data_BND # _chem_comp.id BND _chem_comp.name "methyl 5-acetamido-3,5,9-trideoxy-9-[(phenylcarbonyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid" _chem_comp.type D-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C19 H26 N2 O9" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;ME-A-N-BENZOYL-AMINO-9-DEOXY-NEU5AC; methyl 5-acetamido-3,5,9-trideoxy-9-[(phenylcarbonyl)amino]-D-glycero-alpha-D-galacto-non-2-ulosidonic acid; methyl 5-acetamido-3,5,9-trideoxy-9-[(phenylcarbonyl)amino]-D-glycero-D-galacto-non-2-ulosidonic acid; methyl 5-acetamido-3,5,9-trideoxy-9-[(phenylcarbonyl)amino]-D-glycero-galacto-non-2-ulosidonic acid ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-02-14 _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 426.418 _chem_comp.one_letter_code ? _chem_comp.three_letter_code BND _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 1OD9 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 BND ME-A-N-BENZOYL-AMINO-9-DEOXY-NEU5AC PDB ? 2 BND "methyl 5-acetamido-3,5,9-trideoxy-9-[(phenylcarbonyl)amino]-D-glycero-alpha-D-galacto-non-2-ulosidonic acid" PDB ? 3 BND "methyl 5-acetamido-3,5,9-trideoxy-9-[(phenylcarbonyl)amino]-D-glycero-D-galacto-non-2-ulosidonic acid" PDB ? 4 BND "methyl 5-acetamido-3,5,9-trideoxy-9-[(phenylcarbonyl)amino]-D-glycero-galacto-non-2-ulosidonic 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 BND CY1 CY1 C 0 1 N N N 66.117 39.999 35.798 3.663 1.098 -1.181 CY1 BND 1 BND C1 CX1 C 0 1 N N N 63.387 39.150 34.815 2.351 -0.914 -2.535 C1 BND 2 BND O1A O1A O 0 1 N N N 62.477 39.701 35.476 2.186 -1.468 -1.474 O1A BND 3 BND O1B O1B O 0 1 N N N 63.561 39.332 33.572 2.833 -1.601 -3.582 O1B BND 4 BND C2 CX2 C 0 1 N N R 64.357 38.218 35.587 2.016 0.547 -2.681 C2 BND 5 BND O2 OX2 O 0 1 N N N 65.131 39.029 36.424 3.203 1.325 -2.515 O2 BND 6 BND C3 CX3 C 0 1 N N N 63.629 37.210 36.493 1.434 0.798 -4.074 C3 BND 7 BND C4 CX4 C 0 1 N N S 62.943 36.101 35.644 0.181 -0.066 -4.255 C4 BND 8 BND O4 OX4 O 0 1 N N N 62.499 35.060 36.486 -0.456 0.266 -5.490 O4 BND 9 BND C5 CX5 C 0 1 N N R 63.857 35.467 34.578 -0.775 0.206 -3.089 C5 BND 10 BND N5 NX5 N 0 1 N N N 63.007 34.579 33.780 -1.910 -0.717 -3.159 N5 BND 11 BND C10 C10 C 0 1 N N N 63.327 33.281 33.649 -3.015 -0.374 -3.850 C10 BND 12 BND O10 O10 O 0 1 N N N 64.346 32.762 34.157 -3.071 0.698 -4.413 O10 BND 13 BND C11 C11 C 0 1 N N N 62.393 32.404 32.845 -4.183 -1.324 -3.923 C11 BND 14 BND C6 CX6 C 0 1 N N R 64.487 36.601 33.741 -0.025 0.000 -1.770 C6 BND 15 BND O6 OX6 O 0 1 N N N 65.202 37.530 34.625 1.064 0.916 -1.686 O6 BND 16 BND C7 CX7 C 0 1 N N R 65.415 36.171 32.616 -0.981 0.239 -0.600 C7 BND 17 BND O7 OX7 O 0 1 N N N 66.484 35.434 33.170 -1.482 1.575 -0.659 O7 BND 18 BND C8 CX8 C 0 1 N N R 66.038 37.376 31.888 -0.233 0.033 0.718 C8 BND 19 BND O8 OX8 O 0 1 N N N 65.072 38.309 31.454 0.268 -1.303 0.778 O8 BND 20 BND C9 CX9 C 0 1 N N N 66.872 36.852 30.701 -1.188 0.271 1.889 C9 BND 21 BND NX6 