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 2011-06-04 _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 # 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 # loop_ _software.name _software.version _software.description rdkit 2023.03.3 'Core functionality.' pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.' # loop_ _pdbe_chem_comp_atom_depiction.comp_id _pdbe_chem_comp_atom_depiction.atom_id _pdbe_chem_comp_atom_depiction.element _pdbe_chem_comp_atom_depiction.model_Cartn_x _pdbe_chem_comp_atom_depiction.model_Cartn_y _pdbe_chem_comp_atom_depiction.pdbx_ordinal H2U P P 10.336 -4.683 1 H2U OP1 O 11.218 -5.896 2 H2U OP2 O 11.550 -3.801 3 H2U OP3 O 9.123 -5.564 4 H2U "O5'" O 9.455 -3.469 5 H2U "C5'" C 7.963 -3.626 6 H2U "C4'" C 7.081 -2.412 7 H2U "O4'" O 7.545 -0.986 8 H2U "C3'" C 5.581 -2.412 9 H2U "O3'" O 4.699 -3.626 10 H2U "C1'" C 6.331 -0.104 11 H2U "C2'" C 5.118 -0.986 12 H2U "O2'" O 3.691 -0.522 13 H2U N1 N 6.331 1.396 14 H2U C2 C 7.630 2.146 15 H2U O2 O 8.929 1.396 16 H2U N3 N 7.630 3.646 17 H2U C4 C 6.331 4.396 18 H2U O4 O 6.331 5.896 19 H2U C5 C 5.032 3.646 20 H2U C6 C 5.032 2.146 21 # loop_ _pdbe_chem_comp_bond_depiction.comp_id _pdbe_chem_comp_bond_depiction.atom_id_1 _pdbe_chem_comp_bond_depiction.atom_id_2 _pdbe_chem_comp_bond_depiction.value_order _pdbe_chem_comp_bond_depiction.bond_dir _pdbe_chem_comp_bond_depiction.pdbx_ordinal H2U P OP1 DOUBLE NONE 1 H2U P OP2 SINGLE NONE 2 H2U P OP3 SINGLE NONE 3 H2U P "O5'" SINGLE NONE 4 H2U "O5'" "C5'" SINGLE NONE 5 H2U "C4'" "C5'" SINGLE BEGINDASH 6 H2U "C4'" "O4'" SINGLE NONE 7 H2U "C4'" "C3'" SINGLE NONE 8 H2U "O4'" "C1'" SINGLE NONE 9 H2U "C3'" "O3'" SINGLE BEGINWEDGE 10 H2U "C3'" "C2'" SINGLE NONE 11 H2U "C1'" "C2'" SINGLE NONE 12 H2U "C1'" N1 SINGLE BEGINDASH 13 H2U "C2'" "O2'" SINGLE BEGINWEDGE 14 H2U N1 C2 SINGLE NONE 15 H2U N1 C6 SINGLE NONE 16 H2U C2 O2 DOUBLE NONE 17 H2U C2 N3 SINGLE NONE 18 H2U N3 C4 SINGLE NONE 19 H2U C4 O4 DOUBLE NONE 20 H2U C4 C5 SINGLE NONE 21 H2U C5 C6 SINGLE NONE 22 # loop_ _pdbe_chem_comp_substructure.comp_id _pdbe_chem_comp_substructure.substructure_name _pdbe_chem_comp_substructure.id _pdbe_chem_comp_substructure.substructure_type _pdbe_chem_comp_substructure.substructure_smiles _pdbe_chem_comp_substructure.substructure_inchis _pdbe_chem_comp_substructure.substructure_inchikeys H2U MurckoScaffold S1 scaffold 'O=C1CCN([C@H]2CCCO2)C(=O)N1' InChI=1S/C8H12N2O3/c11-6-3-4-10(8(12)9-6)7-2-1-5-13-7/h7H,1-5H2,(H,9,11,12)/t7-/m1/s1 ZAERJFADDUTCMT-SSDOTTSWSA-N H2U amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N H2U phosphate F2 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N H2U ribose F3 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-UHFFFAOYSA-N # loop_ _pdbe_chem_comp_substructure_mapping.comp_id _pdbe_chem_comp_substructure_mapping.atom_id _pdbe_chem_comp_substructure_mapping.substructure_id _pdbe_chem_comp_substructure_mapping.substructure_ordinal H2U "C4'" S1 1 H2U "O4'" S1 1 H2U "C3'" S1 1 H2U "C1'" S1 1 H2U "C2'" S1 1 H2U N1 S1 1 H2U C2 S1 1 H2U O2 S1 1 H2U N3 S1 1 H2U C4 S1 1 H2U O4 S1 1 H2U C5 S1 1 H2U C6 S1 1 H2U N3 F1 1 H2U C4 F1 1 H2U O4 F1 1 H2U C5 F1 1 H2U OP2 F2 1 H2U P F2 1 H2U OP1 F2 1 H2U OP3 F2 1 H2U "O5'" F2 1 H2U "C2'" F3 1 H2U "C3'" F3 1 H2U "C4'" F3 1 H2U "O4'" F3 1 H2U "C1'" F3 1 H2U "C5'" F3 1 H2U "O5'" F3 1 H2U "O3'" F3 1 H2U "O2'" F3 1 # _pdbe_chem_comp_rdkit_properties.comp_id H2U _pdbe_chem_comp_rdkit_properties.exactmw 326.052 _pdbe_chem_comp_rdkit_properties.amw 326.198 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 11 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 5 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8 _pdbe_chem_comp_rdkit_properties.NumHBD 5 _pdbe_chem_comp_rdkit_properties.NumHBA 9 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21 _pdbe_chem_comp_rdkit_properties.NumAtoms 36 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 