data_5HU # _chem_comp.id 5HU _chem_comp.name "5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2002-09-26 _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 338.208 _chem_comp.one_letter_code U _chem_comp.three_letter_code 5HU _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 1MRS _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 5HU P P P 0 1 N N N 26.429 15.281 8.373 -4.427 1.005 -0.232 P 5HU 1 5HU OP1 O1P O 0 1 N N N 27.421 14.840 9.555 -3.996 1.758 0.967 OP1 5HU 2 5HU OP2 O2P O 0 1 N N N 25.545 16.639 8.835 -5.062 2.024 -1.306 OP2 5HU 3 5HU OP3 O3P O 0 1 N Y N 27.272 15.644 6.985 -5.530 -0.089 0.188 OP3 5HU 4 5HU "O5'" O5* O 0 1 N N N 25.351 14.179 8.129 -3.156 0.262 -0.884 "O5'" 5HU 5 5HU "C5'" C5* C 0 1 N N N 25.344 13.054 7.345 -2.568 -0.533 0.147 "C5'" 5HU 6 5HU "C4'" C4* C 0 1 N N R 23.937 12.428 7.521 -1.348 -1.270 -0.409 "C4'" 5HU 7 5HU "O4'" O4* O 0 1 N N N 23.831 11.013 7.711 -0.264 -0.348 -0.662 "O4'" 5HU 8 5HU "C3'" C3* C 0 1 N N S 22.949 12.897 8.652 -0.764 -2.237 0.651 "C3'" 5HU 9 5HU "O3'" O3* O 0 1 N N N 21.484 13.119 8.436 -1.428 -3.502 0.610 "O3'" 5HU 10 5HU "C2'" C2* C 0 1 N N N 23.502 11.932 9.749 0.708 -2.371 0.193 "C2'" 5HU 11 5HU "C1'" C1* C 0 1 N N R 23.551 10.629 9.042 0.947 -1.123 -0.679 "C1'" 5HU 12 5HU N1 N1 N 0 1 N N N 24.582 9.632 9.383 2.051 -0.334 -0.128 N1 5HU 13 5HU C2 C2 C 0 1 N N N 24.098 8.369 9.646 1.923 0.237 1.083 C2 5HU 14 5HU O2 O2 O 0 1 N N N 22.830 8.136 9.576 0.890 0.090 1.708 O2 5HU 15 5HU N3 N3 N 0 1 N N N 24.918 7.363 9.978 2.922 0.966 1.614 N3 5HU 16 5HU C4 C4 C 0 1 N N N 26.248 7.575 10.059 4.075 1.134 0.936 C4 5HU 17 5HU O4 O4 O 0 1 N N N 27.021 6.550 10.393 4.979 1.794 1.415 O4 5HU 18 5HU C5 C5 C 0 1 N N N 26.801 8.851 9.795 4.222 0.543 -0.342 C5 5HU 19 5HU C5A C5A C 0 1 N N N 28.283 9.041 9.890 5.499 0.718 -1.123 C5A 5HU 20 5HU C6 C6 C 0 1 N N N 25.923 9.880 9.454 3.204 -0.184 -0.851 C6 5HU 21 5HU O5B O5B O 0 1 N N N 28.639 8.853 8.917 5.395 0.024 -2.368 O5B 5HU 22 5HU HO2P HO2P H 0 0 N N N 24.628 16.406 8.922 -5.818 2.446 -0.876 HO2P 5HU 23 5HU HO3P HO3P H 0 0 N N N 26.667 15.713 6.256 -5.783 -0.555 -0.620 HO3P 5HU 24 5HU "H5'" 1H5* H 0 1 N N N 26.138 12.352 7.639 -3.298 -1.258 0.507 "H5'" 5HU 25 5HU "H5''" 2H5* H 0 0 N N N 25.526 13.312 6.291 -2.260 0.110 0.971 "H5''" 5HU 26 5HU "HC4'" HC4* H 0 0 N N N 23.660 12.813 6.528 -1.610 -1.811 -1.319 "HC4'" 5HU 27 5HU "HC3'" HC3* H 0 0 N N N 22.944 13.974 8.878 -0.823 -1.802 1.649 "HC3'" 5HU 28 5HU "HO3'" HO3* H 0 0 N Y N 21.040 12.281 8.390 -0.960 -4.084 1.224 "HO3'" 5HU 29 5HU "H2'" 1H2* H 0 1 N N N 22.884 11.909 10.658 0.844 -3.279 -0.395 "H2'" 5HU 30 5HU "H2''" 2H2* H 0 0 