data_H2U # _chem_comp.id H2U _chem_comp.name "5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H15 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2024-09-27 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces DHU _chem_comp.formula_weight 326.197 _chem_comp.one_letter_code U _chem_comp.three_letter_code H2U _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 1EVV _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI _chem_comp.pdbx_pcm Y # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 H2U P P P 0 1 N N N N N N 51.151 5.354 35.144 -1.087 0.031 -3.989 P H2U 1 H2U OP1 O1P O 0 1 N N N N N N 50.015 6.307 35.028 -1.678 -1.272 -3.613 OP1 H2U 2 H2U OP2 O2P O 0 1 N N N N N N 50.991 4.140 35.990 -2.235 0.986 -4.593 OP2 H2U 3 H2U OP3 O3P O 0 1 N Y N N N N 51.554 4.962 33.633 0.058 -0.197 -5.097 OP3 H2U 4 H2U "O5'" O5* O 0 1 N N N N N N 52.416 6.210 35.629 -0.444 0.725 -2.687 "O5'" H2U 5 H2U "C5'" C5* C 0 1 N N N N N N 52.757 7.421 34.931 0.561 -0.164 -2.199 "C5'" H2U 6 H2U "C4'" C4* C 0 1 N N R N N N 54.234 7.735 35.065 1.216 0.437 -0.955 "C4'" H2U 7 H2U "O4'" O4* O 0 1 N N N N N N 54.537 7.945 36.462 0.236 0.615 0.093 "O4'" H2U 8 H2U "C3'" C3* C 0 1 N N S N N N 55.177 6.613 34.675 2.255 -0.538 -0.359 "C3'" H2U 9 H2U "O3'" O3* O 0 1 N N N N N N 56.463 7.129 34.246 3.574 -0.183 -0.778 "O3'" H2U 10 H2U "C1'" C1* C 0 1 N N R N N N 54.924 6.715 37.047 0.997 0.702 1.318 "C1'" H2U 11 H2U "C2'" C2* C 0 1 N N R N N N 55.101 5.705 35.904 2.107 -0.361 1.168 "C2'" H2U 12 H2U "O2'" O2* O 0 1 N N N N N N 56.186 4.822 36.085 3.331 0.104 1.739 "O2'" H2U 13 H2U N1 N1 N 0 1 N N N N N N 53.888 6.348 38.024 0.148 0.394 2.471 N1 H2U 14 H2U C2 C2 C 0 1 N N N N N N 53.373 7.374 38.806 -0.524 -0.766 2.507 C2 H2U 15 H2U O2 O2 O 0 1 N N N N N N 53.623 8.548 38.592 -0.332 -1.590 1.633 O2 H2U 16 H2U N3 N3 N 0 1 N N N N N N 52.563 6.991 39.847 -1.397 -1.045 3.489 N3 H2U 17 H2U C4 C4 C 0 1 N N N N N N 52.231 5.711 40.243 -1.818 -0.085 4.333 C4 H2U 18 H2U O4 O4 O 0 1 N N N N N N 51.468 5.557 41.200 -2.546 -0.368 5.260 O4 H2U 19 H2U C5 C5 C 0 1 N N N N N N 53.005 4.617 39.555 -1.384 1.343 4.125 C5 H2U 20 H2U C6 C6 C 0 1 N N N N N N 53.410 4.957 38.147 0.040 1.360 3.566 C6 H2U 21 H2U HOP2 2HOP H 0 0 N N N N N N 51.716 3.531 36.064 -2.593 0.534 -5.370 HOP2 H2U 22 H2U HOP3 3HOP H 0 0 N N N N N N 52.279 4.353 33.707 0.415 0.674 -5.313 HOP3 H2U 23 H2U "H5'" 1H5* H 0 1 N N N N N N 52.442 7.380 33.862 1.317 -0.316 -2.970 "H5'" H2U 24 H2U "H5''" 2H5* H 0 0 N N N N N N 52.124 8.277 35.263 0.106 -1.121 -1.943 "H5''" H2U 25 H2U "H4'" H4* H 0 1 N N N N N N 54.389 8.607 34.388 1.688 1.389 -1.198 "H4'" H2U 26 H2U "H3'" H3* H 0 1 N N N N N N 54.921 6.017 33.767 2.026 -1.563 -0.649 "H3'" H2U 27 H2U "HO3'" *HO3 H 0 0 N Y N N N N 57.053 6.426 34.001 4.180 -0.805 -0.353 "HO3'" H2U 28 H2U "H1'" H1* H 0 1 N N N N N N 55.891 6.758 37.600 1.435 1.694 1.423 "H1'" H2U 29 H2U "H2'" H2* H 0 1 N N N N N N 54.269 4.966 35.822 1.803 -1.299 1.633 "H2'" H2U 30 H2U "HO2'" *HO2 H 0 0 N N N N N N 56.138 4.258 36.848 3.998 -0.572 1.562 "HO2'" H2U 31 H2U HN3 HN3 H 0 1 N N N N N N 52.158 7.751 40.393 -1.731 -1.950 3.591 HN3 H2U 32 H2U H51 1H5 H 0 1 N N N N N N 53.894 4.323 40.160 -1.408 1.874 5.076 H51 H2U 33 H2U H52 2H5 H 0 1 N N N N N N 52.437 3.657 39.580 -2.057 1.829 3.419 H52 H2U 34 H2U H61 1H6 H 0 1 N N N N N N 52.582 4.749 37.428 0.743 1.094 4.356 H61 H2U 35 H2U H62 2H6 H 0 1 N N N N N N 54.166 4.235 37.759 0.273 2.358 3.194 H62 H2U 36 # 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 H2U P OP1 DOUB N N 1 H2U P OP2 SING N N 2 H2U P OP3 SING N N 3 H2U P "O5'" SING N N 4 H2U OP2 HOP2 SING N N 5 H2U OP3 HOP3 SING N N 6 H2U "O5'" "C5'" SING N N 7 H2U "C5'" "C4'" SING N N 8 H2U "C5'" "H5'" SING N N 9 H2U "C5'" "H5''" SING N N 10 H2U "C4'" "O4'" SING N N 11 H2U "C4'" "C3'" SING N N 12 H2U "C4'" "H4'" SING N N 13 H2U "O4'" "C1'" SING N N 14 H2U "C3'" "O3'" SING N N 15 H2U "C3'" "C2'" SING N N 16 H2U "C3'" "H3'" SING N N 17 H2U "O3'" "HO3'" SING N N 18 H2U "C1'" "C2'" SING N N 19 H2U "C1'" N1 SING N N 20 H2U "C1'" "H1'" SING N N 21 H2U "C2'" "O2'" SING N N 22 H2U "C2'" "H2'" SING N N 23 H2U "O2'" "HO2'" SING N N 24 H2U N1 C2 SING N N 25 H2U N1 C6 SING N N 26 H2U C2 O2 DOUB N N 27 H2U C2 N3 SING N N 28 H2U N3 C4 SING N N 29 H2U N3 HN3 SING N N 30 H2U C4 O4 DOUB N N 31 H2U C4 C5 SING N N 32 H2U C5 C6 SING N N 33 H2U C5 H51 SING N N 34 H2U C5 H52 SING N N 35 H2U C6 H61 SING N N 36 H2U C6 H62 SING N N 37 # 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 H2U SMILES ACDLabs 10.04 "O=C1N(CCC(=O)N1)C2OC(C(O)C2O)COP(=O)(O)O" H2U SMILES_CANONICAL CACTVS 3.341 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2CCC(=O)NC2=O" H2U SMILES CACTVS 3.341 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2CCC(=O)NC2=O" H2U SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" H2U SMILES "OpenEye OEToolkits" 1.5.0 "C1CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O" H2U InChI InChI 1.03 "InChI=1S/C9H15N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h4,6-8,13-14H,1-3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1" H2U InChIKey InChI 1.03 NBWDKGJHOHJBRJ-XVFCMESISA-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 H2U "SYSTEMATIC NAME" ACDLabs 10.04 ;5'-uridylic acid ; H2U "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(2,4-dioxo-1,3-diazinan-1-yl)-3,4-dihydroxy-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 H2U "Create component" 1999-07-08 EBI H2U "Modify descriptor" 2011-06-04 RCSB H2U "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id H2U _pdbx_chem_comp_pcm.modified_residue_id HIS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom P _pdbx_chem_comp_pcm.modified_residue_id_linking_atom NE2 _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #