 4.322 0.809 H61 HD4 50 HD4 H62 H23 H 0 1 N N N -1.142 43.402 36.583 1.492 3.793 0.108 H62 HD4 51 HD4 HO6 H24 H 0 1 N Y N 0.192 42.573 38.305 1.239 4.535 2.364 HO6 HD4 52 HD4 HO4 H25 H 0 1 N Y N -3.803 42.596 36.396 4.418 3.961 -0.466 HO4 HD4 53 HD4 HO3 H26 H 0 1 N Y N -5.905 46.806 36.298 5.501 1.221 -2.237 HO3 HD4 54 # # 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 HD4 O29 P27 DOUB N N 1 HD4 O3 C3 SING N N 2 HD4 O28 P27 SING N N 3 HD4 O4 C4 SING N N 4 HD4 P27 O26 SING N N 5 HD4 P27 O30 SING N N 6 HD4 C4 C3 SING N N 7 HD4 C4 C5 SING N N 8 HD4 C3 C2 SING N N 9 HD4 O7 C7 DOUB N N 10 HD4 O26 C25 SING N N 11 HD4 C2 N2 SING N N 12 HD4 C2 C1 SING N N 13 HD4 C6 C5 SING N N 14 HD4 C6 O6 SING N N 15 HD4 C7 N2 SING N N 16 HD4 C7 C8 SING N N 17 HD4 C5 O5 SING N N 18 HD4 O5 C1 SING N N 19 HD4 O31 C23 SING N N 20 HD4 C25 C23 SING N N 21 HD4 C1 O1 SING N N 22 HD4 C23 C21 SING N N 23 HD4 O1 C17 SING N N 24 HD4 C21 C17 SING N N 25 HD4 C21 O32 SING N N 26 HD4 C17 C19 SING N N 27 HD4 C19 O20 SING N N 28 HD4 C1 H1 SING N N 29 HD4 C2 H2 SING N N 30 HD4 C5 H5 SING N N 31 HD4 C3 H3 SING N N 32 HD4 C4 H4 SING N N 33 HD4 C8 H81 SING N N 34 HD4 C8 H82 SING N N 35 HD4 C8 H83 SING N N 36 HD4 N2 HN2 SING N N 37 HD4 C17 H10 SING N N 38 HD4 C19 H11 SING N N 39 HD4 C19 H12 SING N N 40 HD4 O20 H13 SING N N 41 HD4 C21 H14 SING N N 42 HD4 C23 H15 SING N N 43 HD4 C25 H16 SING N N 44 HD4 C25 H17 SING N N 45 HD4 O28 H18 SING N N 46 HD4 O30 H19 SING N N 47 HD4 O31 H20 SING N N 48 HD4 O32 H21 SING N N 49 HD4 C6 H61 SING N N 50 HD4 C6 H62 SING N N 51 HD4 O6 HO6 SING N N 52 HD4 O4 HO4 SING N N 53 HD4 O3 HO3 SING N N 54 # # 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 HD4 SMILES ACDLabs 12.01 "C1(OC(CO)C(O)C(COP(O)(O)=O)O)C(NC(C)=O)C(C(C(O1)CO)O)O" HD4 InChI InChI 1.03 "InChI=1S/C13H26NO13P/c1-5(17)14-9-12(21)11(20)8(3-16)27-13(9)26-7(2-15)10(19)6(18)4-25-28(22,23)24/h6-13,15-16,18-21H,2-4H2,1H3,(H,14,17)(H2,22,23,24)/t6-,7+,8+,9+,10-,11+,12+,13+/m0/s1" HD4 InChIKey InChI 1.03 UTDJSTSCOBYMHN-SKCKNYEVSA-N HD4 SMILES_CANONICAL CACTVS 3.385 "CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@H]1O[C@H](CO)[C@@H](O)[C@@H](O)CO[P](O)(O)=O" HD4 SMILES CACTVS 3.385 "CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1O[CH](CO)[CH](O)[CH](O)CO[P](O)(O)=O" HD4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1O[C@H](CO)[C@H]([C@H](COP(=O)(O)O)O)O)CO)O)O" HD4 SMILES "OpenEye OEToolkits" 2.0.6 "CC(=O)NC1C(C(C(OC1OC(CO)C(C(COP(=O)(O)O)O)O)CO)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 HD4 "SYSTEMATIC NAME" ACDLabs 12.01 "4-O-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol" HD4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 ;[(2~{S},3~{S},4~{R})-4-[(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-2, 3,5-tris(oxidanyl)pentyl] dihydrogen phosphate ; # _pdbx_chem_comp_related.comp_id HD4 _pdbx_chem_comp_related.related_comp_id NAG _pdbx_chem_comp_related.relationship_type "Carbohydrate core" _pdbx_chem_comp_related.details ? # # loop_ _pdbx_chem_comp_atom_related.ordinal _pdbx_chem_comp_atom_related.comp_id _pdbx_chem_comp_atom_related.atom_id _pdbx_chem_comp_atom_related.related_comp_id _pdbx_chem_comp_atom_related.related_atom_id _pdbx_chem_comp_atom_related.related_type 1 HD4 C8 NAG C8 "Carbohydrate core" 2 HD4 C5 NAG C5 "Carbohydrate core" 3 HD4 C1 NAG C1 "Carbohydrate core" 4 HD4 C7 NAG C7 "Carbohydrate core" 5 HD4 C6 NAG C6 "Carbohydrate core" 6 HD4 C2 NAG C2 "Carbohydrate core" 7 HD4 C3 NAG C3 "Carbohydrate core" 8 HD4 C4 NAG C4 "Carbohydrate core" 9 HD4 N2 NAG N2 "Carbohydrate core" 10 HD4 O5 NAG O5 "Carbohydrate core" 11 HD4 O1 NAG O1 "Carbohydrate core" 12 HD4 O7 NAG O7 "Carbohydrate core" 13 HD4 O6 NAG O6 "Carbohydrate core" 14 HD4 O4 NAG O4 "Carbohydrate core" 15 HD4 O3 NAG O3 "Carbohydrate core" 16 HD4 H1 NAG H1 "Carbohydrate core" 17 HD4 H2 NAG H2 "Carbohydrate core" 18 HD4 H61 NAG H61 "Carbohydrate core" 19 HD4 H62 NAG H62 "Carbohydrate core" 20 HD4 HO6 NAG HO6 "Carbohydrate core" 21 HD4 HO4 NAG HO4 "Carbohydrate core" 22 HD4 HO3 NAG HO3 "Carbohydrate core" 23 HD4 H5 NAG H5 "Carbohydrate core" 24 HD4 H3 NAG H3 "Carbohydrate core" 25 HD4 H4 NAG H4 "Carbohydrate core" 26 HD4 H81 NAG H81 "Carbohydrate core" 27 HD4 H82 NAG H82 "Carbohydrate core" 28 HD4 H83 NAG H83 "Carbohydrate core" 29 HD4 HN2 NAG HN2 "Carbohydrate core" # # loop_ _pdbx_chem_comp_feature.comp_id _pdbx_chem_comp_feature.type _pdbx_chem_comp_feature.value _pdbx_chem_comp_feature.source _pdbx_chem_comp_feature.support HD4 "CARBOHYDRATE ISOMER" D PDB ? HD4 "CARBOHYDRATE RING" pyranose PDB ? HD4 "CARBOHYDRATE ANOMER" beta PDB ? HD4 "CARBOHYDRATE PRIMARY CARBONYL GROUP" aldose PDB ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site HD4 "Create component" 2018-06-26 RCSB HD4 "Initial release" 2018-08-29 RCSB HD4 "Other modification" 2020-07-03 RCSB HD4 "Modify parent residue" 2020-07-17 RCSB HD4 "Modify name" 2020-07-17 RCSB HD4 "Modify synonyms" 2020-07-17 RCSB HD4 "Modify internal type" 2020-07-17 RCSB HD4 "Modify linking type" 2020-07-17 RCSB HD4 "Modify atom id" 2020-07-17 RCSB HD4 "Modify component atom id" 2020-07-17 RCSB HD4 "Modify leaving atom flag" 2020-07-17 RCSB ##