data_U4M # _chem_comp.id U4M _chem_comp.name "1-{2,5-dideoxy-2-fluoro-4-[(phosphonooxy)methyl]-alpha-L-lyxofuranosyl}pyrimidine-2,4(1H,3H)-dione" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H14 F N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2'-F,4'-alpha-methyl uridine 5--(dihydrogen phosphate)" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-04-06 _chem_comp.pdbx_modified_date 2021-03-13 _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 340.199 _chem_comp.one_letter_code ? _chem_comp.three_letter_code U4M _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 6CXZ _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 U4M "C1'" C1 C 0 1 N N R -7.304 -19.593 10.268 1.365 -1.033 -0.345 "C1'" U4M 1 U4M C2 C2 C 0 1 N N N -5.076 -19.294 9.397 3.421 0.208 -0.719 C2 U4M 2 U4M "C2'" C3 C 0 1 N N R -7.216 -20.255 11.641 1.088 -1.728 1.012 "C2'" U4M 3 U4M "C3'" C4 C 0 1 N N R -7.899 -19.218 12.483 -0.241 -2.469 0.698 "C3'" U4M 4 U4M C4 C5 C 0 1 N N N -3.957 -17.168 9.232 3.794 2.329 0.189 C4 U4M 5 U4M "C4'" C6 C 0 1 N N R -9.091 -18.799 11.575 -0.938 -1.493 -0.275 "C4'" U4M 6 U4M C5 C7 C 0 1 N N N -5.075 -16.543 9.777 2.515 2.282 0.795 C5 U4M 7 U4M "C5'" C8 C 0 1 N N N -9.801 -17.596 12.069 -1.956 -0.641 0.486 "C5'" U4M 8 U4M C6 C9 C 0 1 N N N -6.181 -17.313 10.130 1.742 1.190 0.614 C6 U4M 9 U4M CM C10 C 0 1 N N N -10.175 -19.873 11.503 -1.644 -2.280 -1.381 CM U4M 10 U4M "F2'" F1 F 0 1 N N N -7.870 -21.444 11.537 2.106 -2.632 1.333 "F2'" U4M 11 U4M N1 N1 N 0 1 N N N -6.151 -18.713 9.922 2.204 0.151 -0.148 N1 U4M 12 U4M N3 N2 N 0 1 N N N -3.954 -18.541 9.039 4.213 1.285 -0.554 N3 U4M 13 U4M O2 O1 O 0 1 N N N -5.063 -20.507 9.214 3.814 -0.728 -1.388 O2 U4M 14 U4M "O3'" O2 O 0 1 N N N -8.337 -19.746 13.709 0.015 -3.724 0.064 "O3'" U4M 15 U4M O4 O3 O 0 1 N N N -2.967 -16.513 8.908 4.509 3.303 0.338 O4 U4M 16 U4M "O4'" O4 O 0 1 N N N -8.483 -18.693 10.273 0.072 -0.652 -0.843 "O4'" U4M 17 U4M "O5'" O5 O 0 1 N N N -8.713 -16.530 12.010 -2.678 0.176 -0.437 "O5'" U4M 18 U4M OP1 O6 O 0 1 N N N -9.984 -14.708 13.173 -5.070 0.378 0.636 OP1 U4M 19 U4M OP2 O7 O 0 1 N N N -7.728 -14.227 12.080 -3.296 2.128 1.038 OP2 U4M 20 U4M P P1 P 0 1 N N N -9.017 -14.959 12.086 -3.833 1.202 0.017 P U4M 21 U4M "H1'" H1 H 0 1 N N N -7.427 -20.368 9.497 1.846 -1.728 -1.034 "H1'" U4M 22 U4M "H2'" H2 H 0 1 N N N -6.164 -20.370 11.943 0.950 -0.995 1.807 "H2'" U4M 23 U4M "H3'" H3 H 0 1 N N N -7.234 -18.355 12.631 -0.831 -2.607 1.604 "H3'" U4M 24 U4M H5 H4 H 0 1 N N N -5.085 -15.473 9.925 2.163 3.108 1.395 H5 U4M 25 U4M H6L H5 H 0 1 N N N -10.648 -17.337 11.417 -2.651 -1.292 1.017 H6L U4M 26 U4M "H5'" H6 H 0 1 N N N -10.162 -17.741 13.098 -1.434 -0.006 1.202 "H5'" U4M 27 U4M H6 H7 H 0 1 N N N -7.055 -16.845 10.559 0.763 1.136 1.067 H6 U4M 28 U4M HM3 H8 H 0 1 N N N -10.657 -19.975 12.487 -2.131 -1.586 -2.066 HM3 U4M 29 U4M HM1 H9 H 0 