data_T41 # _chem_comp.id T41 _chem_comp.name ;1-(2-O-METHYL-BETA-D-ARABINOFURANOSYL)THYMIDINE 5'-MONOPHOSPHATE ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H17 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1995-10-15 _chem_comp.pdbx_modified_date 2018-03-14 _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 352.234 _chem_comp.one_letter_code T _chem_comp.three_letter_code T41 _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 214D _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 T41 N1 N1 N 0 1 N N N 3.304 -0.962 4.148 2.146 0.131 -0.498 N1 T41 1 T41 C2 C2 C 0 1 N N N 1.999 -0.558 3.869 2.179 0.508 0.793 C2 T41 2 T41 N3 N3 N 0 1 N N N 1.635 -0.550 2.531 3.214 1.217 1.281 N3 T41 3 T41 C4 C4 C 0 1 N N N 2.434 -0.904 1.457 4.240 1.561 0.478 C4 T41 4 T41 C5 C5 C 0 1 N N N 3.763 -1.335 1.835 4.219 1.171 -0.883 C5 T41 5 T41 C5M C5M C 0 1 N N N 4.743 -1.802 0.787 5.354 1.543 -1.802 C5M T41 6 T41 C6 C6 C 0 1 N N N 4.141 -1.344 3.131 3.168 0.461 -1.346 C6 T41 7 T41 O2 O2 O 0 1 N N N 1.193 -0.223 4.733 1.260 0.204 1.530 O2 T41 8 T41 O4 O4 O 0 1 N N N 1.998 -0.837 0.311 5.177 2.203 0.919 O4 T41 9 T41 "C1'" "C1'" C 0 1 N N R 3.768 -0.931 5.560 1.009 -0.644 -0.999 "C1'" T41 10 T41 "C2'" "C2'" C 0 1 N N S 4.242 -2.213 6.170 0.960 -2.030 -0.317 "C2'" T41 11 T41 "O2'" "O2'" O 0 1 N N N 5.108 -2.927 5.341 1.626 -1.989 0.947 "O2'" T41 12 T41 "C3'" "C3'" C 0 1 N N R 5.025 -1.741 7.386 -0.549 -2.301 -0.126 "C3'" T41 13 T41 "C4'" "C4'" C 0 1 N N R 5.520 -0.359 6.930 -1.233 -1.048 -0.715 "C4'" T41 14 T41 "O3'" "O3'" O 0 1 N N N 4.217 -1.546 8.537 -0.942 -3.471 -0.846 "O3'" T41 15 T41 "O4'" "O4'" O 0 1 N N N 4.820 -0.007 5.743 -0.235 -0.008 -0.631 "O4'" T41 16 T41 "C5'" "C5'" C 0 1 N N N 7.021 -0.314 6.617 -2.463 -0.674 0.115 "C5'" T41 17 T41 "O5'" "O5'" O 0 1 N N N 7.382 -1.246 5.616 -3.147 0.414 -0.511 "O5'" T41 18 T41 "C6'" "C6'" C 0 1 N N N 4.707 -4.254 5.404 2.223 -3.230 1.329 "C6'" T41 19 T41 P P P 0 1 N N N 8.853 -1.233 4.945 -4.489 1.069 0.091 P T41 20 T41 O1P O1P O 0 1 N N N 9.846 -1.426 6.024 -4.247 1.495 1.487 O1P T41 21 T41 O2P O2P O 0 1 N N N 8.836 -2.153 3.787 -4.907 2.346 -0.796 O2P T41 22 T41 O3P O3P O 0 1 N Y N 9.004 0.284 4.394 -5.676 -0.018 0.060 O3P T41 23 T41 H3 H3 H 0 1 N N N 0.702 -0.259 2.321 3.221 1.481 2.215 H3 T41 24 T41 H5M1 H5M1 H 0 0 N N N 5.690 -2.085 1.270 6.100 2.111 -1.246 H5M1 T41 25 T41 H5M2 H5M2 H 0 0 N N N 4.327 -2.672 0.258 5.809 0.637 -2.202 H5M2 T41 26 T41 H5M3 H5M3 H 0 0 N N N 4.926 -0.989 0.069 4.972 2.151 -2.622 H5M3 T41 27 T41 H6 H6 H 0 1 N N N 5.143 -1.665 3.377 3.134 0.155 -2.381 H6 T41 28 T41 "H1'" "H1'" H 0 1 N N N 2.916 -0.590 6.166 1.074 -0.756 -2.081 "H1'" T41 29 T41 "H2'1" "H2'1" H 0 0 N N N 3.385 -2.824 6.489 1.409 -2.787 -0.960 "H2'1" T41 30 T41 "H3'" "H3'" H 0 1 N N N 5.877 -2.409 7.583 -0.787 -2.405 0.933 "H3'" T41 31 T41 "H4'" "H4'" H 0 1 N N N 5.306 0.370 7.726 -1.514 -1.222 -1.754 "H4'" T41 