data_JDT # _chem_comp.id JDT _chem_comp.name ;2'-deoxy-5-ethyluridine 5'-(dihydrogen phosphate) ; _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H17 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2011-04-01 _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 336.235 _chem_comp.one_letter_code ? _chem_comp.three_letter_code JDT _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 2RRQ _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 JDT P P P 0 1 N N N 1.201 12.496 3.195 4.443 1.134 0.031 P JDT 1 JDT N1 N1 N 0 1 N N N -2.152 7.341 2.918 -2.063 -0.461 0.289 N1 JDT 2 JDT C2 C2 C 0 1 N N N -3.227 6.752 2.287 -2.015 -0.183 -1.027 C2 JDT 3 JDT O2 O2 O 0 1 N N N -4.341 7.247 2.266 -1.016 -0.461 -1.662 O2 JDT 4 JDT N3 N3 N 0 1 N N N -2.950 5.556 1.679 -3.057 0.398 -1.650 N3 JDT 5 JDT C4 C4 C 0 1 N N N -1.736 4.904 1.638 -4.172 0.713 -0.959 C4 JDT 6 JDT O4 O4 O 0 1 N N N -1.635 3.838 1.035 -5.115 1.238 -1.522 O4 JDT 7 JDT C5 C5 C 0 1 N N N -0.654 5.577 2.324 -4.236 0.426 0.426 C5 JDT 8 JDT C6 C6 C 0 1 N N N -0.907 6.753 2.915 -3.176 -0.157 1.025 C6 JDT 9 JDT C7 C7 C 0 1 N N N 0.670 4.898 2.447 -5.470 0.768 1.220 C7 JDT 10 JDT "C1'" "C1'" C 0 1 N N R -2.369 8.626 3.611 -0.915 -1.099 0.938 "C1'" JDT 11 JDT "C2'" "C2'" C 0 1 N N N -2.574 8.494 5.121 -0.712 -2.516 0.368 "C2'" JDT 12 JDT "C3'" "C3'" C 0 1 N N S -1.288 9.042 5.713 0.728 -2.493 -0.201 "C3'" JDT 13 JDT "O3'" "O3'" O 0 1 N N N -1.525 9.690 6.965 1.412 -3.713 0.093 "O3'" JDT 14 JDT "C4'" "C4'" C 0 1 N N R -0.852 10.056 4.666 1.361 -1.305 0.566 "C4'" JDT 15 JDT "O4'" "O4'" O 0 1 N N N -1.214 9.439 3.412 0.281 -0.352 0.662 "O4'" JDT 16 JDT "C5'" "C5'" C 0 1 N N N 0.620 10.399 4.685 2.531 -0.716 -0.225 "C5'" JDT 17 JDT "O5'" "O5'" O 0 1 N N N 0.797 11.814 4.579 3.169 0.299 0.554 "O5'" JDT 18 JDT C72 C72 C 0 1 N N N 1.033 4.182 3.713 -5.394 2.225 1.679 C72 JDT 19 JDT OP1 OP1 O 0 1 N N N 2.683 12.559 3.120 5.517 0.197 -0.367 OP2 JDT 20 JDT OP2 OP2 O 0 1 N N N 0.407 13.744 3.058 4.976 2.092 1.210 OP1 JDT 21 JDT OP3 OP3 O 0 1 N Y N 0.666 11.471 2.078 4.014 2.030 -1.236 OP3 JDT 22 JDT HN3 HN3 H 0 1 N N N -3.712 5.106 1.214 -3.006 0.592 -2.599 HN3 JDT 23 JDT H6 H6 H 0 1 N N N -0.096 7.264 3.413 -3.206 -0.384 2.081 H6 JDT 24 JDT H71 H71 H 0 1 N N N 0.699 4.141 1.650 -6.353 0.628 0.597 H7 JDT 25 JDT H72 H72 H 0 1 N N N 1.429 5.683 2.313 -5.533 0.115 2.091 H7A JDT 26 JDT "H1'" "H1'" H 0 1 N N N -3.288 9.058 3.189 -1.081 -1.153 2.014 "H1'" JDT 27 JDT "H2'" "H2'" H 0 1 N N N -3.448 9.070 5.459 -0.798 -3.262 1.158 "H2'" JDT 28 JDT "H2''" "H2''" H 0 0 N N N -2.735 7.446 5.414 -1.433 -2.715 -0.425 "H2'A" JDT 29 JDT "H3'" "H3'" H 0 1 N N N -0.541 8.262 5.921 0.719 -2.304 -1.275 "H3'" JDT 30 JDT "HO3'" "HO3'" H 0 0 N Y N -0.705 10.022 7.311 0.999 -4.498 -0.292 "HO3'" JDT 31 JDT "H4'" "H4'" H 