data_51N # _chem_comp.id 51N _chem_comp.name "5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-1-O-phosphono-alpha-D-ribofuranose" _chem_comp.type D-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C5 H13 O14 P3" _chem_comp.mon_nstd_parent_comp_id RIB _chem_comp.pdbx_synonyms ;1'-ALPHA-PHOSPHORIBOSYL-5'-PYROPHOSPHORIC ACID; 5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-1-O-phosphono-alpha-D-ribose; 5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-1-O-phosphono-D-ribose; 5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-1-O-phosphono-ribose ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-06-15 _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 390.070 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 51N _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 5C1R _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 51N "1'-ALPHA-PHOSPHORIBOSYL-5'-PYROPHOSPHORIC ACID" PDB ? 2 51N "5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-1-O-phosphono-alpha-D-ribose" PDB ? 3 51N "5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-1-O-phosphono-D-ribose" PDB ? 4 51N "5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-1-O-phosphono-ribose" 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 51N C1 C01 C 0 1 N N R -19.034 29.356 18.360 3.187 0.526 -0.426 C1 51N 1 51N O4 O02 O 0 1 N N N -18.408 29.570 16.946 1.775 0.314 -0.324 O4 51N 2 51N C4 C03 C 0 1 N N R -19.243 28.604 16.084 1.136 1.497 0.183 C4 51N 3 51N C3 C04 C 0 1 N N S -20.453 28.694 16.576 2.093 2.660 -0.180 C3 51N 4 51N C2 C05 C 0 1 N N R -20.207 28.811 18.211 3.476 1.977 0.013 C2 51N 5 51N C5 C06 C 0 1 N N N -19.154 29.105 14.637 -0.223 1.697 -0.489 C5 51N 6 51N O1 O07 O 0 1 N N N -18.135 28.463 19.022 3.878 -0.386 0.431 O1 51N 7 51N O08 O08 O 0 1 N N N -16.426 27.982 20.804 5.239 -2.527 1.122 O08 51N 8 51N P09 P09 P 0 1 N N N -17.187 29.109 20.159 4.396 -1.829 -0.059 P09 51N 9 51N O10 O10 O 0 1 N N N -18.165 29.844 21.167 3.133 -2.754 -0.435 O10 51N 10 51N O11 O11 O 0 1 N N N -16.103 29.954 19.639 5.259 -1.665 -1.250 O11 51N 11 51N O3 O12 O 0 1 N N N -21.218 27.523 16.254 1.931 3.760 0.718 O3 51N 12 51N O2 O13 O 0 1 N N N -20.257 27.468 18.713 3.879 2.023 1.383 O2 51N 13 51N O5 O14 O 0 1 N N N -19.563 30.449 14.620 -1.126 0.680 -0.050 O5 51N 14 51N O15 O15 O 0 1 N N N -19.412 33.987 15.212 -5.649 0.018 1.466 O15 51N 15 51N O16 O16 O 0 1 N N N -20.595 32.492 13.571 -3.407 -0.596 0.236 O16 51N 16 51N P17 P17 P 0 1 N N N -19.701 33.775 13.753 -4.953 -1.001 0.431 P17 51N 17 51N O18 O18 O 0 1 N N N -20.503 34.992 13.170 -5.046 -2.500 1.010 O18 51N 18 51N O19 O19 O 0 1 N N N -18.366 33.658 13.106 -5.649 -0.932 -0.873 O19 51N 19 51N P20 P20 P 0 1 N N N -20.132 31.016 13.249 -2.651 0.584 -0.557 P20 51N 20 51N O21 O21 O 0 1 N N N -19.105 30.966 12.198 -3.339 1.869 -0.301 O21 51N 21 51N O22 O22 O 0 1 N N N -21.325 30.275 12.778 -2.674 0.268 -2.136 O22 51N 22 51N H1 H1 H 0 1 N N N -19.076 30.324 18.881 3.510 0.380 -1.457 H1 51N 23 51N H4 H2 H 0 1 N N N -18.821 27.590 16.152 1.018 1.428 1.265 H4 51N 24 51N H3 H3 H 0 1 N N N -20.979 29.603 16.249 1.953 2.975 -1.214 H3 51N 25 51N H2 H4 H 0 1 N N N -21.021 29.418 18.634 4.228 2.436 -0.629 H2 51N 26 51N H51 H5 H 0 1 N N N -19.814 28.505 13.993 -0.621 2.676 -0.220 H51 51N 27 51N H52 H6 H 0 1 N N N -18.118 29.025 14.277 -0.106 1.637 -1.571 H52 51N 28 51N H7 H7 H 0 1 N N N -15.493 28.128 20.698 5.583 -3.402 0.896 H7 51N 29 51N H8 H8 H 0 1 N N N -17.886 30.745 21.279 2.523 -2.905 0.300 H8 51N 30 51N HO3 H9 H 0 1 N Y N -22.092 27.605 16.618 2.510 4.511 0.529 