data_JW5 # _chem_comp.id JW5 _chem_comp.name ;6-(HYDROXYMETHYL)URIDINE 5'-(DIHYDROGEN PHOSPHATE) ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O10 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-06-29 _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 354.207 _chem_comp.one_letter_code N _chem_comp.three_letter_code JW5 _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 ? _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 JW5 O2 O2 O 0 1 N N N 15.259 10.709 38.913 1.106 -0.731 -1.878 O2 JW5 1 JW5 C2 C2 C 0 1 N N N 15.575 10.246 37.790 2.061 -0.846 -1.134 C2 JW5 2 JW5 N3 N3 N 0 1 N N N 16.891 9.977 37.588 3.038 -1.721 -1.439 N3 JW5 3 JW5 C4 C4 C 0 1 N N N 17.328 9.463 36.409 4.103 -1.861 -0.624 C4 JW5 4 JW5 O4 O4 O 0 1 N N N 18.579 9.232 36.239 4.987 -2.652 -0.899 O4 JW5 5 JW5 C5 C5 C 0 1 N N N 16.404 9.221 35.424 4.185 -1.079 0.553 C5 JW5 6 JW5 C6 C6 C 0 1 N N N 15.043 9.515 35.640 3.192 -0.209 0.834 C6 JW5 7 JW5 C7 C7 C 0 1 N N N 14.192 9.519 34.396 3.255 0.636 2.081 C7 JW5 8 JW5 O7 O7 O 0 1 N N N 13.742 10.897 34.167 4.455 0.337 2.798 O7 JW5 9 JW5 N1 N1 N 0 1 N N N 14.658 10.032 36.833 2.130 -0.094 -0.021 N1 JW5 10 JW5 "C1'" C1* C 0 1 N N R 13.235 10.356 37.071 1.054 0.854 0.281 "C1'" JW5 11 JW5 "O4'" O4* O 0 1 N N N 13.099 11.782 37.368 -0.225 0.184 0.270 "O4'" JW5 12 JW5 "C2'" C2* C 0 1 N N R 12.551 9.610 38.217 0.951 1.922 -0.830 "C2'" JW5 13 JW5 "O2'" O2* O 0 1 N N N 11.954 8.379 37.767 1.625 3.119 -0.439 "O2'" JW5 14 JW5 "C3'" C3* C 0 1 N N S 11.499 10.589 38.682 -0.567 2.175 -0.967 "C3'" JW5 15 JW5 "O3'" O3* O 0 1 N N N 10.272 10.452 37.931 -0.877 3.537 -0.664 "O3'" JW5 16 JW5 "C4'" C4* C 0 1 N N R 12.159 11.941 38.438 -1.201 1.231 0.078 "C4'" JW5 17 JW5 "C5'" C5* C 0 1 N N N 12.875 12.472 39.679 -2.510 0.647 -0.456 "C5'" JW5 18 JW5 "O5'" O5* O 0 1 N N N 11.909 12.742 40.669 -3.101 -0.189 0.540 "O5'" JW5 19 JW5 P P P 0 1 N N N 12.238 13.422 42.098 -4.492 -0.970 0.319 P JW5 20 JW5 O1P O1P O 0 1 N N N 12.576 14.869 41.782 -4.402 -1.801 -0.902 O1P JW5 21 JW5 O3P O3P O 0 1 N Y N 10.966 13.258 42.859 -4.787 -1.913 1.590 O3P JW5 22 JW5 O2P O2P O 0 1 N N N 13.414 12.679 42.671 -5.686 0.098 0.154 O2P JW5 23 JW5 HN3 HN3 H 0 1 N N N 17.549 10.160 38.319 2.974 -2.253 -2.247 HN3 JW5 24 JW5 H5 H5 H 0 1 N N N 16.721 8.804 34.480 5.031 -1.177 1.217 H5 JW5 25 JW5 H71 1H7 H 0 1 N N N 14.780 9.166 33.536 3.249 1.691 1.806 H71 JW5 26 JW5 H72 2H7 H 0 1 N N N 13.329 8.848 34.519 2.392 0.419 2.710 H72 JW5 27 JW5 HO7 HO7 H 0 1 N N N 13.645 11.342 35.001 4.562 0.845 3.613 HO7 JW5 28 JW5 "H1'" H1* H 0 1 N N N 12.739 10.041 36.141 1.226 1.326 1.249 "H1'" JW5 29 JW5 "H2'" H2* H 0 1 N N N 13.251 9.313 39.012 1.362 1.541 -1.765 "H2'" JW5 30 JW5 "HO'2" 2HO* H 0 0 N N N 