32 T41 HA HA H 0 1 N N N 4.760 -1.253 9.260 -1.880 -3.689 -0.761 HA T41 33 T41 "H5'1" "H5'1" H 0 0 N N N 7.281 0.697 6.271 -3.131 -1.532 0.182 "H5'1" T41 34 T41 "H5'2" "H5'2" H 0 0 N N N 7.582 -0.544 7.535 -2.149 -0.378 1.116 "H5'2" T41 35 T41 H11 H11 H 0 1 N N N 5.360 -4.866 4.764 1.454 -3.999 1.395 H11 T41 36 T41 H12 H12 H 0 1 N N N 4.775 -4.609 6.443 2.964 -3.521 0.584 H12 T41 37 T41 H13 H13 H 0 1 N N N 3.667 -4.340 5.055 2.708 -3.116 2.299 H13 T41 38 T41 H2P H2P H 0 1 N N N 9.520 -2.805 3.890 -5.710 2.791 -0.490 H2P T41 39 T41 H3P H3P H 0 1 N N N 9.692 0.729 4.874 -5.890 -0.343 -0.825 H3P T41 40 # 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 T41 N1 C2 SING N N 1 T41 N1 C6 SING N N 2 T41 N1 "C1'" SING N N 3 T41 C2 N3 SING N N 4 T41 C2 O2 DOUB N N 5 T41 N3 C4 SING N N 6 T41 N3 H3 SING N N 7 T41 C4 C5 SING N N 8 T41 C4 O4 DOUB N N 9 T41 C5 C5M SING N N 10 T41 C5 C6 DOUB N N 11 T41 C5M H5M1 SING N N 12 T41 C5M H5M2 SING N N 13 T41 C5M H5M3 SING N N 14 T41 C6 H6 SING N N 15 T41 "C1'" "C2'" SING N N 16 T41 "C1'" "O4'" SING N N 17 T41 "C1'" "H1'" SING N N 18 T41 "C2'" "O2'" SING N N 19 T41 "C2'" "C3'" SING N N 20 T41 "C2'" "H2'1" SING N N 21 T41 "O2'" "C6'" SING N N 22 T41 "C3'" "C4'" SING N N 23 T41 "C3'" "O3'" SING N N 24 T41 "C3'" "H3'" SING N N 25 T41 "C4'" "O4'" SING N N 26 T41 "C4'" "C5'" SING N N 27 T41 "C4'" "H4'" SING N N 28 T41 "O3'" HA SING N N 29 T41 "C5'" "O5'" SING N N 30 T41 "C5'" "H5'1" SING N N 31 T41 "C5'" "H5'2" SING N N 32 T41 "O5'" P SING N N 33 T41 "C6'" H11 SING N N 34 T41 "C6'" H12 SING N N 35 T41 "C6'" H13 SING N N 36 T41 P O1P DOUB N N 37 T41 P O2P SING N N 38 T41 P O3P SING N N 39 T41 O2P H2P SING N N 40 T41 O3P H3P SING N N 41 # 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 T41 SMILES ACDLabs 12.01 "N1(C(NC(C(C)=C1)=O)=O)C2C(OC)C(C(O2)COP(=O)(O)O)O" T41 InChI InChI 1.03 "InChI=1S/C11H17N2O9P/c1-5-3-13(11(16)12-9(5)15)10-8(20-2)7(14)6(22-10)4-21-23(17,18)19/h3,6-8,10,14H,4H2,1-2H3,(H,12,15,16)(H2,17,18,19)/t6-,7-,8+,10-/m1/s1" T41 InChIKey InChI 1.03 AMKCISYJIZUJJQ-BDNRQGISSA-N T41 SMILES_CANONICAL CACTVS 3.385 "CO[C@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O" T41 SMILES CACTVS 3.385 "CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O" T41 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)[C@H]2[C@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OC" T41 SMILES "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OC" # 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 T41 "SYSTEMATIC NAME" ACDLabs 12.01 "5-methyl-1-(2-O-methyl-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione" T41 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3R,4S,5R)-4-methoxy-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-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 T41 "Create component" 1995-10-15 PDBJ T41 "Modify descriptor" 2011-06-04 RCSB T41 "Modify parent residue" 2018-03-14 RCSB #