data_3R2 # _chem_comp.id 3R2 _chem_comp.name "2'-deoxy-5'-O-[(R)-{[(R)-{[(1S,3R,4R,5S)-3,4-dihydroxy-5-methylcyclohexyl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-3,4-dihydrothymidine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H28 N2 O13 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-10-10 _chem_comp.pdbx_modified_date 2015-01-23 _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 530.357 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 3R2 _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 4RIF _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 3R2 O4 O4 O 0 1 N N N -3.176 12.918 4.907 7.043 3.547 1.674 O4 3R2 1 3R2 C4 C4 C 0 1 N N N -2.952 11.917 4.227 6.460 2.704 1.016 C4 3R2 2 3R2 N3 N3 N 0 1 N N N -2.543 11.989 2.907 6.032 1.564 1.596 N3 3R2 3 3R2 C2 C2 C 0 1 N N N -2.228 10.947 2.067 5.384 0.635 0.869 C2 3R2 4 3R2 O2 O2 O 0 1 N N N -1.897 11.148 0.902 5.004 -0.388 1.406 O2 3R2 5 3R2 C5 C5 C 0 1 N N N -3.079 10.535 4.762 6.219 2.914 -0.363 C5 3R2 6 3R2 C5M C5M C 0 1 N N N -3.533 10.306 6.155 6.682 4.181 -1.035 C5M 3R2 7 3R2 C6 C6 C 0 1 N N N -2.761 9.524 3.939 5.571 1.963 -1.069 C6 3R2 8 3R2 N1 N1 N 0 1 N N N -2.341 9.697 2.627 5.148 0.823 -0.442 N1 3R2 9 3R2 C1C C1C C 0 1 N N R -2.036 8.534 1.802 4.440 -0.206 -1.207 C1C 3R2 10 3R2 O4C O4C O 0 1 N N N -2.591 7.329 2.351 3.187 -0.534 -0.567 O4C 3R2 11 3R2 C2C C2C C 0 1 N N N -0.540 8.299 1.751 5.242 -1.526 -1.204 C2C 3R2 12 3R2 C3C C3C C 0 1 N N S -0.463 6.822 1.466 4.157 -2.624 -1.117 C3C 3R2 13 3R2 O3C O3C O 0 1 N N N -0.722 6.640 0.071 4.206 -3.468 -2.269 O3C 3R2 14 3R2 C4C C4C C 0 1 N N R -1.663 6.249 2.214 2.829 -1.837 -1.077 C4C 3R2 15 3R2 C5C C5C C 0 1 N N N -1.253 5.819 3.621 1.832 -2.520 -0.139 C5C 3R2 16 3R2 O5C O5C O 0 1 N N N -0.688 4.528 3.516 0.575 -1.845 -0.206 O5C 3R2 17 3R2 PA PA P 0 1 N N N 0.422 3.988 4.586 -0.710 -2.296 0.653 PA 3R2 18 3R2 O1A O1A O 0 1 N N N 1.566 3.301 3.888 -1.004 -3.722 0.389 O1A 3R2 19 3R2 O2A O2A O 0 1 N N N 0.778 5.189 5.602 -0.405 -2.093 2.221 O2A 3R2 20 3R2 O3A O3A O 0 1 N N N -0.333 2.940 5.548 -1.979 -1.399 0.233 O3A 3R2 21 3R2 PB PB P 0 1 N N N -1.816 2.353 5.768 -3.567 -1.529 0.465 PB 3R2 22 3R2 O1B O1B O 0 1 N N N -1.906 1.903 7.207 -4.161 -2.665 -0.509 O1B 3R2 23 3R2 O2B O2B O 0 1 N N N -2.871 3.494 5.354 -3.830 -1.900 1.874 O2B 3R2 24 3R2 O3B O3B O 0 1 N N N -1.945 1.195 4.629 -4.274 -0.120 0.141 O3B 3R2 25 3R2 "C1'" "C1'" C 0 1 N N S -1.903 -0.207 4.913 -5.667 0.119 0.352 "C1'" 3R2 26 3R2 "C2'" "C2'" C 0 1 N N N -0.577 -0.631 5.552 -6.328 0.489 -0.978 "C2'" 3R2 27 3R2 "C3'" "C3'" C 0 1 N N R 0.622 -0.421 4.641 -5.673 1.753 -1.538 "C3'" 3R2 28 3R2 "O3'" "O3'" O 0 1 N N N 1.797 -0.931 5.270 -6.290 2.099 -2.780 "O3'" 3R2 29 3R2 "C4'" "C4'" C 0 1 N N R 0.427 -1.089 3.293 -5.849 2.903 -0.544 "C4'" 3R2 30 3R2 "O4'" "O4'" O 0 1 N N N 1.538 -0.723 2.480 -5.237 4.083 -1.068 "O4'" 3R2 31 3R2 "C5'" "C5'" C 0 1 N N S -0.877 -0.621 2.651 -5.188 2.533 0.785 "C5'" 3R2 32 3R2 "C6'" "C6'" C 0 1 N N N -1.101 -1.226 1.282 -5.363 3.682 1.780 "C6'" 3R2 33 3R2 "C7'" "C7'" C 0 1 N N N -2.074 -0.895 3.562 -5.843 1.268 1.346 "C7'" 3R2 34 3R2 H1 H1 H 0 1 N N N -2.468 12.907 2.518 6.194 1.413 2.540 H1 3R2 35 3R2 H2 H2 H 0 1 N N N -3.736 11.273 6.639 7.181 4.818 -0.304 H2 3R2 36 3R2 H3 H3 H 0 1 N N N -4.451 9.700 6.146 7.377 3.935 -1.837 H3 3R2 37 3R2 H4 H4 H 0 1 N N N -2.748 9.774 6.713 5.822 4.708 -1.448 H4 3R2 38 3R2 H5 H5 H 0 1 N N N -2.836 8.516 4.320 5.378 2.106 -2.122 H5 3R2 39 3R2 H6 H6 H 0 1 N N N -2.410 8.693 0.780 4.267 0.133 -2.228 H6 3R2 40 3R2 H7 H7 H 0 1 N N N -0.064 8.546 2.711 5.814 -1.628 -2.125 H7 3R2 41 3R2 H8 H8 H 0 1 N N N -0.071 8.886 0.948 5.902 -1.570 -0.338 H8 3R2 42 3R2 H9 H9 H 0 1 N N N 0.486 6.378 1.802 4.280 -3.211 -0.206 H9 3R2 43 3R2 H10 H10 H 0 1 N N N -0.680 5.715 -0.141 5.043 -3.940 -2.375 H10 3R2 44 3R2 H11 H11 H 0 1 N N N -2.095 5.402 1.661 2.409 -1.750 -2.080 H11 3R2 45 3R2 H12 H12 H 0 1 N N N -0.512 6.522 4.029 1.703 -3.560 -0.441 H12 3R2 46 3R2 H13 H13 H 0 1 N N N -2.134 5.792 4.279 2.211 -2.483 0.882 H13 3R2 47 3R2 H14 H14 H 0 1 N N N 1.719 5.313 5.629 -0.203 -1.180 2.467 H14 3R2 48 3R2 H15 H15 H 0 1 N N N -2.596 2.385 7.647 -4.024 -2.487 -1.449 H15 3R2 49 3R2 H16 H16 H 0 1 N N N -2.733 -0.494 5.575 -6.134 -0.781 0.751 H16 3R2 50 3R2 H17 H17 H 0 1 N N N -0.638 -1.699 5.808 -6.203 -0.330 -1.686 H17 3R2 51 3R2 H18 H18 H 0 1 N N N -0.427 -0.042 6.469 -7.391 0.671 -0.817 H18 3R2 52 3R2 H19 H19 H 0 1 N N N 0.739 0.660 4.474 -4.610 1.571 -1.699 H19 3R2 53 3R2 H20 H20 H 0 1 N N N 1.914 -0.509 6.113 -6.218 1.414 -3.459 H20 3R2 54 3R2 H21 H21 H 0 1 N N N 0.391 -2.180 3.430 -6.911 3.085 -0.383 H21 3R2 55 3R2 H22 H22 H 0 1 N N N 2.342 -1.019 2.890 -5.607 4.377 -1.912 H22 3R2 56 3R2 H23 H23 H 0 1 N N N -0.806 0.469 2.523 -4.125 2.350 0.624 H23 3R2 57 3R2 H24 H24 H 0 1 N N N -2.051 -0.856 0.868 -6.426 3.864 1.940 H24 3R2 58 3R2 H25 H25 H 0 1 N N N -0.274 -0.940 0.615 -4.892 3.418 2.727 H25 3R2 59 3R2 H26 H26 H 0 1 N N N -1.141 -2.322 1.368 -4.897 4.582 1.380 H26 3R2 60 3R2 H27 H27 H 0 1 N N N -2.987 -0.517 3.079 -6.905 1.451 1.507 H27 3R2 61 3R2 H28 H28 H 0 1 N N N -2.165 -1.980 3.720 -5.372 1.005 2.293 H28 3R2 62 # 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 3R2 O3C C3C SING N N 1 3R2 O2 C2 DOUB N N 2 3R2 "C6'" "C5'" SING N N 3 3R2 C3C C2C SING N N 4 3R2 C3C C4C SING N N 5 3R2 C2C C1C SING N N 6 3R2 C1C O4C SING N N 7 3R2 C1C N1 SING N N 8 3R2 C2 N1 SING N N 9 3R2 C2 N3 SING N N 10 3R2 C4C O4C SING N N 11 3R2 C4C C5C SING N N 12 3R2 "O4'" "C4'" SING N N 13 3R2 N1 C6 SING N N 14 3R2 "C5'" "C4'" SING N N 15 3R2 "C5'" "C7'" SING N N 16 3R2 N3 C4 SING N N 17 3R2 "C4'" "C3'" SING N N 18 3R2 O5C C5C SING N N 19 3R2 O5C PA SING N N 20 3R2 "C7'" "C1'" SING N N 21 3R2 O1A PA DOUB N N 22 3R2 C6 C5 DOUB N N 23 3R2 C4 C5 SING N N 24 3R2 C4 O4 DOUB N N 25 3R2 PA O3A SING N N 26 3R2 PA O2A SING N N 27 3R2 O3B "C1'" SING N N 28 3R2 O3B PB SING N N 29 3R2 "C3'" "O3'" SING N N 30 3R2 "C3'" "C2'" SING N N 31 3R2 C5 C5M SING N N 32 3R2 "C1'" "C2'" SING N N 33 3R2 O2B PB DOUB N N 34 3R2 O3A PB SING N N 35 3R2 PB O1B SING N N 36 3R2 N3 H1 SING N N 37 3R2 C5M H2 SING N N 38 3R2 C5M H3 SING N N 39 3R2 C5M H4 SING N N 40 3R2 C6 H5 SING N N 41 3R2 C1C H6 SING N N 42 3R2 C2C H7 SING N N 43 3R2 C2C H8 SING N N 44 3R2 C3C H9 SING N N 45 3R2 O3C H10 SING N N 46 3R2 C4C H11 SING N N 47 3R2 C5C H12 SING N N 48 3R2 C5C H13 SING N N 49 3R2 O2A H14 SING N N 50 3R2 O1B H15 SING N N 51 3R2 "C1'" H16 SING N N 52 3R2 "C2'" H17 SING N N 53 3R2 "C2'" H18 SING N N 54 3R2 "C3'" H19 SING N N 55 3R2 "O3'" H20 SING N N 56 3R2 "C4'" H21 SING N N 57 3R2 "O4'" H22 SING N N 58 3R2 "C5'" H23 SING N N 59 3R2 "C6'" H24 SING N N 60 3R2 "C6'" H25 SING N N 61 3R2 "C6'" H26 SING N N 62 3R2 "C7'" H27 SING N N 63 3R2 "C7'" H28 SING N N 64 # 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 3R2 SMILES ACDLabs 12.01 "O=P(OC1CC(C)C(O)C(O)C1)(O)OP(=O)(O)OCC3OC(N2C(=O)NC(=O)C(=C2)C)CC3O" 3R2 InChI InChI 1.03 "InChI=1S/C17H28N2O13P2/c1-8-3-10(4-12(21)15(8)22)31-34(27,28)32-33(25,26)29-7-13-11(20)5-14(30-13)19-6-9(2)16(23)18-17(19)24/h6,8,10-15,20-22H,3-5,7H2,1-2H3,(H,25,26)(H,27,28)(H,18,23,24)/t8-,10-,11-,12+,13+,14+,15+/m0/s1" 3R2 InChIKey InChI 1.03 CWVOKCJHBPKJQP-PVMIAKCWSA-N 3R2 SMILES_CANONICAL CACTVS 3.385 "C[C@H]1C[C@@H](C[C@@H](O)[C@@H]1O)O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O" 3R2 SMILES CACTVS 3.385 "C[CH]1C[CH](C[CH](O)[CH]1O)O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O" 3R2 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C[C@H]1C[C@@H](C[C@H]([C@@H]1O)O)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O" 3R2 SMILES "OpenEye OEToolkits" 1.7.6 "CC1CC(CC(C1O)O)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)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 3R2 "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5'-O-[(R)-{[(R)-{[(1S,3R,4R,5S)-3,4-dihydroxy-5-methylcyclohexyl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-3,4-dihydrothymidine" 3R2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(1S,3S,4R,5R)-3-methyl-4,5-bis(oxidanyl)cyclohexyl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 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 3R2 "Create component" 2014-10-10 RCSB 3R2 "Initial release" 2015-01-28 RCSB #