N N N 24.496 12.243 10.103 1.378 -2.369 1.053 "H2''" 5HU 31 5HU "HC1'" HC1* H 0 0 N N N 22.612 10.115 9.296 1.180 -1.424 -1.701 "HC1'" 5HU 32 5HU HN3 HN3 H 0 1 N N N 24.544 6.455 10.166 2.813 1.371 2.489 HN3 5HU 33 5HU H5A1 1H5A H 0 0 N N N 28.740 8.372 10.635 6.333 0.314 -0.550 H5A1 5HU 34 5HU H5A2 2H5A H 0 0 N N N 28.531 10.063 10.212 5.667 1.779 -1.311 H5A2 5HU 35 5HU HC6 HC6 H 0 1 N N N 26.303 10.870 9.247 3.299 -0.645 -1.822 HC6 5HU 36 5HU HO5B HO5B H 0 0 N N N 27.905 8.796 8.316 6.231 0.162 -2.835 HO5B 5HU 37 # 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 5HU P OP1 DOUB N N 1 5HU P OP2 SING N N 2 5HU P OP3 SING N N 3 5HU P "O5'" SING N N 4 5HU OP2 HO2P SING N N 5 5HU OP3 HO3P SING N N 6 5HU "O5'" "C5'" SING N N 7 5HU "C5'" "C4'" SING N N 8 5HU "C5'" "H5'" SING N N 9 5HU "C5'" "H5''" SING N N 10 5HU "C4'" "O4'" SING N N 11 5HU "C4'" "C3'" SING N N 12 5HU "C4'" "HC4'" SING N N 13 5HU "O4'" "C1'" SING N N 14 5HU "C3'" "O3'" SING N N 15 5HU "C3'" "C2'" SING N N 16 5HU "C3'" "HC3'" SING N N 17 5HU "O3'" "HO3'" SING N N 18 5HU "C2'" "C1'" SING N N 19 5HU "C2'" "H2'" SING N N 20 5HU "C2'" "H2''" SING N N 21 5HU "C1'" N1 SING N N 22 5HU "C1'" "HC1'" SING N N 23 5HU N1 C2 SING N N 24 5HU N1 C6 SING N N 25 5HU C2 O2 DOUB N N 26 5HU C2 N3 SING N N 27 5HU N3 C4 SING N N 28 5HU N3 HN3 SING N N 29 5HU C4 O4 DOUB N N 30 5HU C4 C5 SING N N 31 5HU C5 C5A SING N N 32 5HU C5 C6 DOUB N N 33 5HU C5A O5B SING N N 34 5HU C5A H5A1 SING N N 35 5HU C5A H5A2 SING N N 36 5HU C6 HC6 SING N N 37 5HU O5B HO5B SING N N 38 # 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 5HU SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1CO)C2OC(C(O)C2)COP(=O)(O)O" 5HU SMILES_CANONICAL CACTVS 3.341 "OCC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" 5HU SMILES CACTVS 3.341 "OCC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" 5HU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)CO)COP(=O)(O)O)O" 5HU SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=C(C(=O)NC2=O)CO)COP(=O)(O)O)O" 5HU InChI InChI 1.03 "InChI=1S/C10H15N2O9P/c13-3-5-2-12(10(16)11-9(5)15)8-1-6(14)7(21-8)4-20-22(17,18)19/h2,6-8,13-14H,1,3-4H2,(H,11,15,16)(H2,17,18,19)/t6-,7+,8+/m0/s1" 5HU InChIKey InChI 1.03 WEBVWKFGRVLCNS-XLPZGREQSA-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 5HU "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-deoxy-5-(hydroxymethyl)uridine 5'-(dihydrogen phosphate) ; 5HU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-[5-(hydroxymethyl)-2,4-dioxo-pyrimidin-1-yl]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 5HU "Create component" 2002-09-26 RCSB 5HU "Modify descriptor" 2011-06-04 RCSB #