11.823 8.415 36.827 1.591 3.824 -1.100 "HO'2" JW5 31 JW5 "H3'" H3* H 0 1 N N N 11.201 10.436 39.730 -0.908 1.921 -1.971 "H3'" JW5 32 JW5 H3T H3T H 0 1 N Y N 9.535 10.422 38.530 -0.455 4.177 -1.253 H3T JW5 33 JW5 "H4'" H4* H 0 1 N N N 11.380 12.674 38.184 -1.376 1.762 1.014 "H4'" JW5 34 JW5 "H5'1" 1H5* H 0 0 N N N 13.588 11.720 40.049 -3.196 1.457 -0.704 "H5'1" JW5 35 JW5 "H5'2" 2H5* H 0 0 N N N 13.428 13.390 39.431 -2.307 0.058 -1.351 "H5'2" JW5 36 JW5 HOP3 3HOP H 0 0 N N N 11.155 13.223 43.789 -5.611 -2.414 1.525 HOP3 JW5 37 JW5 HOP2 2HOP H 0 0 N N N 14.054 12.522 41.987 -5.803 0.678 0.919 HOP2 JW5 38 # 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 JW5 O2 C2 DOUB N N 1 JW5 C2 N1 SING N N 2 JW5 C2 N3 SING N N 3 JW5 N3 C4 SING N N 4 JW5 N3 HN3 SING N N 5 JW5 C4 C5 SING N N 6 JW5 C4 O4 DOUB N N 7 JW5 C5 C6 DOUB N N 8 JW5 C5 H5 SING N N 9 JW5 C6 C7 SING N N 10 JW5 C6 N1 SING N N 11 JW5 C7 O7 SING N N 12 JW5 C7 H71 SING N N 13 JW5 C7 H72 SING N N 14 JW5 O7 HO7 SING N N 15 JW5 N1 "C1'" SING N N 16 JW5 "C1'" "O4'" SING N N 17 JW5 "C1'" "C2'" SING N N 18 JW5 "C1'" "H1'" SING N N 19 JW5 "O4'" "C4'" SING N N 20 JW5 "C2'" "O2'" SING N N 21 JW5 "C2'" "C3'" SING N N 22 JW5 "C2'" "H2'" SING N N 23 JW5 "O2'" "HO'2" SING N N 24 JW5 "C3'" "O3'" SING N N 25 JW5 "C3'" "C4'" SING N N 26 JW5 "C3'" "H3'" SING N N 27 JW5 "O3'" H3T SING N N 28 JW5 "C4'" "C5'" SING N N 29 JW5 "C4'" "H4'" SING N N 30 JW5 "C5'" "O5'" SING N N 31 JW5 "C5'" "H5'1" SING N N 32 JW5 "C5'" "H5'2" SING N N 33 JW5 "O5'" P SING N N 34 JW5 P O3P SING N N 35 JW5 P O2P SING N N 36 JW5 P O1P DOUB N N 37 JW5 O3P HOP3 SING N N 38 JW5 O2P HOP2 SING N N 39 # 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 JW5 SMILES ACDLabs 10.04 "O=C1NC(=O)N(C(=C1)CO)C2OC(C(O)C2O)COP(=O)(O)O" JW5 SMILES_CANONICAL CACTVS 3.341 "OCC1=CC(=O)NC(=O)N1[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O" JW5 SMILES CACTVS 3.341 "OCC1=CC(=O)NC(=O)N1[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O" JW5 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)CO" JW5 SMILES "OpenEye OEToolkits" 1.5.0 "C1=C(N(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)CO" JW5 InChI InChI 1.03 "InChI=1S/C10H15N2O10P/c13-2-4-1-6(14)11-10(17)12(4)9-8(16)7(15)5(22-9)3-21-23(18,19)20/h1,5,7-9,13,15-16H,2-3H2,(H,11,14,17)(H2,18,19,20)/t5-,7-,8-,9-/m1/s1" JW5 InChIKey InChI 1.03 MSQUFEPNTQRBDI-ZOQUXTDFSA-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 JW5 "SYSTEMATIC NAME" ACDLabs 10.04 ;6-(hydroxymethyl)uridine 5'-(dihydrogen phosphate) ; JW5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-3,4-dihydroxy-5-[6-(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 JW5 "Create component" 2007-06-29 RCSB JW5 "Modify descriptor" 2011-06-04 RCSB #