1 N N N -10.928 -19.585 10.754 -0.912 -2.875 -1.927 HM1 U4M 30 U4M HM2 H10 H 0 1 N N N -9.721 -20.833 11.216 -2.391 -2.939 -0.938 HM2 U4M 31 U4M H3 H11 H 0 1 N N N -3.152 -18.991 8.645 5.088 1.309 -0.972 H3 U4M 32 U4M H6M H12 H 0 1 N N N -7.585 -19.990 14.236 0.529 -4.340 0.603 H6M U4M 33 U4M H1 H13 H 0 1 N N N -9.628 -14.062 13.772 -5.472 -0.250 0.020 H1 U4M 34 U4M OP3 OP3 O 0 1 N Y N -9.776 -14.665 10.695 -4.334 2.044 -1.260 OP3 U4M 35 U4M HOP3 HOP3 H 0 0 N Y N -9.245 -14.087 10.160 -5.032 2.684 -1.060 HOP3 U4M 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 U4M O4 C4 DOUB N N 1 U4M N3 C4 SING N N 2 U4M N3 C2 SING N N 3 U4M O2 C2 DOUB N N 4 U4M C4 C5 SING N N 5 U4M C2 N1 SING N N 6 U4M C5 C6 DOUB N N 7 U4M N1 C6 SING N N 8 U4M N1 "C1'" SING N N 9 U4M "C1'" "O4'" SING N N 10 U4M "C1'" "C2'" SING N N 11 U4M "O4'" "C4'" SING N N 12 U4M CM "C4'" SING N N 13 U4M "F2'" "C2'" SING N N 14 U4M "C4'" "C5'" SING N N 15 U4M "C4'" "C3'" SING N N 16 U4M "C2'" "C3'" SING N N 17 U4M "O5'" "C5'" SING N N 18 U4M "O5'" P SING N N 19 U4M OP2 P DOUB N N 20 U4M P OP1 SING N N 21 U4M "C3'" "O3'" SING N N 22 U4M "C1'" "H1'" SING N N 23 U4M "C2'" "H2'" SING N N 24 U4M "C3'" "H3'" SING N N 25 U4M C5 H5 SING N N 26 U4M "C5'" H6L SING N N 27 U4M "C5'" "H5'" SING N N 28 U4M C6 H6 SING N N 29 U4M CM HM3 SING N N 30 U4M CM HM1 SING N N 31 U4M CM HM2 SING N N 32 U4M N3 H3 SING N N 33 U4M "O3'" H6M SING N N 34 U4M OP1 H1 SING N N 35 U4M P OP3 SING N N 36 U4M OP3 HOP3 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 U4M SMILES ACDLabs 12.01 "C1(OC(C(C1F)O)(COP(O)(=O)O)C)N2C(NC(C=C2)=O)=O" U4M InChI InChI 1.03 "InChI=1S/C10H14FN2O8P/c1-10(4-20-22(17,18)19)7(15)6(11)8(21-10)13-3-2-5(14)12-9(13)16/h2-3,6-8,15H,4H2,1H3,(H,12,14,16)(H2,17,18,19)/t6-,7+,8-,10-/m1/s1" U4M InChIKey InChI 1.03 ZQJMYOGITIALJZ-IBCQBUCCSA-N U4M SMILES_CANONICAL CACTVS 3.385 "C[C@]1(CO[P](O)(O)=O)O[C@H]([C@H](F)[C@@H]1O)N2C=CC(=O)NC2=O" U4M SMILES CACTVS 3.385 "C[C]1(CO[P](O)(O)=O)O[CH]([CH](F)[CH]1O)N2C=CC(=O)NC2=O" U4M SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C[C@]1([C@H]([C@H]([C@@H](O1)N2C=CC(=O)NC2=O)F)O)COP(=O)(O)O" U4M SMILES "OpenEye OEToolkits" 2.0.6 "CC1(C(C(C(O1)N2C=CC(=O)NC2=O)F)O)COP(=O)(O)O" # # 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 U4M "SYSTEMATIC NAME" ACDLabs 12.01 "1-{2,5-dideoxy-2-fluoro-4-[(phosphonooxy)methyl]-alpha-L-lyxofuranosyl}pyrimidine-2,4(1H,3H)-dione" U4M "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-fluoranyl-2-methyl-3-oxidanyl-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 U4M "Create component" 2018-04-06 RCSB U4M "Modify synonyms" 2018-04-12 RCSB U4M "Initial release" 2018-08-29 RCSB U4M "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id U4M _pdbx_chem_comp_synonyms.name "2'-F,4'-alpha-methyl uridine 5--(dihydrogen phosphate)" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##