data_DO8 # _chem_comp.id DO8 _chem_comp.name "3-deoxy-8-O-phosphono-alpha-D-manno-oct-2-ulopyranosonic acid" _chem_comp.type "D-saccharide, alpha linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C8 H15 O11 P" _chem_comp.mon_nstd_parent_comp_id KDO _chem_comp.pdbx_synonyms ;3-DEOXY-D-MANNO-2-OCTULOSONATE-8-PHOSPHATE; 3-deoxy-8-O-phosphono-alpha-D-manno-oct-2-ulosonic acid; 3-deoxy-8-O-phosphono-D-manno-oct-2-ulosonic acid; 3-deoxy-8-O-phosphono-manno-oct-2-ulosonic acid ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-08-18 _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 318.172 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DO8 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code ? _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 DO8 3-DEOXY-D-MANNO-2-OCTULOSONATE-8-PHOSPHATE PDB ? 2 DO8 "3-deoxy-8-O-phosphono-alpha-D-manno-oct-2-ulosonic acid" PDB ? 3 DO8 "3-deoxy-8-O-phosphono-D-manno-oct-2-ulosonic acid" PDB ? 4 DO8 "3-deoxy-8-O-phosphono-manno-oct-2-ulosonic acid" 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 DO8 C1 C1 C 0 1 N N N 7.160 -12.399 279.146 -2.487 -2.367 0.205 C1 DO8 1 DO8 O1B O1A O 0 1 N N N 6.208 -12.869 279.801 -2.793 -2.574 1.495 O1B DO8 2 DO8 O1A O1B O 0 1 N N N 8.221 -12.041 279.772 -2.394 -3.304 -0.552 O1A DO8 3 DO8 C2 C2 C 0 1 N N R 7.002 -12.248 277.639 -2.259 -0.965 -0.300 C2 DO8 4 DO8 C3 C3 C 0 1 N N N 5.994 -13.360 277.148 -3.482 -0.104 0.025 C3 DO8 5 DO8 C4 C4 C 0 1 N N R 5.588 -13.045 275.710 -3.256 1.310 -0.521 C4 DO8 6 DO8 O4 O4 O 0 1 N N N 4.635 -14.097 275.365 -4.321 2.164 -0.098 O4 DO8 7 DO8 C5 C5 C 0 1 N N R 4.928 -11.669 275.625 -1.923 1.838 0.023 C5 DO8 8 DO8 O5 O5 O 0 1 N N N 3.731 -11.621 276.449 -2.018 2.007 1.438 O5 DO8 9 DO8 C6 C6 C 0 1 N N R 6.002 -10.565 276.056 -0.818 0.830 -0.303 C6 DO8 10 DO8 O6 O6 O 0 1 N N N 6.550 -10.828 277.432 -1.102 -0.417 0.328 O6 DO8 11 DO8 C7 C7 C 0 1 N N R 5.481 -9.004 276.169 0.523 1.364 0.205 C7 DO8 12 DO8 O7 O7 O 0 1 N N N 5.010 -7.913 277.036 0.810 2.612 -0.429 O7 DO8 13 DO8 C8 C8 C 0 1 N N N 4.920 -8.860 274.688 1.629 0.359 -0.123 C8 DO8 14 DO8 P1 P1 P 0 1 N N N 5.023 -6.015 275.167 3.974 -0.297 0.070 P1 DO8 15 DO8 O2P O2P O 0 1 N N N 3.699 -6.253 276.222 5.362 0.071 0.797 O2P DO8 16 DO8 O3P O3P O 0 1 N N N 6.451 -5.736 276.001 4.190 -0.308 -1.526 O3P DO8 17 DO8 O8 O O 0 1 N N N 5.248 -7.465 274.219 2.860 0.801 0.452 O8 DO8 18 DO8 O1P O1P O 0 1 N N N 4.613 -4.669 274.243 3.522 -1.634 0.515 O1P DO8 19 DO8 O2 O2 O 0 1 N Y N 8.336 -12.481 276.955 -2.062 -0.996 -1.715 O2 DO8 20 DO8 HO1B H1A H 0 0 N N N 5.422 -13.134 279.337 -2.939 -3.473 1.819 HO1B DO8 21 DO8 H31 H31 H 0 1 N N N 6.405 -14.390 277.260 -4.367 -0.537 -0.441 H31 DO8 22 DO8 H32 H32 H 0 1 N N N 5.115 -13.471 277.826 -3.621 -0.060 1.105 H32 DO8 23 DO8 H4 H4 H 0 1 N N N 6.460 -13.017 275.016 -3.221 1.281 -1.611 H4 DO8 24 DO8 HO4 HO4 H 0 1 N Y N 4.382 -13.901 274.470 -5.138 1.787 -0.452 HO4 DO8 25 DO8 H5 H5 H 0 1 N N N 4.599 -11.461 274.579 -1.691 2.795 -0.445 H5 DO8 26 DO8 HO5 HO5 H 0 1 N Y N 3.320 -10.765 276.396 -2.729 2.644 1.596 HO5 DO8 27 DO8 H6 H6 H 0 1 N N N 6.732 -10.660 275.219 -0.765 0.687 -1.382 H6 DO8 28 DO8 H7 H7 H 0 1 N N N 6.197 -8.775 276.992 0.471 1.508 1.284 H7 DO8 29 DO8 HO7 HO7 H 0 1 N Y N 4.709 -7.014 277.101 0.847 2.441 -1.380 HO7 DO8 30 DO8 H81 H81 H 0 1 N N N 5.297 -9.651 273.999 1.367 -0.616 0.286 H81 DO8 31 DO8 H82 H82 H 0 1 N N N 3.835 -9.103 274.606 1.741 0.282 -1.205 H82 DO8 32 DO8 HOP2 HOP2 H 0 0 N N N 2.890 -6.411 275.749 6.000 -0.610 0.542 HOP2 DO8 33 DO8 HOP3 HOP3 H 0 0 N N N 7.186 -5.603 275.414 4.484 0.580 -1.774 HOP3 DO8 34 DO8 HO2 HO2 H 0 1 N Y N 8.237 -12.386 276.014 -1.287 -1.552 -1.877 HO2 DO8 35 # # 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 DO8 C1 O1B SING N N 1 DO8 C1 O1A DOUB N N 2 DO8 C1 C2 SING N N 3 DO8 O1B HO1B SING N N 4 DO8 C2 C3 SING N N 5 DO8 C2 O6 SING N N 6 DO8 C2 O2 SING N N 7 DO8 C3 C4 SING N N 8 DO8 C3 H31 SING N N 9 DO8 C3 H32 SING N N 10 DO8 C4 O4 SING N N 11 DO8 C4 C5 SING N N 12 DO8 C4 H4 SING N N 13 DO8 O4 HO4 SING N N 14 DO8 C5 O5 SING N N 15 DO8 C5 C6 SING N N 16 DO8 C5 H5 SING N N 17 DO8 O5 HO5 SING N N 18 DO8 C6 O6 SING N N 19 DO8 C6 C7 SING N N 20 DO8 C6 H6 SING N N 21 DO8 C7 O7 SING N N 22 DO8 C7 C8 SING N N 23 DO8 C7 H7 SING N N 24 DO8 O7 HO7 SING N N 25 DO8 C8 O8 SING N N 26 DO8 C8 H81 SING N N 27 DO8 C8 H82 SING N N 28 DO8 P1 O2P SING N N 29 DO8 P1 O3P SING N N 30 DO8 P1 O8 SING N N 31 DO8 P1 O1P DOUB N N 32 DO8 O2P HOP2 SING N N 33 DO8 O3P HOP3 SING N N 34 DO8 O2 HO2 SING N N 35 # # 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 DO8 SMILES ACDLabs 10.04 "O=P(O)(O)OCC(O)C1OC(O)(C(=O)O)CC(O)C1O" DO8 SMILES_CANONICAL CACTVS 3.341 "O[C@H](CO[P](O)(O)=O)[C@H]1O[C@](O)(C[C@@H](O)[C@H]1O)C(O)=O" DO8 SMILES CACTVS 3.341 "O[CH](CO[P](O)(O)=O)[CH]1O[C](O)(C[CH](O)[CH]1O)C(O)=O" DO8 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@H]([C@H]([C@H](O[C@]1(C(=O)O)O)[C@@H](COP(=O)(O)O)O)O)O" DO8 SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(C(OC1(C(=O)O)O)C(COP(=O)(O)O)O)O)O" DO8 InChI InChI 1.03 "InChI=1S/C8H15O11P/c9-3-1-8(14,7(12)13)19-6(5(3)11)4(10)2-18-20(15,16)17/h3-6,9-11,14H,1-2H2,(H,12,13)(H2,15,16,17)/t3-,4-,5-,6-,8-/m1/s1" DO8 InChIKey InChI 1.03 IZZNRKJLBIYBJN-HXUQBWEZSA-N # # 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 DO8 "SYSTEMATIC NAME" ACDLabs 10.04 "3-deoxy-8-O-phosphono-alpha-D-manno-oct-2-ulopyranosonic acid" DO8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,4R,5R,6R)-2,4,5-trihydroxy-6-[(1R)-1-hydroxy-2-phosphonooxy-ethyl]oxane-2-carboxylic acid" # _pdbx_chem_comp_related.comp_id DO8 _pdbx_chem_comp_related.related_comp_id KDO _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 DO8 C1 KDO C1 "Carbohydrate core" 2 DO8 C2 KDO C2 "Carbohydrate core" 3 DO8 C3 KDO C3 "Carbohydrate core" 4 DO8 C4 KDO C4 "Carbohydrate core" 5 DO8 C5 KDO C5 "Carbohydrate core" 6 DO8 C6 KDO C6 "Carbohydrate core" 7 DO8 C7 KDO C7 "Carbohydrate core" 8 DO8 C8 KDO C8 "Carbohydrate core" 9 DO8 O8 KDO O8 "Carbohydrate core" 10 DO8 O1B KDO O1B "Carbohydrate core" 11 DO8 O1A KDO O1A "Carbohydrate core" 12 DO8 O2 KDO O2 "Carbohydrate core" 13 DO8 O4 KDO O4 "Carbohydrate core" 14 DO8 O5 KDO O5 "Carbohydrate core" 15 DO8 O6 KDO O6 "Carbohydrate core" 16 DO8 O7 KDO O7 "Carbohydrate core" 17 DO8 HO1B KDO HO1B "Carbohydrate core" 18 DO8 H31 KDO H31 "Carbohydrate core" 19 DO8 H32 KDO H32 "Carbohydrate core" 20 DO8 H4 KDO H4 "Carbohydrate core" 21 DO8 H5 KDO H5 "Carbohydrate core" 22 DO8 H6 KDO H6 "Carbohydrate core" 23 DO8 H7 KDO H7 "Carbohydrate core" 24 DO8 H81 KDO H81 "Carbohydrate core" 25 DO8 H82 KDO H82 "Carbohydrate core" 26 DO8 HO2 KDO HO2 "Carbohydrate core" 27 DO8 HO4 KDO HO4 "Carbohydrate core" 28 DO8 HO5 KDO HO5 "Carbohydrate core" 29 DO8 HO7 KDO HO7 "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 DO8 "CARBOHYDRATE ISOMER" D PDB ? DO8 "CARBOHYDRATE RING" pyranose PDB ? DO8 "CARBOHYDRATE ANOMER" alpha PDB ? DO8 "CARBOHYDRATE PRIMARY CARBONYL GROUP" ketose 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 DO8 "Create component" 2004-08-18 RCSB DO8 "Modify descriptor" 2011-06-04 RCSB DO8 "Other modification" 2020-07-03 RCSB DO8 "Modify parent residue" 2020-07-17 RCSB DO8 "Modify name" 2020-07-17 RCSB DO8 "Modify synonyms" 2020-07-17 RCSB DO8 "Modify internal type" 2020-07-17 RCSB DO8 "Modify linking type" 2020-07-17 RCSB DO8 "Modify atom id" 2020-07-17 RCSB DO8 "Modify component atom id" 2020-07-17 RCSB DO8 "Modify leaving atom flag" 2020-07-17 RCSB ##