NX6 N 0 1 N N N 67.583 37.943 30.034 -0.472 0.074 3.152 NX6 BND 22 BND C12 C12 C 0 1 N N N 68.812 38.318 30.384 -1.117 0.232 4.324 C12 BND 23 BND O12 O12 O 0 1 N N N 69.525 37.552 31.004 -2.294 0.538 4.334 O12 BND 24 BND C1G C1G C 0 1 Y N N 69.411 39.656 30.072 -0.395 0.033 5.599 C1G BND 25 BND CD1 CD1 C 0 1 Y N N 68.780 40.542 29.199 -1.060 0.196 6.815 CD1 BND 26 BND CE1 CE1 C 0 1 Y N N 69.339 41.777 28.901 -0.380 0.008 8.000 CE1 BND 27 BND CD2 CD2 C 0 1 Y N N 70.620 40.030 30.647 0.954 -0.323 5.591 CD2 BND 28 BND CE2 CE2 C 0 1 Y N N 71.202 41.275 30.362 1.624 -0.502 6.783 CE2 BND 29 BND C1Z C1Z C 0 1 Y N N 70.553 42.144 29.487 0.958 -0.339 7.986 C1Z BND 30 BND HY11 HY11 H 0 0 N N N 66.915 39.436 35.292 4.513 1.748 -0.974 HY11 BND 31 BND HY12 HY12 H 0 0 N N N 65.594 40.632 35.066 2.859 1.315 -0.478 HY12 BND 32 BND HY13 HY13 H 0 0 N N N 66.557 40.632 36.583 3.967 0.057 -1.075 HY13 BND 33 BND HO1B H1B H 0 0 N N N 64.251 38.914 33.070 3.048 -2.539 -3.488 HO1B BND 34 BND H32 HX31 H 0 1 N N N 64.357 36.745 37.174 1.168 1.850 -4.174 H32 BND 35 BND H31 HX32 H 0 1 N N N 62.857 37.744 37.066 2.172 0.533 -4.831 H31 BND 36 BND H4 HX4 H 0 1 N N N 62.114 36.604 35.125 0.461 -1.119 -4.260 H4 BND 37 BND HO4 HA H 0 1 N Y N 61.509 35.044 36.499 0.185 0.090 -6.192 HO4 BND 38 BND H5 HX5 H 0 1 N N N 64.685 34.882 35.005 -1.136 1.233 -3.146 H5 BND 39 BND HN5 HB H 0 1 N N N 62.193 34.938 33.335 -1.865 -1.575 -2.709 HN5 BND 40 BND H111 H111 H 0 0 N N N 62.622 31.346 33.042 -4.978 -0.878 -4.520 H111 BND 41 BND H113 H112 H 0 0 N N N 61.353 32.614 33.135 -3.863 -2.258 -4.384 H113 BND 42 BND H112 H113 H 0 0 N N N 62.525 32.614 31.773 -4.552 -1.524 -2.917 H112 BND 43 BND H6 HX6 H 0 1 N N N 63.632 37.078 33.239 0.354 -1.020 -1.726 H6 BND 44 BND H7 HX7 H 0 1 N N N 64.818 35.583 31.903 -1.812 -0.463 -0.660 H7 BND 45 BND HO7 HC H 0 1 N Y N 66.302 34.465 33.076 -0.717 2.164 -0.603 HO7 BND 46 BND H8 HX8 H 0 1 N N N 66.682 37.917 32.597 0.597 0.735 0.778 H8 BND 47 BND HO8 HD H 0 1 N Y N 64.283 37.827 31.100 -0.497 -1.892 0.722 HO8 BND 48 BND H92 HX91 H 0 1 N N N 67.604 36.120 31.072 -1.571 1.291 1.844 H92 BND 49 BND H91 HX92 H 0 1 N N N 66.191 36.384 29.975 -2.019 -0.431 1.829 H91 BND 50 BND HE HE H 0 1 N N N 67.131 38.424 29.290 0.466 -0.169 3.144 HE BND 51 BND HD1 HD1 H 0 1 N N N 67.856 40.267 28.755 -2.105 0.468 6.828 HD1 BND 52 BND HE1 HE1 H 0 1 N N N 68.847 42.438 28.232 -0.893 0.134 8.942 HE1 BND 53 BND HD2 HD2 H 0 1 N N N 71.111 39.364 31.312 1.474 -0.451 4.653 HD2 BND 54 BND HE2 HE2 H 0 1 N N N 72.125 41.551 30.807 2.669 -0.774 6.779 HE2 BND 55 BND H1Z H1Z H 0 1 N N N 70.983 43.089 29.265 1.486 -0.485 8.916 H1Z BND 56 # # 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 BND CY1 O2 SING N N 1 BND CY1 HY11 SING N N 2 BND CY1 HY12 SING N N 3 BND CY1 HY13 SING N N 4 BND C1 O1A DOUB N N 5 BND C1 O1B SING N N 6 BND C1 C2 SING N N 7 BND O1B HO1B SING N N 8 BND C2 O2 SING N N 9 BND C2 C3 SING N N 10 BND C2 O6 SING