data_1FZ # _chem_comp.id 1FZ _chem_comp.name "5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H18 N3 O13 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-01-18 _chem_comp.pdbx_modified_date 2013-04-05 _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 481.184 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 1FZ _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 4IR1 _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 1FZ O2 O2 O 0 1 N N N 28.880 26.277 72.639 3.268 -0.588 -1.466 O2 1FZ 1 1FZ O4 O4 O 0 1 N N N 33.328 26.887 72.192 5.893 -3.978 -0.312 O4 1FZ 2 1FZ C4 C4 C 0 1 N N N 32.188 26.748 71.664 5.504 -2.838 -0.135 C4 1FZ 3 1FZ C5 C5 C 0 1 N N N 32.010 26.749 70.162 6.048 -2.051 0.910 C5 1FZ 4 1FZ C6 C6 C 0 1 N N N 30.722 26.585 69.665 5.598 -0.790 1.085 C6 1FZ 5 1FZ C5M C5M C 0 1 N N N 33.167 26.927 69.201 7.114 -2.615 1.814 C5M 1FZ 6 1FZ N3 N3 N 0 1 N N N 31.085 26.590 72.425 4.555 -2.311 -0.934 N3 1FZ 7 1FZ C2 C2 C 0 1 N N N 29.865 26.411 71.892 4.125 -1.051 -0.737 C2 1FZ 8 1FZ N1 N1 N 0 1 N N N 29.663 26.406 70.483 4.629 -0.295 0.255 N1 1FZ 9 1FZ "C1'" C1* C 0 1 N N R 28.287 26.243 69.950 4.141 1.073 0.445 C1* 1FZ 10 1FZ "C2'" C2* C 0 1 N N N 27.736 27.586 69.541 4.505 1.934 -0.780 C2* 1FZ 11 1FZ "C3'" C3* C 0 1 N N S 27.938 27.619 68.037 3.140 2.447 -1.302 C3* 1FZ 12 1FZ "O3'" O3* O 0 1 N N N 26.954 28.453 67.433 3.228 3.816 -1.701 O3* 1FZ 13 1FZ "O4'" O4* O 0 1 N N N 28.237 25.405 68.784 2.709 1.070 0.559 O4* 1FZ 14 1FZ "C4'" C4* C 0 1 N N R 27.796 26.164 67.638 2.236 2.292 -0.052 C4* 1FZ 15 1FZ "C5'" C5* C 0 1 N N N 28.596 25.780 66.408 0.768 2.157 -0.463 C5* 1FZ 16 1FZ "O5'" O5* O 0 1 N N N 29.946 26.150 66.625 -0.053 2.133 0.707 O5* 1FZ 17 1FZ PA PA P 0 1 N N N 30.882 26.852 65.477 -1.656 2.000 0.650 PA 1FZ 18 1FZ O1A O1A O 0 1 N N N 30.410 26.391 64.094 -2.190 2.909 -0.389 O1A 1FZ 19 1FZ O2A O2A O 0 1 N N N 32.331 26.453 65.760 -2.279 2.396 2.080 O2A 1FZ 20 1FZ N3A N3A N 0 1 N N N 30.704 28.449 65.536 -2.075 0.413 0.275 N3A 1FZ 21 1FZ PB PB P 0 1 N N N 29.445 29.324 64.966 -3.746 0.230 0.206 PB 1FZ 22 1FZ O1B O1B O 0 1 N N N 28.676 30.091 66.004 -4.345 1.203 -0.928 O1B 1FZ 23 1FZ O2B O2B O 0 1 N N N 28.422 28.549 64.182 -4.336 0.580 1.517 O2B 1FZ 24 1FZ O3B O3B O 0 1 N N N 30.232 30.427 64.110 -4.105 -1.298 -0.154 O3B 1FZ 25 1FZ PG PG P 0 1 N N N 30.746 30.126 62.609 -5.483 -2.104 -0.363 PG 1FZ 26 1FZ O1G O1G O 0 1 N N N 30.805 28.627 62.392 -6.168 -2.375 1.068 O1G 1FZ 27 1FZ O3G O3G O 0 1 N N N 29.772 30.735 61.661 -6.399 -1.304 -1.206 O3G 1FZ 28 1FZ O2G O2G O 0 1 N N N 32.080 30.825 62.444 -5.177 -3.509 -1.087 O2G 1FZ 29 1FZ H1 H1 H 0 1 N N N 30.565 26.601 68.597 6.001 -0.176 1.876 H1 1FZ 30 1FZ H2 H2 H 0 1 N N N 34.102 27.042 69.769 7.340 -3.638 1.515 H2 1FZ 31 1FZ H3 H3 H 0 1 N N N 33.240 26.045 68.548 8.015 -2.006 1.736 H3 1FZ 32 1FZ H4 H4 H 0 1 N N N 32.999 27.824 68.587 6.758 -2.607 2.844 H4 1FZ 33 1FZ H5 H5 H 0 1 N N N 31.179 26.607 73.420 4.180 -2.842 -1.654 H5 1FZ 34 1FZ H6 H6 H 0 1 N N N 27.644 25.822 70.737 4.584 1.503 1.344 H6 1FZ 35 1FZ H7 H7 H 0 1 N N N 28.290 28.402 70.029 5.139 2.770 -0.485 H7 1FZ 36 1FZ H8 H8 H 0 1 N N N 26.669 27.665 69.795 5.002 1.329 -1.538 H8 1FZ 37 1FZ H9 H9 H 0 1 N N N 28.954 27.972 67.805 2.779 1.827 -2.122 H9 1FZ 38 1FZ H10 H10 H 0 1 N N N 27.085 29.351 67.713 3.852 3.976 -2.423 H10 1FZ 39 1FZ H11 H11 H 0 1 N N N 26.733 25.955 67.445 2.370 3.135 0.626 H11 1FZ 40 1FZ H12 H12 H 0 1 N N N 28.202 26.309 65.527 0.486 3.004 -1.087 H12 1FZ 41 1FZ H13 H13 H 0 1 N N N 28.529 24.694 66.244 0.631 1.232 -1.022 H13 1FZ 42 1FZ H14 H14 H 0 1 N N N 32.682 25.983 65.013 -1.972 1.840 2.810 H14 1FZ 43 1FZ H15 H15 H 0 1 N N N 31.506 28.815 65.064 -1.668 -0.233 0.935 H15 1FZ 44 1FZ H16 H16 H 0 1 N N N 27.749 29.904 65.915 -4.002 1.031 -1.816 H16 1FZ 45 1FZ H17 H17 H 0 1 N N N 30.207 28.384 61.695 -5.623 -2.895 1.674 H17 1FZ 46 1FZ H18 H18 H 0 1 N N N 32.006 31.496 61.776 -5.964 -4.049 -1.245 H18 1FZ 47 # 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 1FZ O3G PG DOUB N N 1 1FZ O1G PG SING N N 2 1FZ O2G PG SING N N 3 1FZ PG O3B SING N N 4 1FZ O1A PA DOUB N N 5 1FZ O3B PB SING N N 6 1FZ O2B PB DOUB N N 7 1FZ PB N3A SING N N 8 1FZ PB O1B SING N N 9 1FZ PA N3A SING N N 10 1FZ PA O2A SING N N 11 1FZ PA "O5'" SING N N 12 1FZ "C5'" "O5'" SING N N 13 1FZ "C5'" "C4'" SING N N 14 1FZ "O3'" "C3'" SING N N 15 1FZ "C4'" "C3'" SING N N 16 1FZ "C4'" "O4'" SING N N 17 1FZ "C3'" "C2'" SING N N 18 1FZ "O4'" "C1'" SING N N 19 1FZ C5M C5 SING N N 20 1FZ "C2'" "C1'" SING N N 21 1FZ C6 C5 DOUB N N 22 1FZ C6 N1 SING N N 23 1FZ "C1'" N1 SING N N 24 1FZ C5 C4 SING N N 25 1FZ N1 C2 SING N N 26 1FZ C4 O4 DOUB N N 27 1FZ C4 N3 SING N N 28 1FZ C2 N3 SING N N 29 1FZ C2 O2 DOUB N N 30 1FZ C6 H1 SING N N 31 1FZ C5M H2 SING N N 32 1FZ C5M H3 SING N N 33 1FZ C5M H4 SING N N 34 1FZ N3 H5 SING N N 35 1FZ "C1'" H6 SING N N 36 1FZ "C2'" H7 SING N N 37 1FZ "C2'" H8 SING N N 38 1FZ "C3'" H9 SING N N 39 1FZ "O3'" H10 SING N N 40 1FZ "C4'" H11 SING N N 41 1FZ "C5'" H12 SING N N 42 1FZ "C5'" H13 SING N N 43 1FZ O2A H14 SING N N 44 1FZ N3A H15 SING N N 45 1FZ O1B H16 SING N N 46 1FZ O1G H17 SING N N 47 1FZ O2G H18 SING N N 48 # 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 1FZ SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O" 1FZ InChI InChI 1.03 "InChI=1S/C10H18N3O13P3/c1-5-3-13(10(16)11-9(5)15)8-2-6(14)7(25-8)4-24-27(17,18)12-28(19,20)26-29(21,22)23/h3,6-8,14H,2,4H2,1H3,(H,11,15,16)(H2,21,22,23)(H3,12,17,18,19,20)/t6-,7+,8+/m0/s1" 1FZ InChIKey InChI 1.03 YRKUYVYMPXAOAT-XLPZGREQSA-N 1FZ SMILES_CANONICAL CACTVS 3.370 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O" 1FZ SMILES CACTVS 3.370 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O" 1FZ SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O" 1FZ SMILES "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(NP(=O)(O)OP(=O)(O)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 1FZ "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine" 1FZ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-N-[oxidanyl(phosphonooxy)phosphoryl]phosphonamidic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 1FZ "Create component" 2013-01-18 RCSB 1FZ "Initial release" 2013-04-10 RCSB #