12 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 3 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.778 _pdbe_chem_comp_rdkit_properties.NumRings 2 _pdbe_chem_comp_rdkit_properties.NumAromaticRings 0 _pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2 _pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2 _pdbe_chem_comp_rdkit_properties.NumHeterocycles 2 _pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0 _pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2 _pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2 _pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0 _pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0 _pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 4 _pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0 _pdbe_chem_comp_rdkit_properties.labuteASA 139.713 _pdbe_chem_comp_rdkit_properties.tpsa 165.860 _pdbe_chem_comp_rdkit_properties.CrippenClogP -2.516 _pdbe_chem_comp_rdkit_properties.CrippenMR 63.532 _pdbe_chem_comp_rdkit_properties.chi0v 10.410 _pdbe_chem_comp_rdkit_properties.chi1v 6.238 _pdbe_chem_comp_rdkit_properties.chi2v 2.237 _pdbe_chem_comp_rdkit_properties.chi3v 2.237 _pdbe_chem_comp_rdkit_properties.chi4v 1.350 _pdbe_chem_comp_rdkit_properties.chi0n 24.516 _pdbe_chem_comp_rdkit_properties.chi1n 11.857 _pdbe_chem_comp_rdkit_properties.chi2n 1.922 _pdbe_chem_comp_rdkit_properties.chi3n 1.922 _pdbe_chem_comp_rdkit_properties.chi4n 1.155 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.070 _pdbe_chem_comp_rdkit_properties.kappa1 5.532 _pdbe_chem_comp_rdkit_properties.kappa2 5.969 _pdbe_chem_comp_rdkit_properties.kappa3 3.771 _pdbe_chem_comp_rdkit_properties.Phi 1.572 # loop_ _pdbe_chem_comp_external_mappings.comp_id _pdbe_chem_comp_external_mappings.source _pdbe_chem_comp_external_mappings.resource _pdbe_chem_comp_external_mappings.resource_id H2U UniChem PDBe H2U H2U UniChem 'KEGG LIGAND' C04639 H2U UniChem ChEBI 74673 H2U UniChem SureChEMBL SCHEMBL11178912 H2U UniChem Nikkaji J2.752.464H H2U UniChem 'EPA CompTox Dashboard' DTXSID30331490 H2U UniChem BRENDA 106269 H2U UniChem BRENDA 90350 H2U UniChem PubChem 440416 # loop_ _pdbe_chem_comp_rdkit_conformer.comp_id _pdbe_chem_comp_rdkit_conformer.atom_id _pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit _pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit _pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit _pdbe_chem_comp_rdkit_conformer.rdkit_method _pdbe_chem_comp_rdkit_conformer.rdkit_ordinal H2U P -4.523 0.806 0.375 ETKDGv3 1 H2U OP1 -4.916 1.749 -0.741 ETKDGv3 2 H2U OP2 -5.897 -0.023 0.911 ETKDGv3 3 H2U OP3 -3.867 1.688 1.663 ETKDGv3 4 H2U "O5'" -3.387 -0.331 -0.196 ETKDGv3 5 H2U "C5'" -2.221 0.359 -0.580 ETKDGv3 6 H2U "C4'" -1.178 -0.643 -1.085 ETKDGv3 7 H2U "O4'" -0.030 0.046 -1.520 ETKDGv3 8 H2U "C3'" -0.742 -1.625 0.001 ETKDGv3 9 H2U "O3'" -1.598 -2.737 0.130 ETKDGv3 10 H2U "C1'" 1.086 -0.789 -1.277 ETKDGv3 11 H2U "C2'" 0.662 -1.992 -0.420 ETKDGv3 12 H2U "O2'" 0.669 -3.167 -1.191 ETKDGv3 13 H2U N1 2.147 -0.022 -0.603 ETKDGv3 14 H2U C2 3.533 -0.236 -0.929 ETKDGv3 15 H2U O2 3.883 -1.196 -1.669 ETKDGv3 16 H2U N3 4.524 0.653 -0.407 ETKDGv3 17 H2U C4 4.124 1.804 0.343 ETKDGv3 18 H2U O4 4.996 2.585 0.809 ETKDGv3 19 H2U C5 2.666 2.116 0.520 ETKDGv3 20 H2U C6 1.845 0.823 0.563 ETKDGv3 21 H2U HOP2 -6.509 0.684 1.238 ETKDGv3 22 H2U HOP3 -4.582 2.320 1.929 ETKDGv3 23 H2U "H5'" -2.443 1.067 -1.410 ETKDGv3 24 H2U "H5''" -1.789 0.926 0.276 ETKDGv3 25 H2U "H4'" -1.603 -1.187 -1.959 ETKDGv3 26 H2U "H3'" -0.689 -1.105 0.984 ETKDGv3 27 H2U "HO3'" -1.774 -3.109 -0.774 ETKDGv3 28 H2U "H1'" 1.453 -1.138 -2.268 ETKDGv3 29 H2U "H2'" 1.307 -2.124 0.481 ETKDGv3 30 H2U "HO2'" 1.619 -3.445 -1.271 ETKDGv3 31 H2U HN3 5.537 0.473 -0.589 ETKDGv3 32 H2U H51 2.325 2.743 -0.331 ETKDGv3 33 H2U H52 2.509 2.683 1.463 ETKDGv3 34 H2U H61 0.767 1.081 0.605 ETKDGv3 35 H2U H62 2.094 0.262 1.490 ETKDGv3 36 #