data_3DR # _chem_comp.id 3DR _chem_comp.name "1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C5 H11 O6 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "ABASIC DIDEOXYRIBOSE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2021-03-01 _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 198.111 _chem_comp.one_letter_code N _chem_comp.three_letter_code 3DR _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 1QUM _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 3DR "O5'" O5* O 0 1 N N N 112.167 6.416 10.589 -0.442 0.550 -0.918 "O5'" 3DR 1 3DR P P P 0 1 N N N 112.629 4.952 10.119 -0.015 -0.051 -2.349 P 3DR 2 3DR OP1 O1P O 0 1 N N N 114.115 4.865 10.298 -0.290 -1.505 -2.375 OP1 3DR 3 3DR OP2 O2P O 0 1 N N N 111.840 3.992 10.990 -0.861 0.675 -3.510 OP2 3DR 4 3DR OP3 O3P O 0 1 N Y N 112.197 4.879 8.655 1.556 0.202 -2.590 OP3 3DR 5 3DR "C2'" C2* C 0 1 N N N 111.338 8.596 14.187 -0.260 -0.503 3.709 "C2'" 3DR 6 3DR "C5'" C5* C 0 1 N N N 112.570 6.867 11.902 0.338 -0.131 0.065 "C5'" 3DR 7 3DR "C4'" C4* C 0 1 N N R 112.284 8.336 12.033 -0.020 0.396 1.456 "C4'" 3DR 8 3DR "O4'" O4* O 0 1 N N N 110.865 8.573 11.860 -1.415 0.144 1.745 "O4'" 3DR 9 3DR "C1'" C1* C 0 1 N N N 110.237 8.649 13.126 -1.525 0.209 3.184 "C1'" 3DR 10 3DR "C3'" C3* C 0 1 N N S 112.551 8.990 13.382 0.751 -0.377 2.548 "C3'" 3DR 11 3DR "O3'" O3* O 0 1 N N N 112.665 10.395 13.264 1.902 0.360 2.965 "O3'" 3DR 12 3DR HOP2 2HOP H 0 0 N N N 112.113 3.125 10.711 -0.575 0.287 -4.349 HOP2 3DR 13 3DR HOP3 3HOP H 0 0 N N N 112.470 4.012 8.376 1.691 1.159 -2.566 HOP3 3DR 14 3DR "H2'" 1H2* H 0 1 N N N 111.151 9.211 15.097 -0.471 -1.552 3.918 "H2'" 3DR 15 3DR "H2''" 2H2* H 0 0 N N N 111.424 7.628 14.734 0.117 -0.004 4.601 "H2''" 3DR 16 3DR "H5'" 1H5* H 0 1 N N N 112.097 6.270 12.716 1.397 0.042 -0.126 "H5'" 3DR 17 3DR "H5''" 2H5* H 0 0 N N N 113.635 6.622 12.124 0.130 -1.200 0.017 "H5''" 3DR 18 3DR "H4'1" 1H4* H 0 0 N N N 112.973 8.768 11.270 0.194 1.462 1.524 "H4'1" 3DR 19 3DR "H1'1" 1H1* H 0 0 N N N 109.454 7.868 13.271 -2.422 -0.312 3.519 "H1'1" 3DR 20 3DR "H1'2" 2H1* H 0 0 N N N 109.574 9.539 13.230 -1.542 1.246 3.517 "H1'2" 3DR 21 3DR "H3'" H3* H 0 1 N N N 113.511 8.666 13.847 1.041 -1.363 2.185 "H3'" 3DR 22 3DR "HO3'" HO3* H 0 0 N Y N 113.429 10.643 12.756 2.325 -0.154 3.665 "HO3'" 3DR 23 # # 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 3DR "O5'" P SING N N 1 3DR "O5'" "C5'" SING N N 2 3DR P OP1 DOUB N N 3 3DR P OP2 SING N N 4 3DR P OP3 SING N N 5 3DR OP2 HOP2 SING N N 6 3DR OP3 HOP3 SING N N 7 3DR "C2'" "C1'" SING N N 8 3DR "C2'" "C3'" SING N N 9 3DR "C2'" "H2'" SING N N 10 3DR "C2'" "H2''" SING N N 11 3DR "C5'" "C4'" SING N N 12 3DR "C5'" "H5'" SING N N 13 3DR "C5'" "H5''" SING N N 14 3DR "C4'" "O4'" SING N N 15 3DR "C4'" "C3'" SING N N 16 3DR "C4'" "H4'1" SING N N 17 3DR "O4'" "C1'" SING N N 18 3DR "C1'" "H1'1" SING N N 19 3DR "C1'" "H1'2" SING N N 20 3DR "C3'" "O3'" SING N N 21 3DR "C3'" "H3'" SING N N 22 3DR "O3'" "HO3'" SING N N 23 # # 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 3DR SMILES ACDLabs 10.04 "O=P(OCC1OCCC1O)(O)O" 3DR SMILES_CANONICAL CACTVS 3.341 "O[C@H]1CCO[C@@H]1CO[P](O)(O)=O" 3DR SMILES CACTVS 3.341 "O[CH]1CCO[CH]1CO[P](O)(O)=O" 3DR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1CO[C@@H]([C@H]1O)COP(=O)(O)O" 3DR SMILES "OpenEye OEToolkits" 1.5.0 "C1COC(C1O)COP(=O)(O)O" 3DR InChI InChI 1.03 "InChI=1S/C5H11O6P/c6-4-1-2-10-5(4)3-11-12(7,8)9/h4-6H,1-3H2,(H2,7,8,9)/t4-,5+/m0/s1" 3DR InChIKey InChI 1.03 BVOBPNSQIRMLCA-CRCLSJGQSA-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 3DR "SYSTEMATIC NAME" ACDLabs 10.04 "1,4-anhydro-2-deoxy-5-O-phosphono-D-erythro-pentitol" 3DR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S)-3-hydroxyoxolan-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 3DR "Create component" 1999-07-08 RCSB 3DR "Modify descriptor" 2011-06-04 RCSB 3DR "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 3DR _pdbx_chem_comp_synonyms.name "ABASIC DIDEOXYRIBOSE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##