data_TLO # _chem_comp.id TLO _chem_comp.name "5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H20 N2 O11 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "thymidine diphosphate phenol" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-10-29 _chem_comp.pdbx_modified_date 2020-06-17 _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 478.284 _chem_comp.one_letter_code ? _chem_comp.three_letter_code TLO _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 3PFG _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 TLO N1 N1 N 0 1 N N N -4.972 5.207 35.692 4.821 -0.504 0.437 N1 TLO 1 TLO C2 C2 C 0 1 N N N -3.884 5.847 36.170 4.856 -0.682 -0.896 C2 TLO 2 TLO O2 O2 O 0 1 N N N -3.785 7.106 36.098 4.281 0.107 -1.621 O2 TLO 3 TLO N3 N3 N 0 1 N N N -2.869 5.168 36.776 5.519 -1.720 -1.438 N3 TLO 4 TLO C4 C4 C 0 1 N N N -2.947 3.806 36.856 6.162 -2.603 -0.648 C4 TLO 5 TLO O4 O4 O 0 1 N N N -1.961 3.253 37.380 6.763 -3.542 -1.138 O4 TLO 6 TLO C5 C5 C 0 1 N N N -4.059 3.108 36.354 6.133 -2.428 0.757 C5 TLO 7 TLO C6 C6 C 0 1 N N N -5.057 3.859 35.752 5.460 -1.377 1.274 C6 TLO 8 TLO PA PA P 0 1 N N N -9.358 1.816 32.709 -1.481 1.662 -0.484 PA TLO 9 TLO PB PB P 0 1 N N N -7.760 2.499 30.318 -3.863 -0.084 -0.242 PB TLO 10 TLO CG CG C 0 1 Y N N -7.376 0.326 28.949 -5.884 -1.122 0.786 CG TLO 11 TLO CZ CZ C 0 1 Y N N -5.780 -1.843 28.416 -8.384 -2.171 0.234 CZ TLO 12 TLO "C1'" "C1'" C 0 1 N N R -6.015 5.933 34.963 4.096 0.639 0.998 "C1'" TLO 13 TLO O1A O1A O 0 1 N N N -9.073 0.749 33.750 -2.074 3.153 -0.351 O1A TLO 14 TLO O1B O1B O 0 1 N N N -6.299 2.738 30.328 -3.534 -1.331 -1.206 O1B TLO 15 TLO "C2'" "C2'" C 0 1 N N N -5.933 5.607 33.454 4.716 1.965 0.502 "C2'" TLO 16 TLO O2A O2A O 0 1 N N N -10.606 1.699 31.858 -1.328 1.318 -1.916 O2A TLO 17 TLO O2B O2B O 0 1 N N N -8.670 3.709 30.151 -4.700 0.895 -0.971 O2B TLO 18 TLO "C3'" "C3'" C 0 1 N N S -7.389 5.598 33.006 3.499 2.895 0.298 "C3'" TLO 19 TLO "O3'" "O3'" O 0 1 N N N -7.808 6.984 32.817 3.594 4.037 1.152 "O3'" TLO 20 TLO O3A O3A O 0 1 N N N -8.074 1.797 31.740 -2.489 0.619 0.214 O3A TLO 21 TLO O3B O3B O 0 1 N N N -8.186 1.390 29.247 -4.657 -0.606 1.058 O3B TLO 22 TLO "C4'" "C4'" C 0 1 N N R -8.106 5.163 34.246 2.288 2.022 0.696 "C4'" TLO 23 TLO "O4'" "O4'" O 0 1 N N N -7.271 5.478 35.366 2.737 0.662 0.510 "O4'" TLO 24 TLO "C5'" "C5'" C 0 1 N N N -8.262 3.661 34.241 1.095 2.318 -0.215 "C5'" TLO 25 TLO "O5'" "O5'" O 0 1 N N N -9.294 3.308 33.278 -0.045 1.588 0.241 "O5'" TLO 26 TLO C5M C5M C 0 1 N N N -4.093 1.586 36.515 6.843 -3.401 1.662 C5M TLO 27 TLO CD1 CD1 C 0 1 Y N N -7.414 -0.803 29.778 -6.024 -2.474 0.508 CD1 TLO 28 TLO CD2 CD2 C 0 1 Y N N -6.546 0.386 27.851 -7.001 -0.298 0.792 CD2 TLO 29 TLO CE1 CE1 C 0 1 Y N N -6.609 -1.902 29.529 -7.273 -2.996 0.233 CE1 TLO 30 TLO CE2 CE2 C 0 1 Y N N -5.750 -0.719 27.603 -8.248 -0.825 0.516 CE2 TLO 31 TLO HN3 HN3 H 0 1 N N N -2.083 5.657 37.154 5.534 -1.833 -2.402 HN3 TLO 32 TLO H6 H6 H 0 1 N N N -5.914 3.360 35.325 5.428 -1.227 2.343 H6 TLO 33 TLO HZ HZ H 0 1 N N N -5.148 -2.686 28.179 -9.359 -2.581 0.018 HZ TLO 34 TLO "H1'" "H1'" H 0 1 N N N -5.875 7.006 35.160 4.108 0.598 2.087 "H1'" TLO 35 TLO HO1A HO1A H 0 0 N N N -9.764 0.097 33.733 -2.200 3.446 0.562 HO1A TLO 36 TLO HO1B HO1B H 0 0 N N N -6.129 3.667 30.223 -2.987 -2.014 -0.793 HO1B TLO 37 TLO "H2'" "H2'" H 0 1 N N N -5.350 6.365 32.910 5.390 2.376 1.253 "H2'" TLO 38 TLO "H2'A" "H2'A" H 0 0 N N N -5.453 4.633 33.279 5.243 1.811 -0.440 "H2'A" TLO 39 TLO "H3'" "H3'" H 0 1 N N N -7.562 4.994 32.103 3.423 3.202 -0.745 "H3'" TLO 40 