N N 11 BND C3 C4 SING N N 12 BND C3 H32 SING N N 13 BND C3 H31 SING N N 14 BND C4 O4 SING N N 15 BND C4 C5 SING N N 16 BND C4 H4 SING N N 17 BND O4 HO4 SING N N 18 BND C5 N5 SING N N 19 BND C5 C6 SING N N 20 BND C5 H5 SING N N 21 BND N5 C10 SING N N 22 BND N5 HN5 SING N N 23 BND C10 O10 DOUB N N 24 BND C10 C11 SING N N 25 BND C11 H111 SING N N 26 BND C11 H113 SING N N 27 BND C11 H112 SING N N 28 BND C6 O6 SING N N 29 BND C6 C7 SING N N 30 BND C6 H6 SING N N 31 BND C7 O7 SING N N 32 BND C7 C8 SING N N 33 BND C7 H7 SING N N 34 BND O7 HO7 SING N N 35 BND C8 O8 SING N N 36 BND C8 C9 SING N N 37 BND C8 H8 SING N N 38 BND O8 HO8 SING N N 39 BND C9 NX6 SING N N 40 BND C9 H92 SING N N 41 BND C9 H91 SING N N 42 BND NX6 C12 SING N N 43 BND NX6 HE SING N N 44 BND C12 O12 DOUB N N 45 BND C12 C1G SING N N 46 BND C1G CD1 DOUB Y N 47 BND C1G CD2 SING Y N 48 BND CD1 CE1 SING Y N 49 BND CD1 HD1 SING N N 50 BND CE1 C1Z DOUB Y N 51 BND CE1 HE1 SING N N 52 BND CD2 CE2 DOUB Y N 53 BND CD2 HD2 SING N N 54 BND CE2 C1Z SING Y N 55 BND CE2 HE2 SING N N 56 BND C1Z H1Z SING N N 57 # # 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 BND SMILES ACDLabs 10.04 "O=C(c1ccccc1)NCC(O)C(O)C2OC(OC)(C(=O)O)CC(O)C2NC(=O)C" BND SMILES_CANONICAL CACTVS 3.341 "CO[C@@]1(C[C@H](O)[C@@H](NC(C)=O)[C@@H](O1)[C@H](O)[C@H](O)CNC(=O)c2ccccc2)C(O)=O" BND SMILES CACTVS 3.341 "CO[C]1(C[CH](O)[CH](NC(C)=O)[CH](O1)[CH](O)[CH](O)CNC(=O)c2ccccc2)C(O)=O" BND SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC(=O)N[C@@H]1[C@H](C[C@@](O[C@H]1[C@@H]([C@@H](CNC(=O)c2ccccc2)O)O)(C(=O)O)OC)O" BND SMILES "OpenEye OEToolkits" 1.5.0 "CC(=O)NC1C(CC(OC1C(C(CNC(=O)c2ccccc2)O)O)(C(=O)O)OC)O" BND InChI InChI 1.03 "InChI=1S/C19H26N2O9/c1-10(22)21-14-12(23)8-19(29-2,18(27)28)30-16(14)15(25)13(24)9-20-17(26)11-6-4-3-5-7-11/h3-7,12-16,23-25H,8-9H2,1-2H3,(H,20,26)(H,21,22)(H,27,28)/t12-,13+,14+,15+,16+,19+/m0/s1" BND InChIKey InChI 1.03 ULZLCALWUIQOMB-YRIWUQCMSA-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 BND "SYSTEMATIC NAME" ACDLabs 10.04 "methyl 5-(acetylamino)-3,5,9-trideoxy-9-[(phenylcarbonyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid" BND "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,4S,5R,6R)-5-acetamido-6-[(1R,2R)-3-benzamido-1,2-dihydroxy-propyl]-4-hydroxy-2-methoxy-oxane-2-carboxylic acid" # # 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 BND "CARBOHYDRATE ISOMER" D PDB ? BND "CARBOHYDRATE RING" pyranose PDB ? BND "CARBOHYDRATE ANOMER" alpha PDB ? BND "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 BND "Create component" 2003-02-14 EBI BND "Modify descriptor" 2011-06-04 RCSB BND "Other modification" 2020-07-03 RCSB BND "Modify name" 2020-07-17 RCSB BND "Modify synonyms" 2020-07-17 RCSB BND "Modify internal type" 2020-07-17 RCSB BND "Modify linking type" 2020-07-17 RCSB BND "Modify atom id" 2020-07-17 RCSB BND "Modify component atom id" 2020-07-17 RCSB BND "Modify leaving atom flag" 2020-07-17 RCSB ##