data_N # _chem_comp.id N _chem_comp.name ;ANY 5'-MONOPHOSPHATE NUCLEOTIDE ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C5 H11 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "1-DEOXY-RIBOFURANOSE-5'-PHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-13 _chem_comp.pdbx_modified_date 2024-09-27 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ROB _chem_comp.formula_weight 214.110 _chem_comp.one_letter_code N _chem_comp.three_letter_code N _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 1G9T _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 N OP3 O3P O 0 1 N Y N N N N 10.761 86.955 65.197 3.772 -0.872 -0.895 OP3 N 1 N P P P 0 1 N N N N N N 10.142 87.086 66.531 2.816 -0.013 0.074 P N 2 N OP1 O1P O 0 1 N N N N N N 10.847 88.090 67.347 2.933 -0.520 1.459 OP1 N 3 N OP2 O2P O 0 1 N N N N N N 8.692 87.283 66.512 3.257 1.535 0.030 OP2 N 4 N "O5'" O5* O 0 1 N N N N N N 10.538 85.720 67.176 1.289 -0.150 -0.420 "O5'" N 5 N "C5'" C5* C 0 1 N N N N N N 9.666 84.781 67.791 0.187 0.412 0.294 "C5'" N 6 N "C4'" C4* C 0 1 N N R N N N 10.002 83.443 67.242 -1.114 0.098 -0.447 "C4'" N 7 N "O4'" O4* O 0 1 N N N N N N 11.364 83.072 67.508 -1.366 -1.316 -0.414 "O4'" N 8 N "C3'" C3* C 0 1 N N S N N N 9.128 82.397 67.841 -2.298 0.790 0.257 "C3'" N 9 N "O3'" O3* O 0 1 N N N N N N 8.611 81.562 66.790 -2.947 1.700 -0.634 "O3'" N 10 N "C2'" C2* C 0 1 N N S N N N 10.023 81.630 68.762 -3.249 -0.372 0.632 "C2'" N 11 N "O2'" O2* O 0 1 N N N N N N 9.798 80.229 68.647 -4.612 -0.012 0.400 "O2'" N 12 N "C1'" C1* C 0 1 N N N N N N 11.479 81.977 68.419 -2.798 -1.488 -0.344 "C1'" N 13 N HOP3 3HOP H 0 0 N N N N N N 10.082 86.927 64.534 4.709 -0.836 -0.656 HOP3 N 14 N HOP2 2HOP H 0 0 N N N N N N 8.366 87.326 67.403 3.205 1.934 -0.850 HOP2 N 15 N "H5'" 1H5* H 0 1 N N N N N N 9.806 84.790 68.882 0.147 -0.016 1.296 "H5'" N 16 N "H5''" 2H5* H 0 0 N N N N N N 8.615 85.033 67.585 0.313 1.493 0.366 "H5''" N 17 N "H4'" H4* H 0 1 N N N N N N 9.849 83.511 66.155 -1.044 0.439 -1.480 "H4'" N 18 N "H3'" H3* H 0 1 N N N N N N 8.263 82.806 68.383 -1.958 1.312 1.152 "H3'" N 19 N "HO3'" H3T H 0 0 N Y N N N N 8.497 82.079 66.001 -3.700 2.163 -0.243 "HO3'" N 20 N "H2'" H2* H 0 1 N N N N N N 9.806 81.908 69.804 -3.100 -0.678 1.668 "H2'" N 21 N "HO2'" 2HO* H 0 0 N N N N N N 9.748 79.990 67.729 -5.246 -0.708 0.620 "HO2'" N 22 N "H1'" H1* H 0 1 N N N N N N 11.997 81.123 67.957 -3.250 -1.346 -1.326 "H1'" N 23 N "H1'2" 2H1* H 0 0 N N N N N N 12.074 82.229 69.309 -3.047 -2.472 0.055 "H1'2" N 24 # 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 N OP3 P SING N N 1 N OP3 HOP3 SING N N 2 N P OP1 DOUB N N 3 N P OP2 SING N N 4 N P "O5'" SING N N 5 N OP2 HOP2 SING N N 6 N "O5'" "C5'" SING N N 7 N "C5'" "C4'" SING N N 8 N "C5'" "H5'" SING N N 9 N "C5'" "H5''" SING N N 10 N "C4'" "O4'" SING N N 11 N "C4'" "C3'" SING N N 12 N "C4'" "H4'" SING N N 13 N "O4'" "C1'" SING N N 14 N "C3'" "O3'" SING N N 15 N "C3'" "C2'" SING N N 16 N "C3'" "H3'" SING N N 17 N "O3'" "HO3'" SING N N 18 N "C2'" "O2'" SING N N 19 N "C2'" "C1'" SING N N 20 N "C2'" "H2'" SING N N 21 N "O2'" "HO2'" SING N N 22 N "C1'" "H1'" SING N N 23 N "C1'" "H1'2" SING N N 24 # 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 N SMILES ACDLabs 10.04 "O=P(OCC1OCC(O)C1O)(O)O" N InChI InChI 1.03 "InChI=1S/C5H11O7P/c6-3-1-11-4(5(3)7)2-12-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5-/m0/s1" N InChIKey InChI 1.03 CYZZKTRFOOKUMT-LMVFSUKVSA-N N SMILES_CANONICAL CACTVS 3.385 "O[C@H]1CO[C@H](CO[P](O)(O)=O)[C@H]1O" N SMILES CACTVS 3.385 "O[CH]1CO[CH](CO[P](O)(O)=O)[CH]1O" N SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 "C1[C@@H]([C@@H]([C@H](O1)COP(=O)(O)O)O)O" N SMILES "OpenEye OEToolkits" 1.7.5 "C1C(C(C(O1)COP(=O)(O)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 N "SYSTEMATIC NAME" ACDLabs 10.04 1,4-anhydro-5-O-phosphono-D-ribitol N "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4S)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site N "Create component" 1999-07-13 RCSB N "Modify descriptor" 2011-06-04 RCSB N "Modify descriptor" 2012-01-05 RCSB N "Modify coordinates" 2012-01-05 RCSB N "Modify synonyms" 2020-06-05 PDBE N "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id N _pdbx_chem_comp_synonyms.name "1-DEOXY-RIBOFURANOSE-5'-PHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id N _pdbx_chem_comp_pcm.modified_residue_id GLU _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Nucleotide monophosphate" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom "C3'" _pdbx_chem_comp_pcm.modified_residue_id_linking_atom OE2 _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #