data_9RC # _chem_comp.id 9RC _chem_comp.name "5'-O-[(S)-hydroxy(4-nitrophenoxy)phosphoryl]thymidine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H18 N3 O10 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms PNP-TMP _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-06-28 _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 443.302 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 9RC _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 6A4D _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 9RC OAJ O1 O 0 1 N N N -15.167 -31.961 -19.707 3.648 -0.124 -1.584 OAJ 9RC 1 9RC CAE C1 C 0 1 N N N -14.499 -32.964 -19.968 4.433 -0.688 -0.847 CAE 9RC 2 9RC NAI N1 N 0 1 N N N -15.049 -34.218 -19.756 5.107 -1.765 -1.295 NAI 9RC 3 9RC CAL C2 C 0 1 N N N -14.312 -35.372 -20.053 5.981 -2.402 -0.490 CAL 9RC 4 9RC OAS O2 O 0 1 N N N -14.847 -36.466 -19.842 6.591 -3.376 -0.894 OAS 9RC 5 9RC CAT C3 C 0 1 N N N -13.018 -35.261 -20.584 6.185 -1.928 0.828 CAT 9RC 6 9RC CAU C4 C 0 1 N N N -12.252 -36.393 -20.910 7.157 -2.621 1.747 CAU 9RC 7 9RC CAF C5 C 0 1 N N N -12.491 -33.996 -20.773 5.497 -0.846 1.251 CAF 9RC 8 9RC NAB N2 N 0 1 N N N -13.257 -32.852 -20.457 4.622 -0.225 0.402 NAB 9RC 9 9RC CAA C6 C 0 1 N N R -12.730 -31.496 -20.628 3.875 0.949 0.860 CAA 9RC 10 9RC OAC O3 O 0 1 N N N -12.635 -31.146 -21.984 2.469 0.754 0.633 OAC 9RC 11 9RC CAD C7 C 0 1 N N N -11.311 -31.431 -20.123 4.302 2.190 0.052 CAD 9RC 12 9RC CAH C8 C 0 1 N N S -10.879 -30.140 -20.692 2.989 2.689 -0.598 CAH 9RC 13 9RC OAK O4 O 0 1 N N N -11.180 -29.150 -19.744 2.908 4.115 -0.555 OAK 9RC 14 9RC CAG C9 C 0 1 N N R -11.761 -30.004 -21.923 1.911 2.046 0.311 CAG 9RC 15 9RC CAR C10 C 0 1 N N N -10.886 -30.106 -23.128 0.591 1.888 -0.447 CAR 9RC 16 9RC OAQ O5 O 0 1 N N N -11.766 -30.160 -24.240 -0.387 1.305 0.417 OAQ 9RC 17 9RC PAP P1 P 0 1 N N N -11.153 -30.316 -25.686 -1.896 0.995 -0.051 PAP 9RC 18 9RC OAO O6 O 0 1 N N N -12.410 -30.089 -26.657 -1.872 0.146 -1.263 OAO 9RC 19 9RC OAN O7 O 0 1 N N N -10.770 -31.740 -25.818 -2.652 2.378 -0.379 OAN 9RC 20 9RC OAM O8 O 0 1 N N N -10.019 -29.242 -25.603 -2.676 0.224 1.128 OAM 9RC 21 9RC CAV C11 C 0 1 Y N N -8.970 -28.713 -26.346 -3.929 -0.179 0.791 CAV 9RC 22 9RC CAW C12 C 0 1 Y N N -8.194 -27.635 -25.783 -4.128 -1.431 0.227 CAW 9RC 23 9RC CAY C13 C 0 1 Y N N -7.131 -27.011 -26.531 -5.403 -1.838 -0.114 CAY 9RC 24 9RC CBA C14 C 0 1 Y N N -6.807 -27.472 -27.845 -6.480 -0.999 0.105 CBA 9RC 25 9RC NBB N3 N 1 1 N N N -5.825 -26.978 -28.690 -7.845 -1.439 -0.262 NBB 9RC 26 9RC OBD O9 O -1 1 N N N -4.829 -27.950 -29.539 -8.019 -2.538 -0.757 OBD 9RC 27 9RC OBC O10 O 0 1 N N N -5.780 -25.622 -28.925 -8.795 -0.701 -0.069 OBC 9RC 28 9RC CAZ C15 C 0 1 Y N N -7.584 -28.526 -28.336 -6.285 0.249 0.667 CAZ 9RC 29 9RC CAX C16 C 0 1 Y N N -8.646 -29.151 -27.641 -5.012 0.659 1.015 CAX 9RC 30 9RC H1 H1 H 0 1 N N N -15.976 -34.300 -19.389 4.962 -2.083 -2.199 H1 9RC 31 9RC H2 H2 H 0 1 N N N -12.831 -37.303 -20.694 7.610 -3.466 1.227 H2 9RC 32 9RC H3 H3 H 0 1 N N N -11.996 -36.367 -21.979 7.936 -1.920 2.048 H3 9RC 33 9RC H4 H4 H 0 1 N N N -11.329 -36.396 -20.312 6.630 -2.980 2.631 H4 9RC 34 9RC H5 H5 H 0 1 N N N -11.490 -33.883 -21.164 5.639 -0.470 2.253 H5 9RC 35 9RC H6 H6 H 0 1 N N N -13.351 -30.775 -20.076 4.062 1.116 1.921 H6 9RC 36 9RC H7 H7 H 0 1 N N N -10.706 -32.266 -20.506 4.714 2.953 0.713 H7 9RC 37 