data_3R3 # _chem_comp.id 3R3 _chem_comp.name "[[[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-oxidanyl-phosphoryl]amino]phosphonic acid" _chem_comp.type D-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C5 H14 N O13 P3" _chem_comp.mon_nstd_parent_comp_id RIB _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-10-13 _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 389.085 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 3R3 _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 4WN3 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 3R3 O3B O3B O 0 1 N N N -7.649 -19.628 -1.520 -4.667 -1.540 -0.986 O3B 3R3 1 3R3 PB PB P 0 1 N N N -8.450 -20.616 -0.623 -3.625 -1.846 0.020 PB 3R3 2 3R3 O1B O1B O 0 1 N N N -9.802 -20.104 -0.448 -4.209 -1.577 1.496 O1B 3R3 3 3R3 O2B O2B O 0 1 N N N -7.712 -21.001 0.610 -3.189 -3.390 -0.111 O2B 3R3 4 3R3 N3A N3A N 0 1 N N N -8.668 -21.988 -1.494 -2.287 -0.860 -0.242 N3A 3R3 5 3R3 PA PA P 0 1 N N N -7.566 -23.110 -2.076 -2.700 0.766 -0.114 PA 3R3 6 3R3 O1A O1A O 0 1 N N N -8.222 -23.861 -3.238 -3.229 1.035 1.242 O1A 3R3 7 3R3 O2A O2A O 0 1 N N N -6.915 -23.884 -0.964 -3.826 1.122 -1.209 O2A 3R3 8 3R3 O1 O1 O 0 1 N N N -6.338 -22.233 -2.718 -1.396 1.674 -0.371 O1 3R3 9 3R3 C1 C1 C 0 1 N N R -4.964 -22.641 -2.794 -0.305 1.747 0.550 C1 3R3 10 3R3 O4 O4 O 0 1 N N N -4.889 -23.576 -3.866 0.680 0.762 0.216 O4 3R3 11 3R3 C4 C4 C 0 1 N N R -4.668 -22.832 -5.086 1.919 1.403 -0.125 C4 3R3 12 3R3 C3 C3 C 0 1 N N S -4.293 -21.387 -4.730 1.875 2.776 0.591 C3 3R3 13 3R3 O3 O3 O 0 1 N N N -5.429 -20.588 -5.181 2.694 3.735 -0.081 O3 3R3 14 3R3 C2 C2 C 0 1 N N R -4.135 -21.418 -3.206 0.368 3.133 0.455 C2 3R3 15 3R3 O2 O2 O 0 1 N N N -4.688 -20.247 -2.583 0.102 3.741 -0.811 O2 3R3 16 3R3 C5 C5 C 0 1 N N N -3.703 -23.537 -5.994 3.103 0.577 0.382 C5 3R3 17 3R3 O5 O5 O 0 1 N N N -4.543 -24.523 -6.637 3.196 -0.634 -0.370 O5 3R3 18 3R3 P P P 0 1 N N N -3.765 -25.759 -7.279 4.330 -1.746 -0.105 P 3R3 19 3R3 O1P O1P O 0 1 N N N -2.984 -26.403 -6.130 4.127 -2.381 1.360 O1P 3R3 20 3R3 O2P O2P O 0 1 N N N -4.714 -26.800 -7.832 4.213 -2.906 -1.215 O2P 3R3 21 3R3 O3P O3P O 0 1 N N N -2.818 -25.014 -8.261 5.667 -1.116 -0.189 O3P 3R3 22 3R3 H1A H1 H 0 1 N N N -9.894 -19.284 -0.919 -3.579 -1.756 2.207 H1A 3R3 23 3R3 H2A H2 H 0 1 N N N -6.869 -20.564 0.624 -3.912 -4.016 0.028 H2A 3R3 24 3R3 H3A H3 H 0 1 N N N -9.148 -21.677 -2.314 -1.863 -1.056 -1.137 H3A 3R3 25 3R3 H4A H4 H 0 1 N N N -6.998 -24.815 -1.134 -3.547 0.969 -2.123 H4A 3R3 26 3R3 H1 H5 H 0 1 N N N -4.599 -23.059 -1.844 -0.666 1.580 1.565 H1 3R3 27 3R3 H4 H6 H 0 1 N N N -5.628 -22.781 -5.620 1.988 1.541 -1.204 H4 3R3 28 3R3 H3 H7 H 0 1 N N N -3.354 -21.089 -5.220 2.162 2.682 1.639 H3 3R3 29 3R3 HO3 H8 H 0 1 N Y N -5.267 -19.671 -4.992 2.697 4.609 0.332 HO3 3R3 30 3R3 H2 H9 H 0 1 N N N -3.079 -21.564 -2.934 0.047 3.779 1.272 H2 3R3 31 3R3 HO2 H10 H 0 1 N Y N -4.571 -20.303 -1.642 -0.825 3.982 -0.944 HO2 3R3 32 3R3 H51 H11 H 0 1 N N N -2.895 -24.016 -5.421 4.023 1.150 0.264 H51 3R3 33 3R3 H52 H12 H 0 1 N N N -3.270 -22.843 -6.729 2.955 0.340 1.436 H52 3R3 34 3R3 H13 H13 H 0 1 N N N -2.057 -26.223 -6.236 3.270 -2.812 1.487 H13 3R3 35 3R3 H14 H14 H 0 1 N N N -4.599 -26.866 -8.773 4.867 -3.612 -1.117 H14 3R3 36 # # 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 3R3 O3P P DOUB N N 1 3R3 O2P P SING N N 2 3R3 P O5 SING N N 3 3R3 P O1P SING N N 4 3R3 O5 C5 SING N N 5 3R3 C5 C4 SING N N 6 3R3 O3 C3 SING N N 7 3R3 C4 C3 SING N N 8 3R3 C4 O4 SING N N 9 3R3 C3 C2 SING N N 10 3R3 O4 C1 SING N N 11 3R3 O1A PA DOUB N N 12 3R3 C2 C1 SING N N 13 3R3 C2 O2 SING N N 14 3R3 C1 O1 SING N N 15 3R3 O1 PA SING N N 16 3R3 PA N3A SING N N 17 3R3 PA O2A SING N N 18 3R3 O3B PB DOUB N N 19 3R3 N3A PB SING N N 20 3R3 PB O1B SING N N 21 3R3 PB O2B SING N N 22 3R3 O1B H1A SING N N 23 3R3 O2B H2A SING N N 24 3R3 N3A H3A SING N N 25 3R3 O2A H4A SING N N 26 3R3 C1 H1 SING N N 27 3R3 C4 H4 SING N N 28 3R3 C3 H3 SING N N 29 3R3 O3 HO3 SING N N 30 3R3 C2 H2 SING N N 31 3R3 O2 HO2 SING N N 32 3R3 C5 H51 SING N N 33 3R3 C5 H52 SING N N 34 3R3 O1P H13 SING N N 35 3R3 O2P H14 SING N N 36 # # 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 3R3 InChI InChI 1.03 "InChI=1S/C5H14NO13P3/c7-3-2(1-17-22(14,15)16)18-5(4(3)8)19-21(12,13)6-20(9,10)11/h2-5,7-8H,1H2,(H2,14,15,16)(H4,6,9,10,11,12,13)/t2-,3-,4-,5-/m1/s1" 3R3 InChIKey InChI 1.03 FCRMTSGXHCKCEX-TXICZTDVSA-N 3R3 SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@H](O[C@@H]1CO[P](O)(O)=O)O[P](O)(=O)N[P](O)(O)=O" 3R3 SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)O[P](O)(=O)N[P](O)(O)=O" 3R3 SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "C([C@@H]1[C@H]([C@H]([C@H](O1)OP(=O)(NP(=O)(O)O)O)O)O)OP(=O)(O)O" 3R3 SMILES "OpenEye OEToolkits" 1.9.2 "C(C1C(C(C(O1)OP(=O)(NP(=O)(O)O)O)O)O)OP(=O)(O)O" # _pdbx_chem_comp_identifier.comp_id 3R3 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 1.9.2 _pdbx_chem_comp_identifier.identifier "[[[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-oxidanyl-phosphoryl]amino]phosphonic acid" # _pdbx_chem_comp_related.comp_id 3R3 _pdbx_chem_comp_related.related_comp_id RIB _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 3R3 C1 RIB C1 "Carbohydrate core" 2 3R3 C2 RIB C2 "Carbohydrate core" 3 3R3 C3 RIB C3 "Carbohydrate core" 4 3R3 C4 RIB C4 "Carbohydrate core" 5 3R3 C5 RIB C5 "Carbohydrate core" 6 3R3 O1 RIB O1 "Carbohydrate core" 7 3R3 O2 RIB O2 "Carbohydrate core" 8 3R3 O3 RIB O3 "Carbohydrate core" 9 3R3 O4 RIB O4 "Carbohydrate core" 10 3R3 O5 RIB O5 "Carbohydrate core" 11 3R3 HO2 RIB HO2 "Carbohydrate core" 12 3R3 H51 RIB H51 "Carbohydrate core" 13 3R3 H52 RIB H52 "Carbohydrate core" 14 3R3 H1 RIB H1 "Carbohydrate core" 15 3R3 H4 RIB H4 "Carbohydrate core" 16 3R3 H3 RIB H3 "Carbohydrate core" 17 3R3 HO3 RIB HO3 "Carbohydrate core" 18 3R3 H2 RIB H2 "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 3R3 "CARBOHYDRATE ISOMER" D PDB ? 3R3 "CARBOHYDRATE RING" furanose PDB ? 3R3 "CARBOHYDRATE ANOMER" alpha PDB ? 3R3 "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 3R3 "Create component" 2014-10-13 EBI 3R3 "Initial release" 2015-12-23 RCSB 3R3 "Other modification" 2020-07-03 RCSB 3R3 "Modify parent residue" 2020-07-17 RCSB 3R3 "Modify internal type" 2020-07-17 RCSB 3R3 "Modify linking type" 2020-07-17 RCSB 3R3 "Modify atom id" 2020-07-17 RCSB 3R3 "Modify component atom id" 2020-07-17 RCSB 3R3 "Modify leaving atom flag" 2020-07-17 RCSB ##