data_P2U # _chem_comp.id P2U _chem_comp.name "2'-DEOXY-PSEUDOURIDINE-5'MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H13 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2000-03-23 _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 308.182 _chem_comp.one_letter_code U _chem_comp.three_letter_code P2U _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 1EMH _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 P2U N1 N1 N 0 1 N N N 20.024 3.141 7.922 -0.531 1.102 4.630 N1 P2U 1 P2U C2 C2 C 0 1 N N N 19.663 2.852 6.608 -1.245 -0.035 4.706 C2 P2U 2 P2U N3 N3 N 0 1 N N N 18.303 2.620 6.394 -1.203 -0.946 3.716 N3 P2U 3 P2U C4 C4 C 0 1 N N N 17.319 2.642 7.353 -0.443 -0.728 2.624 C4 P2U 4 P2U C5 C5 C 0 1 N N N 17.768 2.944 8.637 0.317 0.462 2.534 C5 P2U 5 P2U C6 C6 C 0 1 N N N 19.097 3.191 8.875 0.256 1.359 3.542 C6 P2U 6 P2U O2 O2 O 0 1 N N N 20.437 2.790 5.658 -1.939 -0.243 5.683 O2 P2U 7 P2U O4 O4 O 0 1 N N N 16.149 2.436 7.079 -0.404 -1.551 1.728 O4 P2U 8 P2U "C1'" C1* C 0 1 N N R 16.948 3.993 9.433 1.180 0.727 1.327 "C1'" P2U 9 P2U "C2'" C2* C 0 1 N N N 15.578 3.417 9.876 2.247 -0.378 1.175 "C2'" P2U 10 P2U "C3'" C3* C 0 1 N N S 15.511 3.494 11.397 2.360 -0.584 -0.351 "C3'" P2U 11 P2U "C4'" C4* C 0 1 N N R 16.899 3.927 11.820 1.347 0.419 -0.944 "C4'" P2U 12 P2U "O3'" O3* O 0 1 N N N 14.450 4.353 11.819 3.683 -0.284 -0.800 "O3'" P2U 13 P2U "O4'" O4* O 0 1 N N N 17.652 4.286 10.635 0.393 0.650 0.118 "O4'" P2U 14 P2U "C5'" C5* C 0 1 N N N 17.438 2.788 12.593 0.647 -0.177 -2.167 "C5'" P2U 15 P2U "O5'" O5* O 0 1 N N N 18.411 3.275 13.263 -0.333 0.741 -2.650 "O5'" P2U 16 P2U P P P 0 1 N N N 19.339 2.338 14.133 -1.026 0.052 -3.930 P P2U 17 P2U OP1 O1P O 0 1 N N N 20.521 3.168 14.467 -1.657 -1.223 -3.522 OP1 P2U 18 P2U OP2 O2P O 0 1 N N N 19.520 1.032 13.467 -2.149 1.038 -4.529 OP2 P2U 19 P2U OP3 O3P O 0 1 N Y N 18.481 2.081 15.459 0.089 -0.236 -5.054 OP3 P2U 20 P2U HN1 HN1 H 0 1 N N N 20.538 4.021 7.927 -0.575 1.746 5.354 HN1 P2U 21 P2U HN3 HN3 H 0 1 N N N 17.998 2.414 5.442 -1.724 -1.761 3.787 HN3 P2U 22 P2U H6 H6 H 0 1 N N N 19.440 3.444 9.892 0.827 2.274 3.489 H6 P2U 23 P2U "H1'" H1* H 0 1 N N N 16.800 4.884 8.779 1.655 1.705 1.409 "H1'" P2U 24 P2U "H2'" 1H2* H 0 1 N N N 14.715 3.919 9.378 1.917 -1.297 1.661 "H2'" P2U 25 P2U "H2''" 2H2* H 0 0 N N N 15.394 2.388 9.486 3.201 -0.048 1.588 "H2''" P2U 26 P2U "H3'" H3* H 0 1 N N N 15.258 2.524 11.887 2.088 -1.604 -0.620 "H3'" P2U 27 P2U "H4'" H4* H 0 1 N N N 