data_NXD # _chem_comp.id NXD _chem_comp.name "methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid" _chem_comp.type D-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C14 H23 N3 O10" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;METHYL 5-(ACETYLAMINO)-9-{[AMINO(OXO)ACETYL]AMINO}-3,5,9-TRIDEOXY-D-GLYCERO-ALPHA-D-GLUCO-NON-2-ULOPYRANOSIDONIC ACID; ALPHA METHYL -9-(AMINOOXALYL-AMINO)-9-DEOXYNEU5AC; OXAMIDO-NEU5AC; methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-alpha-D-galacto-non-2-ulosidonic acid; methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-D-galacto-non-2-ulosidonic acid; methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-galacto-non-2-ulosidonic acid ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-02-28 _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 393.347 _chem_comp.one_letter_code ? _chem_comp.three_letter_code NXD _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 2G5R _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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 NXD C11 C11 C 0 1 N N N -5.337 13.357 30.493 -3.265 4.267 1.158 C11 NXD 1 NXD C10 C10 C 0 1 N N N -3.822 13.569 30.313 -3.169 3.075 0.242 C10 NXD 2 NXD O10 O10 O 0 1 N N N -3.294 14.628 30.654 -3.719 3.095 -0.839 O10 NXD 3 NXD N5 N5 N 0 1 N N N -3.135 12.554 29.782 -2.473 1.986 0.624 N5 NXD 4 NXD C5 C5 C 0 1 N N R -3.736 11.283 29.348 -2.380 0.826 -0.267 C5 NXD 5 NXD C4 C4 C 0 1 N N S -3.254 10.133 30.233 -3.607 -0.072 -0.070 C4 NXD 6 NXD O4 O4 O 0 1 N N N -3.683 10.361 31.576 -4.781 0.611 -0.515 O4 NXD 7 NXD C3 C3 C 0 1 N N N -3.805 8.781 29.733 -3.415 -1.352 -0.890 C3 NXD 8 NXD C2 C2 C 0 1 N N R -3.504 8.562 28.230 -2.075 -1.988 -0.514 C2 NXD 9 NXD C1 C1 C 0 1 N N N -2.000 8.274 28.042 -2.062 -2.293 0.962 C1 NXD 10 NXD O1B O1A O 0 1 N N N -1.427 7.467 28.773 -0.895 -2.364 1.623 O1B NXD 11 NXD O1A O1B O 0 1 N N N -1.360 8.848 27.160 -3.101 -2.474 1.551 O1A NXD 12 NXD O2 O2 O 0 1 N N N -4.280 7.426 27.769 -1.900 -3.200 -1.250 O2 NXD 13 NXD CB CB C 0 1 N N N -4.238 7.196 26.338 -0.602 -3.699 -0.924 CB NXD 14 NXD O6 O6 O 0 1 N N N -3.910 9.735 27.450 -1.010 -1.090 -0.820 O6 NXD 15 NXD C6 C6 C 0 1 N N R -3.348 11.004 27.884 -1.119 0.025 0.063 C6 NXD 16 NXD C7 C7 C 0 1 N N R -3.791 12.083 26.885 0.110 0.922 -0.100 C7 NXD 17 NXD O7 O7 O 0 1 N N N -5.230 12.152 26.834 0.119 1.485 -1.413 O7 NXD 18 NXD C8 C8 C 0 1 N N R -3.222 11.837 25.477 1.379 0.092 0.107 C8 NXD 19 NXD O8 O8 O 0 1 N N N -1.928 11.216 25.547 1.370 -0.471 1.420 O8 NXD 20 NXD C9 C9 C 0 1 N N N -3.125 13.162 24.728 2.607 0.989 -0.055 C9 NXD 21 NXD NAB NAB N 0 1 N N N -2.927 12.963 23.287 3.822 0.173 0.024 NAB NXD 22 NXD CAC CAC C 0 1 N N N -3.918 12.704 22.433 5.032 0.753 -0.093 CAC NXD 23 NXD OAD OAD O 0 1 N N N -5.101 12.593 