data_DXD # _chem_comp.id DXD _chem_comp.name "(1S,3S,4R)-4-(PHOSPHOOXYMETHYL)-CYCLOPENTANE-1,3-DIOL" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C6 H13 O6 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-09-12 _chem_comp.pdbx_modified_date 2011-06-04 _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 212.138 _chem_comp.one_letter_code N _chem_comp.three_letter_code DXD _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1XCY _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 DXD P P P 0 1 N N N -1.296 6.916 17.265 1.755 3.925 -1.042 P DXD 1 DXD OP1 O1P O 0 1 N N N -1.669 8.268 17.741 2.705 4.578 -0.082 OP1 DXD 2 DXD OP2 O2P O 0 1 N N N -0.595 5.976 18.169 0.189 4.242 -0.789 OP2 DXD 3 DXD "O5'" O5* O 0 1 N N N -2.609 6.188 16.685 1.819 2.308 -1.075 "O5'" DXD 4 DXD "C5'" C5* C 0 1 N N N -3.244 6.674 15.491 0.952 1.614 -1.956 "C5'" DXD 5 DXD "C4'" C4* C 0 1 N N R -4.484 5.795 15.039 1.197 0.121 -1.806 "C4'" DXD 6 DXD "C1'" C1* C 0 1 N N S -4.838 3.600 16.242 0.860 -1.899 -0.577 "C1'" DXD 7 DXD "C6'" C6* C 0 1 N N N -4.290 4.221 14.957 0.950 -0.388 -0.388 "C6'" DXD 8 DXD "O6'" O6* O 0 1 N N N -6.167 3.214 15.912 2.168 -2.463 -0.581 "O6'" DXD 9 DXD "C2'" C2* C 0 1 N N N -4.933 4.747 17.251 0.233 -2.107 -1.959 "C2'" DXD 10 DXD "C3'" C3* C 0 1 N N S -5.519 5.879 16.361 0.236 -0.731 -2.635 "C3'" DXD 11 DXD "O3'" O3* O 0 1 N N N -6.859 5.615 15.905 0.675 -0.815 -3.979 "O3'" DXD 12 DXD OP3 O3P O 0 1 N Y N ? ? ? 1.969 4.326 -2.594 OP3 DXD 13 DXD HOP2 2HOP H 0 0 N N N -0.356 5.109 17.864 -0.092 5.173 -0.662 HOP2 DXD 14 DXD "H5'1" 1H5* H 0 0 N N N -2.446 6.875 14.776 -0.082 1.854 -1.702 "H5'1" DXD 15 DXD "H5'2" 2H5* H 0 0 N N N -3.648 7.667 15.688 1.158 1.929 -2.981 "H5'2" DXD 16 DXD "H4'" H4* H 0 1 N N N -4.645 6.100 14.005 2.233 -0.081 -2.107 "H4'" DXD 17 DXD "H1'" H1* H 0 1 N N N -4.390 2.651 16.536 0.289 -2.385 0.220 "H1'" DXD 18 DXD "H6'1" 1H6* H 0 0 N N N -4.964 3.729 14.256 1.758 -0.094 0.288 "H6'1" DXD 19 DXD "H6'2" 2H6* H 0 0 N N N -3.327 3.826 14.633 0.001 0.003 -0.002 "H6'2" DXD 20 DXD "H7'" H7* H 0 1 N N N -6.621 4.014 15.637 2.101 -3.316 -1.038 "H7'" DXD 21 DXD "H2'1" 1H2* H 0 0 N N N -5.547 4.553 18.130 0.765 -2.860 -2.551 "H2'1" DXD 22 DXD "H2'2" 2H2* H 0 0 N N N -3.920 4.950 17.599 -0.805 -2.444 -1.851 "H2'2" DXD 23 DXD "H3'" H3* H 0 1 N N N -5.689 6.685 17.076 -0.775 -0.307 -2.630 "H3'" DXD 24 DXD "HO3'" H3T H 0 0 N Y N -7.444 5.663 16.652 1.311 -1.550 -4.025 "HO3'" DXD 25 DXD HOP3 3HOP H 0 0 N N N 0.239 -0.867 -0.305 2.063 5.273 -2.831 HOP3 DXD 26 # 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 DXD P OP1 DOUB N N 1 DXD P OP2 SING N N 2 DXD P "O5'" SING N N 3 DXD P OP3 SING N N 4 DXD OP2 HOP2 SING N N 5 DXD "O5'" "C5'" SING N N 6 DXD "C5'" "C4'" SING N N 7 DXD "C5'" "H5'1" SING N N 8 DXD "C5'" "H5'2" SING N N 9 DXD "C4'" "C6'" SING N N 10 DXD "C4'" "C3'" SING N N 11 DXD "C4'" "H4'" SING N N 12 DXD "C1'" "C6'" SING N N 13 DXD "C1'" "O6'" SING N N 14 DXD "C1'" "C2'" SING N N 15 DXD "C1'" "H1'" SING N N 16 DXD "C6'" "H6'1" SING N N 17 DXD "C6'" "H6'2" SING N N 18 DXD "O6'" "H7'" SING N N 19 DXD "C2'" "C3'" SING N N 20 DXD "C2'" "H2'1" SING N N 21 DXD "C2'" "H2'2" SING N N 22 DXD "C3'" "O3'" SING N N 23 DXD "C3'" "H3'" SING N N 24 DXD "O3'" "HO3'" SING N N 25 DXD OP3 HOP3 SING N N 26 # 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 DXD SMILES ACDLabs 10.04 "O=P(OCC1CC(O)CC1O)(O)O" DXD SMILES_CANONICAL CACTVS 3.341 "O[C@@H]1C[C@H](O)[C@@H](CO[P](O)(O)=O)C1" DXD SMILES CACTVS 3.341 "O[CH]1C[CH](O)[CH](CO[P](O)(O)=O)C1" DXD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H](C[C@@H]([C@H]1COP(=O)(O)O)O)O" DXD SMILES "OpenEye OEToolkits" 1.5.0 "C1C(CC(C1COP(=O)(O)O)O)O" DXD InChI InChI 1.03 "InChI=1S/C6H13O6P/c7-5-1-4(6(8)2-5)3-12-13(9,10)11/h4-8H,1-3H2,(H2,9,10,11)/t4-,5+,6+/m1/s1" DXD InChIKey InChI 1.03 BSAJVOLDMHTVPM-SRQIZXRXSA-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 DXD "SYSTEMATIC NAME" ACDLabs 10.04 "[(1R,2S,4S)-2,4-dihydroxycyclopentyl]methyl dihydrogen phosphate" DXD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(1R,2S,4S)-2,4-dihydroxycyclopentyl]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 DXD "Create component" 2004-09-12 RCSB DXD "Modify descriptor" 2011-06-04 RCSB #