TLO "HO3'" "HO3'" H 0 0 N N N -8.715 7.006 32.537 4.371 4.589 0.985 "HO3'" TLO 41 TLO "H4'" "H4'" H 0 1 N N N -9.087 5.658 34.297 2.023 2.194 1.739 "H4'" TLO 42 TLO "H5'" "H5'" H 0 1 N N N -7.310 3.188 33.957 0.877 3.386 -0.191 "H5'" TLO 43 TLO "H5'A" "H5'A" H 0 0 N N N -8.553 3.313 35.243 1.334 2.019 -1.235 "H5'A" TLO 44 TLO H5M H5M H 0 1 N N N -5.020 1.191 36.074 7.323 -4.173 1.061 H5M TLO 45 TLO H5MA H5MA H 0 0 N N N -3.226 1.144 36.002 7.597 -2.871 2.244 H5MA TLO 46 TLO H5MB H5MB H 0 0 N N N -4.057 1.330 37.584 6.122 -3.862 2.337 H5MB TLO 47 TLO HD1 HD1 H 0 1 N N N -8.083 -0.816 30.626 -5.157 -3.118 0.506 HD1 TLO 48 TLO HD2 HD2 H 0 1 N N N -6.518 1.256 27.212 -6.895 0.754 1.013 HD2 TLO 49 TLO HE1 HE1 H 0 1 N N N -6.625 -2.769 30.173 -7.382 -4.047 0.012 HE1 TLO 50 TLO HE2 HE2 H 0 1 N N N -5.086 -0.706 26.751 -9.116 -0.183 0.516 HE2 TLO 51 # # 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 TLO "C1'" N1 SING N N 1 TLO N1 C6 SING N N 2 TLO N1 C2 SING N N 3 TLO O2 C2 DOUB N N 4 TLO C2 N3 SING N N 5 TLO N3 C4 SING N N 6 TLO N3 HN3 SING N N 7 TLO C5 C4 SING N N 8 TLO C4 O4 DOUB N N 9 TLO C6 C5 DOUB N N 10 TLO C5 C5M SING N N 11 TLO C6 H6 SING N N 12 TLO O3A PA SING N N 13 TLO O2A PA DOUB N N 14 TLO PA "O5'" SING N N 15 TLO PA O1A SING N N 16 TLO O3B PB SING N N 17 TLO O2B PB DOUB N N 18 TLO PB O1B SING N N 19 TLO PB O3A SING N N 20 TLO CD2 CG DOUB Y N 21 TLO CG O3B SING N N 22 TLO CG CD1 SING Y N 23 TLO CE2 CZ DOUB Y N 24 TLO CZ CE1 SING Y N 25 TLO CZ HZ SING N N 26 TLO "C2'" "C1'" SING N N 27 TLO "C1'" "O4'" SING N N 28 TLO "C1'" "H1'" SING N N 29 TLO O1A HO1A SING N N 30 TLO O1B HO1B SING N N 31 TLO "C3'" "C2'" SING N N 32 TLO "C2'" "H2'" SING N N 33 TLO "C2'" "H2'A" SING N N 34 TLO "O3'" "C3'" SING N N 35 TLO "C3'" "C4'" SING N N 36 TLO "C3'" "H3'" SING N N 37 TLO "O3'" "HO3'" SING N N 38 TLO "C5'" "C4'" SING N N 39 TLO "C4'" "O4'" SING N N 40 TLO "C4'" "H4'" SING N N 41 TLO "O5'" "C5'" SING N N 42 TLO "C5'" "H5'" SING N N 43 TLO "C5'" "H5'A" SING N N 44 TLO C5M H5M SING N N 45 TLO C5M H5MA SING N N 46 TLO C5M H5MB SING N N 47 TLO CE1 CD1 DOUB Y N 48 TLO CD1 HD1 SING N N 49 TLO CE2 CD2 SING Y N 50 TLO CD2 HD2 SING N N 51 TLO CE1 HE1 SING N N 52 TLO CE2 HE2 SING N N 53 # # 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 TLO SMILES ACDLabs 12.01 "O=P(Oc1ccccc1)(O)OP(=O)(O)OCC3OC(N2C(=O)NC(=O)C(=C2)C)CC3O" TLO SMILES_CANONICAL CACTVS 3.370 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)Oc3ccccc3)O2)C(=O)NC1=O" TLO SMILES CACTVS 3.370 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)Oc3ccccc3)O2)C(=O)NC1=O" TLO SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@@](=O)(O)Oc3ccccc3)O" TLO SMILES "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)Oc3ccccc3)O" TLO InChI InChI 1.03 "InChI=1S/C16H20N2O11P2/c1-10-8-18(16(21)17-15(10)20)14-7-12(19)13(27-14)9-26-30(22,23)29-31(24,25)28-11-5-3-2-4-6-11/h2-6,8,12-14,19H,7,9H2,1H3,(H,22,23)(H,24,25)(H,17,20,21)/t12-,13+,14+/m0/s1" TLO InChIKey InChI 1.03 BANJVYKYIQPYKP-BFHYXJOUSA-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 TLO "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine" TLO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] phenyl hydrogen 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 TLO "Create component" 2010-10-29 RCSB TLO "Modify aromatic_flag" 2011-06-04 RCSB TLO "Modify descriptor" 2011-06-04 RCSB TLO "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id TLO _pdbx_chem_comp_synonyms.name "thymidine diphosphate phenol" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##