22.763 5.117 1.952 -0.264 OAD NXD 24 NXD CAF CAF C 0 1 N N N -3.538 12.534 20.962 6.271 -0.079 -0.012 CAF NXD 25 NXD OAG OAG O 0 1 N N N -2.350 12.656 20.674 6.187 -1.277 0.160 OAG NXD 26 NXD NAK NAK N 0 1 N N N -4.480 12.271 20.056 7.482 0.501 -0.129 NAK NXD 27 NXD H111 H111 H 0 0 N N N -5.636 12.417 30.006 -2.713 4.066 2.076 H111 NXD 28 NXD H113 H112 H 0 0 N N N -5.881 14.196 30.035 -2.840 5.141 0.663 H113 NXD 29 NXD H112 H113 H 0 0 N N N -5.576 13.306 31.566 -4.311 4.458 1.398 H112 NXD 30 NXD HN5 HN5 H 0 1 N N N -2.147 12.665 29.672 -2.034 1.969 1.489 HN5 NXD 31 NXD H5 H5 H 0 1 N N N -4.830 11.361 29.434 -2.338 1.164 -1.302 H5 NXD 32 NXD H4 H4 H 0 1 N N N -2.156 10.093 30.191 -3.710 -0.325 0.985 H4 NXD 33 NXD HO4 HO4 H 0 1 N Y N -2.925 10.412 32.147 -5.523 0.005 -0.384 HO4 NXD 34 NXD H32 H31 H 0 1 N N N -4.897 8.782 29.869 -3.417 -1.109 -1.952 H32 NXD 35 NXD H31 H32 H 0 1 N N N -3.333 7.972 30.310 -4.223 -2.050 -0.672 H31 NXD 36 NXD HO1B H1A H 0 0 N N N -0.512 7.408 28.525 -0.887 -2.560 2.570 HO1B NXD 37 NXD HB1 HB1 H 0 1 N N N -5.125 6.622 26.033 0.142 -2.923 -1.108 HB1 NXD 38 NXD HB2 HB2 H 0 1 N N N -3.330 6.630 26.084 -0.576 -3.986 0.127 HB2 NXD 39 NXD HB3 HB3 H 0 1 N N N -4.227 8.162 25.811 -0.380 -4.568 -1.544 HB3 NXD 40 NXD H6 H6 H 0 1 N N N -2.248 10.991 27.882 -1.174 -0.331 1.091 H6 NXD 41 NXD H7 H7 H 0 1 N N N -3.390 13.044 27.239 0.076 1.723 0.639 H7 NXD 42 NXD HO7 HO7 H 0 1 N Y N -5.578 12.167 27.718 0.149 0.745 -2.034 HO7 NXD 43 NXD H8 H8 H 0 1 N N N -3.899 11.157 24.938 1.413 -0.709 -0.631 H8 NXD 44 NXD HO8 HO8 H 0 1 N Y N -1.594 11.079 24.668 1.339 0.269 2.042 HO8 NXD 45 NXD H92 H91 H 0 1 N N N -2.258 13.714 25.120 2.568 1.488 -1.023 H92 NXD 46 NXD H91 H92 H 0 1 N N N -4.059 13.722 24.881 2.619 1.736 0.738 H91 NXD 47 NXD HAB HAB H 0 1 N N N -1.997 13.025 22.925 3.754 -0.785 0.161 HAB NXD 48 NXD HAK1 HAK1 H 0 0 N N N -4.324 12.147 19.076 7.549 1.459 -0.266 HAK1 NXD 49 NXD HAK2 HAK2 H 0 0 N N N -5.367 12.218 20.514 8.286 -0.039 -0.076 HAK2 NXD 50 # # 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 NXD C11 C10 SING N N 1 NXD C11 H111 SING N N 2 NXD C11 H113 SING N N 3 NXD C11 H112 SING N N 4 NXD C10 O10 DOUB N N 5 NXD C10 N5 SING N N 6 NXD N5 C5 SING N N 7 NXD N5 HN5 SING N N 8 NXD C5 C4 SING N N 9 NXD C5 C6 SING N N 10 NXD C5 H5 SING N N 11 NXD C4 O4 SING N N 12 NXD C4 C3 SING N N 13 NXD C4 H4 SING N N 14 NXD O4 HO4 SING N N 15 NXD C3 C2 SING N N 16 NXD C3 H32 SING N N 17 NXD C3 H31 SING N N 18 NXD C2 C1 SING N N 19 NXD C2 O2 SING N N 20 NXD C2 O6 SING N N 21 NXD C1 O1B SING N N 22 NXD C1 O1A DOUB N N 23 NXD O1B HO1B SING N N 24 NXD O2 CB SING N N 25 NXD CB HB1 SING N N 26 NXD CB HB2 SING N N 27 NXD CB HB3 SING N N 28 NXD O6 C6 SING N N 29 NXD C6 C7 SING N N 30 NXD C6 H6 SING N N 31 NXD C7 O7 SING N N 32 NXD C7 C8 SING N N 33 NXD C7 H7 SING N N 34 NXD O7 HO7 SING N N 35 NXD C8 O8 SING N N 36 NXD C8 C9 SING N N 37 NXD C8 H8 SING N N 38 NXD O8 HO8 SING N N 39 NXD C9 NAB SING N N 40 NXD C9 H92 SING N N 41 NXD C9 H91 SING N N 42 NXD NAB CAC SING N N 43 NXD NAB HAB SING N N 44 NXD CAC OAD DOUB N N 45 NXD CAC CAF SING N N 46 NXD CAF OAG DOUB N N 47 NXD CAF NAK SING N N 48 NXD NAK HAK1 SING N N 49 NXD NAK HAK2 SING N N 50 # # 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 NXD SMILES ACDLabs 10.04 "O=C(N)C(=O)NCC(O)C(O)C1OC(OC)(C(=O)O)CC(O)C1NC(=O)C" NXD 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)C(N)=O)C(O)=O" NXD SMILES CACTVS 3.341 "CO[C]1(C[CH](O)[CH](NC(C)=O)[CH](O1)[CH](O)[CH](O)CNC(=O)C(N)=O)C(O)=O" NXD 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)C(=O)N)O)O)(C(=O)O)OC)O" NXD SMILES "OpenEye OEToolkits" 1.5.0 "CC(=O)NC1C(CC(OC1C(C(CNC(=O)C(=O)N)O)O)(C(=O)O)OC)O" NXD InChI InChI 1.03 "InChI=1S/C14H23N3O10/c1-5(18)17-8-6(19)3-14(26-2,13(24)25)27-10(8)9(21)7(20)4-16-12(23)11(15)22/h6-10,19-21H,3-4H2,1-2H3,(H2,15,22)(H,16,23)(H,17,18)(H,24,25)/t6-,7+,8+,9+,10+,14+/m0/s1" NXD InChIKey InChI 1.03 KJWFCLCEUZUZFP-BYBVIHBISA-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 NXD "SYSTEMATIC NAME" ACDLabs 10.04 ;methyl 5-(acetylamino)-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid ; NXD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,4S,5R,6R)-5-acetamido-6-[(1R,2R)-1,2-dihydroxy-3-(oxamoylamino)propyl]-4-hydroxy-2-methoxy-oxane-2-carboxylic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site NXD "Create component" 2006-02-28 RCSB NXD "Modify descriptor" 2011-06-04 RCSB NXD "Modify synonyms" 2020-05-27 PDBE NXD "Other modification" 2020-07-03 RCSB NXD "Modify name" 2020-07-17 RCSB NXD "Modify synonyms" 2020-07-17 RCSB NXD "Modify linking type" 2020-07-17 RCSB NXD "Modify atom id" 2020-07-17 RCSB NXD "Modify component atom id" 2020-07-17 RCSB NXD "Modify leaving atom flag" 2020-07-17 RCSB # # 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 NXD "CARBOHYDRATE ISOMER" D PDB ? NXD "CARBOHYDRATE RING" pyranose PDB ? NXD "CARBOHYDRATE ANOMER" alpha PDB ? NXD "CARBOHYDRATE PRIMARY CARBONYL GROUP" ketose PDB ? # # 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 NXD "METHYL 5-(ACETYLAMINO)-9-{[AMINO(OXO)ACETYL]AMINO}-3,5,9-TRIDEOXY-D-GLYCERO-ALPHA-D-GLUCO-NON-2-ULOPYRANOSIDONIC ACID" PDB ? 2 NXD "ALPHA METHYL -9-(AMINOOXALYL-AMINO)-9-DEOXYNEU5AC" PDB ? 3 NXD OXAMIDO-NEU5AC PDB ? 4 NXD "methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-alpha-D-galacto-non-2-ulosidonic acid" PDB ? 5 NXD "methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-D-galacto-non-2-ulosidonic acid" PDB ? 6 NXD "methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-galacto-non-2-ulosidonic acid" PDB ? ##