9RC H8 H8 H 0 1 N N N -11.272 -31.423 -19.024 5.029 1.916 -0.712 H8 9RC 38 9RC H9 H9 H 0 1 N N N -9.815 -30.155 -20.970 2.900 2.328 -1.623 H9 9RC 39 9RC H10 H10 H 0 1 N N N -10.617 -29.255 -18.986 3.616 4.564 -1.036 H10 9RC 40 9RC H11 H11 H 0 1 N N N -12.316 -29.054 -21.908 1.768 2.638 1.215 H11 9RC 41 9RC H12 H12 H 0 1 N N N -10.273 -31.018 -23.080 0.244 2.867 -0.780 H12 9RC 42 9RC H13 H13 H 0 1 N N N -10.230 -29.226 -23.201 0.743 1.243 -1.311 H13 9RC 43 9RC H14 H14 H 0 1 N N N -11.351 -32.169 -26.435 -2.705 2.985 0.372 H14 9RC 44 9RC H15 H15 H 0 1 N N N -8.413 -27.289 -24.784 -3.287 -2.086 0.055 H15 9RC 45 9RC H16 H16 H 0 1 N N N -6.577 -26.192 -26.097 -5.559 -2.812 -0.553 H16 9RC 46 9RC H17 H17 H 0 1 N N N -7.355 -28.892 -29.326 -7.127 0.902 0.837 H17 9RC 47 9RC H18 H18 H 0 1 N N N -9.201 -29.955 -28.101 -4.860 1.634 1.454 H18 9RC 48 # # 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 9RC OBD NBB SING N N 1 9RC OBC NBB DOUB N N 2 9RC NBB CBA SING N N 3 9RC CAZ CBA DOUB Y N 4 9RC CAZ CAX SING Y N 5 9RC CBA CAY SING Y N 6 9RC CAX CAV DOUB Y N 7 9RC OAO PAP DOUB N N 8 9RC CAY CAW DOUB Y N 9 9RC CAV CAW SING Y N 10 9RC CAV OAM SING N N 11 9RC OAN PAP SING N N 12 9RC PAP OAM SING N N 13 9RC PAP OAQ SING N N 14 9RC OAQ CAR SING N N 15 9RC CAR CAG SING N N 16 9RC OAC CAG SING N N 17 9RC OAC CAA SING N N 18 9RC CAG CAH SING N N 19 9RC CAU CAT SING N N 20 9RC CAF CAT DOUB N N 21 9RC CAF NAB SING N N 22 9RC CAH CAD SING N N 23 9RC CAH OAK SING N N 24 9RC CAA NAB SING N N 25 9RC CAA CAD SING N N 26 9RC CAT CAL SING N N 27 9RC NAB CAE SING N N 28 9RC CAL OAS DOUB N N 29 9RC CAL NAI SING N N 30 9RC CAE NAI SING N N 31 9RC CAE OAJ DOUB N N 32 9RC NAI H1 SING N N 33 9RC CAU H2 SING N N 34 9RC CAU H3 SING N N 35 9RC CAU H4 SING N N 36 9RC CAF H5 SING N N 37 9RC CAA H6 SING N N 38 9RC CAD H7 SING N N 39 9RC CAD H8 SING N N 40 9RC CAH H9 SING N N 41 9RC OAK H10 SING N N 42 9RC CAG H11 SING N N 43 9RC CAR H12 SING N N 44 9RC CAR H13 SING N N 45 9RC OAN H14 SING N N 46 9RC CAW H15 SING N N 47 9RC CAY H16 SING N N 48 9RC CAZ H17 SING N N 49 9RC CAX H18 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 9RC SMILES ACDLabs 12.01 "O=C1NC(=O)C(C)=CN1C2CC(O)C(O2)COP(Oc3ccc([N+]([O-])=O)cc3)(=O)O" 9RC InChI InChI 1.03 "InChI=1S/C16H18N3O10P/c1-9-7-18(16(22)17-15(9)21)14-6-12(20)13(28-14)8-27-30(25,26)29-11-4-2-10(3-5-11)19(23)24/h2-5,7,12-14,20H,6,8H2,1H3,(H,25,26)(H,17,21,22)/t12-,13+,14+/m0/s1" 9RC InChIKey InChI 1.03 RWOAVOYBVRQNIZ-BFHYXJOUSA-N 9RC SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)Oc3ccc(cc3)[N+]([O-])=O)O2)C(=O)NC1=O" 9RC SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)Oc3ccc(cc3)[N+]([O-])=O)O2)C(=O)NC1=O" 9RC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)Oc3ccc(cc3)[N+](=O)[O-])O" 9RC SMILES "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)Oc3ccc(cc3)[N+](=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 9RC "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(S)-hydroxy(4-nitrophenoxy)phosphoryl]thymidine" 9RC "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl (4-nitrophenyl) 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 9RC "Create component" 2018-06-28 PDBJ 9RC "Initial release" 2019-03-13 RCSB 9RC "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 9RC _pdbx_chem_comp_synonyms.name PNP-TMP _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##