16.935 4.835 12.465 1.849 1.349 -1.212 "H4'" P2U 28 P2U "HO3'" H3T H 0 0 N Y N 14.408 4.401 12.766 4.273 -0.922 -0.376 "HO3'" P2U 29 P2U "H5'" 1H5* H 0 1 N N N 16.676 2.264 13.217 1.382 -0.369 -2.948 "H5'" P2U 30 P2U "H5''" 2H5* H 0 0 N N N 17.716 1.908 11.967 0.162 -1.112 -1.887 "H5''" P2U 31 P2U HOP2 2HOP H 0 0 N N N 20.078 0.468 13.990 -2.538 0.588 -5.291 HOP2 P2U 32 P2U HOP3 3HOP H 0 0 N N N 19.039 1.517 15.982 0.474 0.618 -5.291 HOP3 P2U 33 # 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 P2U N1 C2 SING N N 1 P2U N1 C6 SING N N 2 P2U N1 HN1 SING N N 3 P2U C2 N3 SING N N 4 P2U C2 O2 DOUB N N 5 P2U N3 C4 SING N N 6 P2U N3 HN3 SING N N 7 P2U C4 C5 SING N N 8 P2U C4 O4 DOUB N N 9 P2U C5 C6 DOUB N N 10 P2U C5 "C1'" SING N N 11 P2U C6 H6 SING N N 12 P2U "C1'" "C2'" SING N N 13 P2U "C1'" "O4'" SING N N 14 P2U "C1'" "H1'" SING N N 15 P2U "C2'" "C3'" SING N N 16 P2U "C2'" "H2'" SING N N 17 P2U "C2'" "H2''" SING N N 18 P2U "C3'" "C4'" SING N N 19 P2U "C3'" "O3'" SING N N 20 P2U "C3'" "H3'" SING N N 21 P2U "C4'" "O4'" SING N N 22 P2U "C4'" "C5'" SING N N 23 P2U "C4'" "H4'" SING N N 24 P2U "O3'" "HO3'" SING N N 25 P2U "C5'" "O5'" SING N N 26 P2U "C5'" "H5'" SING N N 27 P2U "C5'" "H5''" SING N N 28 P2U "O5'" P SING N N 29 P2U P OP1 DOUB N N 30 P2U P OP2 SING N N 31 P2U P OP3 SING N N 32 P2U OP2 HOP2 SING N N 33 P2U OP3 HOP3 SING N N 34 # 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 P2U SMILES ACDLabs 10.04 "O=P(OCC2OC(C1=CNC(=O)NC1=O)CC2O)(O)O" P2U SMILES_CANONICAL CACTVS 3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)C2=CNC(=O)NC2=O" P2U SMILES CACTVS 3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)C2=CNC(=O)NC2=O" P2U SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1C2=CNC(=O)NC2=O)COP(=O)(O)O)O" P2U SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1C2=CNC(=O)NC2=O)COP(=O)(O)O)O" P2U InChI InChI 1.03 "InChI=1S/C9H13N2O8P/c12-5-1-6(4-2-10-9(14)11-8(4)13)19-7(5)3-18-20(15,16)17/h2,5-7,12H,1,3H2,(H2,15,16,17)(H2,10,11,13,14)/t5-,6+,7+/m0/s1" P2U InChIKey InChI 1.03 QJNQHNJPOXCQQR-RRKCRQDMSA-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 P2U "SYSTEMATIC NAME" ACDLabs 10.04 "(1R)-1,4-anhydro-2-deoxy-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-erythro-pentitol" P2U "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(2,4-dioxo-1H-pyrimidin-5-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 P2U "Create component" 2000-03-23 RCSB P2U "Modify descriptor" 2011-06-04 RCSB #