HO3 51N 31 51N HO2 H10 H 0 1 N Y N -20.121 27.476 19.653 4.736 1.610 1.555 HO2 51N 32 51N H11 H11 H 0 1 N N N -18.472 33.993 15.352 -5.243 0.025 2.343 H11 51N 33 51N H12 H12 H 0 1 N N N -19.980 35.428 12.508 -5.950 -2.812 1.152 H12 51N 34 51N H13 H13 H 0 1 N N N -21.163 29.934 11.906 -2.240 -0.562 -2.377 H13 51N 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 51N O21 P20 DOUB N N 1 51N O22 P20 SING N N 2 51N O19 P17 DOUB N N 3 51N O18 P17 SING N N 4 51N P20 O16 SING N N 5 51N P20 O5 SING N N 6 51N O16 P17 SING N N 7 51N P17 O15 SING N N 8 51N O5 C5 SING N N 9 51N C5 C4 SING N N 10 51N C4 C3 SING N N 11 51N C4 O4 SING N N 12 51N O3 C3 SING N N 13 51N C3 C2 SING N N 14 51N O4 C1 SING N N 15 51N C2 C1 SING N N 16 51N C2 O2 SING N N 17 51N C1 O1 SING N N 18 51N O1 P09 SING N N 19 51N O11 P09 DOUB N N 20 51N P09 O08 SING N N 21 51N P09 O10 SING N N 22 51N C1 H1 SING N N 23 51N C4 H4 SING N N 24 51N C3 H3 SING N N 25 51N C2 H2 SING N N 26 51N C5 H51 SING N N 27 51N C5 H52 SING N N 28 51N O08 H7 SING N N 29 51N O10 H8 SING N N 30 51N O3 HO3 SING N N 31 51N O2 HO2 SING N N 32 51N O15 H11 SING N N 33 51N O18 H12 SING N N 34 51N O22 H13 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 51N SMILES ACDLabs 12.01 "C1(OP(O)(O)=O)OC(C(C1O)O)COP(OP(O)(O)=O)(=O)O" 51N InChI InChI 1.03 "InChI=1S/C5H13O14P3/c6-3-2(1-16-22(14,15)19-21(11,12)13)17-5(4(3)7)18-20(8,9)10/h2-7H,1H2,(H,14,15)(H2,8,9,10)(H2,11,12,13)/t2-,3-,4-,5-/m1/s1" 51N InChIKey InChI 1.03 FPVTZUUYHCKWRL-TXICZTDVSA-N 51N SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)O[P](O)(O)=O" 51N SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)O[P](O)(O)=O" 51N SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "C([C@@H]1[C@H]([C@H]([C@H](O1)OP(=O)(O)O)O)O)OP(=O)(O)OP(=O)(O)O" 51N SMILES "OpenEye OEToolkits" 1.9.2 "C(C1C(C(C(O1)OP(=O)(O)O)O)O)OP(=O)(O)OP(=O)(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 51N "SYSTEMATIC NAME" ACDLabs 12.01 "5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-1-O-phosphono-alpha-D-ribofuranose" 51N "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(2R,3S,4R,5R)-3,4-bis(oxidanyl)-5-phosphonooxy-oxolan-2-yl]methyl phosphono hydrogen phosphate" # _pdbx_chem_comp_related.comp_id 51N _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 51N C1 RIB C1 "Carbohydrate core" 2 51N C4 RIB C4 "Carbohydrate core" 3 51N C3 RIB C3 "Carbohydrate core" 4 51N C2 RIB C2 "Carbohydrate core" 5 51N C5 RIB C5 "Carbohydrate core" 6 51N O4 RIB O4 "Carbohydrate core" 7 51N O1 RIB O1 "Carbohydrate core" 8 51N O3 RIB O3 "Carbohydrate core" 9 51N O2 RIB O2 "Carbohydrate core" 10 51N O5 RIB O5 "Carbohydrate core" 11 51N H1 RIB H1 "Carbohydrate core" 12 51N HO2 RIB HO2 "Carbohydrate core" 13 51N H4 RIB H4 "Carbohydrate core" 14 51N H3 RIB H3 "Carbohydrate core" 15 51N H2 RIB H2 "Carbohydrate core" 16 51N H51 RIB H51 "Carbohydrate core" 17 51N H52 RIB H52 "Carbohydrate core" 18 51N HO3 RIB HO3 "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 51N "CARBOHYDRATE ISOMER" D PDB ? 51N "CARBOHYDRATE RING" furanose PDB ? 51N "CARBOHYDRATE ANOMER" alpha PDB ? 51N "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 51N "Create component" 2015-06-15 RCSB 51N "Initial release" 2016-07-20 RCSB 51N "Other modification" 2020-07-03 RCSB 51N "Modify parent residue" 2020-07-17 RCSB 51N "Modify synonyms" 2020-07-17 RCSB 51N "Modify internal type" 2020-07-17 RCSB 51N "Modify linking type" 2020-07-17 RCSB 51N "Modify atom id" 2020-07-17 RCSB 51N "Modify component atom id" 2020-07-17 RCSB 51N "Modify leaving atom flag" 2020-07-17 RCSB ##