0 1 N N N -1.339 11.024 4.853 1.686 -1.618 1.558 "H4'" JDT 32 JDT "H5'" "H5'" H 0 1 N N N 1.062 10.048 5.629 3.249 -1.504 -0.453 "H5'" JDT 33 JDT "H5''" "H5''" H 0 0 N N N 1.118 9.907 3.837 2.160 -0.282 -1.153 "H5'A" JDT 34 JDT H72A H72A H 0 0 N N N 1.021 4.893 4.552 -6.286 2.472 2.253 H72A JDT 35 JDT H72B H72B H 0 0 N N N 0.305 3.379 3.902 -4.510 2.364 2.302 H72B JDT 36 JDT H72C H72C H 0 0 N N N 2.039 3.749 3.614 -5.330 2.877 0.808 H72 JDT 37 JDT HOP2 HOP2 H 0 0 N N N 0.993 14.480 2.930 5.744 2.626 0.965 HOP1 JDT 38 JDT HOP3 HOP3 H 0 0 N N N 1.403 11.113 1.597 3.312 2.668 -1.047 HOP3 JDT 39 # 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 JDT P "O5'" SING N N 1 JDT P OP1 DOUB N N 2 JDT P OP2 SING N N 3 JDT P OP3 SING N N 4 JDT N1 C2 SING N N 5 JDT N1 C6 SING N N 6 JDT N1 "C1'" SING N N 7 JDT C2 O2 DOUB N N 8 JDT C2 N3 SING N N 9 JDT N3 C4 SING N N 10 JDT C4 O4 DOUB N N 11 JDT C4 C5 SING N N 12 JDT C5 C6 DOUB N N 13 JDT C5 C7 SING N N 14 JDT C7 C72 SING N N 15 JDT "C1'" "C2'" SING N N 16 JDT "C1'" "O4'" SING N N 17 JDT "C2'" "C3'" SING N N 18 JDT "C3'" "O3'" SING N N 19 JDT "C3'" "C4'" SING N N 20 JDT "C4'" "O4'" SING N N 21 JDT "C4'" "C5'" SING N N 22 JDT "C5'" "O5'" SING N N 23 JDT N3 HN3 SING N N 24 JDT C6 H6 SING N N 25 JDT C7 H71 SING N N 26 JDT C7 H72 SING N N 27 JDT "C1'" "H1'" SING N N 28 JDT "C2'" "H2'" SING N N 29 JDT "C2'" "H2''" SING N N 30 JDT "C3'" "H3'" SING N N 31 JDT "O3'" "HO3'" SING N N 32 JDT "C4'" "H4'" SING N N 33 JDT "C5'" "H5'" SING N N 34 JDT "C5'" "H5''" SING N N 35 JDT C72 H72A SING N N 36 JDT C72 H72B SING N N 37 JDT C72 H72C SING N N 38 JDT OP2 HOP2 SING N N 39 JDT OP3 HOP3 SING N N 40 # 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 JDT SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)CC)CC2O" JDT SMILES_CANONICAL CACTVS 3.370 "CCC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" JDT SMILES CACTVS 3.370 "CCC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" JDT SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CCC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" JDT SMILES "OpenEye OEToolkits" 1.7.0 "CCC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O" JDT InChI InChI 1.03 "InChI=1S/C11H17N2O8P/c1-2-6-4-13(11(16)12-10(6)15)9-3-7(14)8(21-9)5-20-22(17,18)19/h4,7-9,14H,2-3,5H2,1H3,(H,12,15,16)(H2,17,18,19)/t7-,8+,9+/m0/s1" JDT InChIKey InChI 1.03 PKJQLAZOOFOCPH-DJLDLDEBSA-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 JDT "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-deoxy-5-ethyluridine 5'-(dihydrogen phosphate) ; JDT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3S,5R)-5-(5-ethyl-2,4-dioxo-pyrimidin-1-yl)-3-hydroxy-oxolan-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 JDT "Create component" 2011-04-01 PDBJ JDT "Modify descriptor" 2011-06-04 RCSB #