data_2BT # _chem_comp.id 2BT _chem_comp.name "2'-O-BUTYL-THYMIDINE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C14 H23 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms "2'-O-BUTYL-5-METHYLURIDINE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-12-16 _chem_comp.pdbx_modified_date 2021-03-01 _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 394.314 _chem_comp.one_letter_code T _chem_comp.three_letter_code 2BT _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1WV5 _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 2BT P P P 0 1 N N N -4.736 31.251 0.586 2.787 0.324 -4.407 P 2BT 1 2BT OP3 O3P O 0 1 N Y N -5.868 30.549 0.016 1.198 0.588 -4.548 OP3 2BT 2 2BT OP2 O2P O 0 1 N N N -3.411 30.594 0.625 2.921 -1.270 -4.647 OP2 2BT 3 2BT "O5'" O5* O 0 1 N N N -4.531 32.593 -0.257 3.063 0.476 -2.819 "O5'" 2BT 4 2BT "C5'" C5* C 0 1 N N N -5.546 33.600 -0.327 2.282 -0.292 -1.921 "C5'" 2BT 5 2BT "C4'" C4* C 0 1 N N R -5.014 34.963 -0.718 2.725 0.023 -0.498 "C4'" 2BT 6 2BT "O4'" O4* O 0 1 N N N -4.260 35.459 0.380 2.470 1.422 -0.246 "O4'" 2BT 7 2BT "C1'" C1* C 0 1 N N R -3.268 36.323 -0.111 1.373 1.543 0.675 "C1'" 2BT 8 2BT N1 N1 N 0 1 N N N -1.948 35.753 0.243 0.452 2.524 0.177 N1 2BT 9 2BT C2 C2 C 0 1 N N N -0.858 36.585 0.261 -0.300 3.336 1.055 C2 2BT 10 2BT O2 O2 O 0 1 N N N -0.914 37.763 -0.025 -0.225 3.269 2.283 O2 2BT 11 2BT N3 N3 N 0 1 N N N 0.313 35.996 0.642 -1.159 4.248 0.431 N3 2BT 12 2BT C4 C4 C 0 1 N N N 0.495 34.674 0.942 -1.338 4.427 -0.932 C4 2BT 13 2BT O4 O4 O 0 1 N N N 1.587 34.252 1.284 -2.112 5.251 -1.413 O4 2BT 14 2BT C5 C5 C 0 1 N N N -0.675 33.881 0.929 -0.514 3.537 -1.792 C5 2BT 15 2BT C5M C5M C 0 1 N N N -0.620 32.620 1.697 -0.651 3.669 -3.275 C5M 2BT 16 2BT C6 C6 C 0 1 N N N -1.835 34.434 0.585 0.309 2.663 -1.199 C6 2BT 17 2BT "C2'" C2* C 0 1 N N R -3.525 36.491 -1.603 0.748 0.163 0.786 "C2'" 2BT 18 2BT "O2'" O2* O 0 1 N N N -4.479 37.524 -1.886 0.137 -0.058 2.041 "O2'" 2BT 19 2BT "CA'" CA* C 0 1 N N N -4.022 38.855 -1.725 -0.332 -1.396 2.174 "CA'" 2BT 20 2BT "CB'" CB* C 0 1 N N N -5.024 39.764 -2.386 -0.992 -1.552 3.536 "CB'" 2BT 21 2BT "CC'" CC* C 0 1 N N N -4.354 41.065 -2.829 -1.506 -2.973 3.753 "CC'" 2BT 22 2BT "C3'" C3* C 0 1 N N R -4.029 35.074 -1.858 1.940 -0.742 0.560 "C3'" 2BT 23 2BT "O3'" O3* O 0 1 N N N -4.671 34.899 -3.113 2.742 -0.809 1.739 "O3'" 2BT 24 2BT "CD'" CD* C 0 1 N N N ? ? ? -2.126 -3.136 5.131 "CD'" 2BT 25 2BT OP1 O1P O 0 1 N N N ? ? ? 3.659 1.172 -5.286 OP1 2BT 26 2BT HOP3 3HOP H 0 0 N N N -6.718 30.970 -0.009 0.799 0.616 -5.443 HOP3 2BT 27 2BT HOP2 2HOP H 0 0 N N N -2.668 31.054 0.998 2.886 -1.617 -5.563 HOP2 2BT 28 2BT "H5'" 1H5* H 0 1 N N N -6.368 33.285 -1.010 1.229 -0.035 -2.051 "H5'" 2BT 29 2BT "H5''" 2H5* H 0 0 N N N -6.113 33.656 0.631 2.428 -1.352 -2.133 "H5''" 2BT 30 2BT "H4'" H4* H 0 1 N N N -5.943 35.496 -1.026 3.804 -0.139 -0.410 "H4'" 2BT 31 2BT "H1'" H1* H 0 1 N N N -3.286 37.343 0.337 1.754 1.910 1.633 "H1'" 2BT 32 2BT HN3 HN3 H 0 1 N N N 1.130 36.602 0.709 -1.709 4.843 1.045 HN3 2BT 33 2BT H71 1H5M H 0 1 N N N -1.542 31.994 1.686 -1.057 2.748 -3.690 H71 2BT 34 2BT H72 2H5M H 0 1 N N N 0.251 32.011 1.359 0.324 3.866 -3.719 H72 2BT 35 2BT H73 3H5M H 0 1 N N N -0.321 32.833 2.749 -1.320 4.497 -3.510 H73 2BT 36 2BT H6 H6 H 0 1 N N N -2.725 33.782 0.583 0.928 1.995 -1.790 H6 2BT 37 2BT "H2'" H2* H 0 1 N N N -2.670 36.820 -2.238 -0.000 0.004 -0.000 "H2'" 2BT 38 2BT "HA'1" 1HA* H 0 0 N N N -3.830 39.122 -0.659 0.521 -2.075 2.072 "HA'1" 2BT 39 2BT "HA'2" 2HA* H 0 0 N N N -2.983 39.006 -2.102 -1.045 -1.596 1.368 "HA'2" 2BT 40 2BT "HB'1" 1HB* H 0 0 N N N -5.548 39.259 -3.230 -1.815 -0.833 3.625 "HB'1" 2BT 41 2BT "HB'2" 2HB* H 0 0 N N N -5.906 39.953 -1.732 -0.274 -1.284 4.321 "HB'2" 2BT 42 2BT "HC'1" 1HC* H 0 0 N N N -4.349 42.010 -3.420 -0.682 -3.688 3.642 "HC'1" 2BT 43 2BT "HC'2" 2HC* H 0 0 N N N -4.000 42.102 -2.622 -2.254 -3.219 2.991 "HC'2" 2BT 44 2BT "H3'" H3* H 0 1 N N N -3.219 34.308 -1.898 1.675 -1.764 0.277 "H3'" 2BT 45 2BT "HO3'" H3T H 0 0 N Y N -4.051 34.968 -3.829 3.447 -0.153 1.628 "HO3'" 2BT 46 2BT "HD'1" 1HD* H 0 0 N N N 0.488 0.948 -0.323 -1.394 -2.927 5.918 "HD'1" 2BT 47 2BT "HD'2" 2HD* H 0 0 N N N -0.004 -0.945 0.591 -2.975 -2.458 5.263 "HD'2" 2BT 48 2BT "HD'3" 3HD* H 0 0 N N N -0.353 -1.037 -0.206 -2.486 -4.161 5.266 "HD'3" 2BT 49 # # 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 2BT P OP3 SING N N 1 2BT P OP2 SING N N 2 2BT P "O5'" SING N N 3 2BT P OP1 DOUB N N 4 2BT OP3 HOP3 SING N N 5 2BT OP2 HOP2 SING N N 6 2BT "O5'" "C5'" SING N N 7 2BT "C5'" "C4'" SING N N 8 2BT "C5'" "H5'" SING N N 9 2BT "C5'" "H5''" SING N N 10 2BT "C4'" "O4'" SING N N 11 2BT "C4'" "C3'" SING N N 12 2BT "C4'" "H4'" SING N N 13 2BT "O4'" "C1'" SING N N 14 2BT "C1'" N1 SING N N 15 2BT "C1'" "C2'" SING N N 16 2BT "C1'" "H1'" SING N N 17 2BT N1 C2 SING N N 18 2BT N1 C6 SING N N 19 2BT C2 O2 DOUB N N 20 2BT C2 N3 SING N N 21 2BT N3 C4 SING N N 22 2BT N3 HN3 SING N N 23 2BT C4 O4 DOUB N N 24 2BT C4 C5 SING N N 25 2BT C5 C5M SING N N 26 2BT C5 C6 DOUB N N 27 2BT C5M H71 SING N N 28 2BT C5M H72 SING N N 29 2BT C5M H73 SING N N 30 2BT C6 H6 SING N N 31 2BT "C2'" "O2'" SING N N 32 2BT "C2'" "C3'" SING N N 33 2BT "C2'" "H2'" SING N N 34 2BT "O2'" "CA'" SING N N 35 2BT "CA'" "CB'" SING N N 36 2BT "CA'" "HA'1" SING N N 37 2BT "CA'" "HA'2" SING N N 38 2BT "CB'" "CC'" SING N N 39 2BT "CB'" "HB'1" SING N N 40 2BT "CB'" "HB'2" SING N N 41 2BT "CC'" "CD'" SING N N 42 2BT "CC'" "HC'1" SING N N 43 2BT "CC'" "HC'2" SING N N 44 2BT "C3'" "O3'" SING N N 45 2BT "C3'" "H3'" SING N N 46 2BT "O3'" "HO3'" SING N N 47 2BT "CD'" "HD'1" SING N N 48 2BT "CD'" "HD'2" SING N N 49 2BT "CD'" "HD'3" SING N N 50 # # 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 2BT SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2OCCCC)COP(=O)(O)O" 2BT SMILES_CANONICAL CACTVS 3.341 "CCCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O" 2BT SMILES CACTVS 3.341 "CCCCO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O" 2BT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CCCCO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)C)COP(=O)(O)O)O" 2BT SMILES "OpenEye OEToolkits" 1.5.0 "CCCCOC1C(C(OC1N2C=C(C(=O)NC2=O)C)COP(=O)(O)O)O" 2BT InChI InChI 1.03 "InChI=1S/C14H23N2O9P/c1-3-4-5-23-11-10(17)9(7-24-26(20,21)22)25-13(11)16-6-8(2)12(18)15-14(16)19/h6,9-11,13,17H,3-5,7H2,1-2H3,(H,15,18,19)(H2,20,21,22)/t9-,10-,11-,13-/m1/s1" 2BT InChIKey InChI 1.03 WSAMAMLAATZRPR-PRULPYPASA-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 2BT "SYSTEMATIC NAME" ACDLabs 10.04 "2'-O-butyl-5-methyluridine 5'-(dihydrogen phosphate)" 2BT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-4-butoxy-3-hydroxy-5-(5-methyl-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 2BT "Create component" 2004-12-16 RCSB 2BT "Modify linking type" 2011-06-04 RCSB 2BT "Modify descriptor" 2011-06-04 RCSB 2BT "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 2BT _pdbx_chem_comp_synonyms.name "2'-O-BUTYL-5-METHYLURIDINE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##