data_P1D # _chem_comp.id P1D _chem_comp.name ;((2S,3AS,4R,6S)-4-(HYDROXYMETHYL)-6-(4-OXO-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-TETRAHYDROFURO[3,4-D][1,3]DIOXO L-2-YL)METHYLPHOSPHONIC ACID ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C13 H16 N3 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "9-DEAZAINOSINE-2',3'-O-ETHYLIDENEPHOSPHONATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2005-08-04 _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 373.255 _chem_comp.one_letter_code ? _chem_comp.three_letter_code P1D _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 2AI2 _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 P1D O3 O3 O 0 1 N N N 68.130 -40.506 96.449 4.319 0.185 0.389 O3 P1D 1 P1D P P P 0 1 N N N 66.583 -40.898 96.634 3.741 -1.317 0.441 P P1D 2 P1D O4 O4 O 0 1 N N N 65.769 -39.618 97.137 4.883 -2.313 0.987 O4 P1D 3 P1D O2 O2 O 0 1 N N N 65.966 -41.382 95.372 2.571 -1.365 1.346 O2 P1D 4 P1D C1P C1P C 0 1 N N N 66.457 -42.156 97.927 3.236 -1.833 -1.233 C1P P1D 5 P1D C1 C1 C 0 1 N N S 65.218 -43.061 97.773 2.067 -0.965 -1.703 C1 P1D 6 P1D "O3'" "O3'" O 0 1 N N N 65.041 -43.786 99.008 2.431 0.424 -1.660 "O3'" P1D 7 P1D "O2'" "O2'" O 0 1 N N N 65.318 -44.106 96.783 0.948 -1.113 -0.804 "O2'" P1D 8 P1D "C2'" "C2'" C 0 1 N N S 65.798 -45.317 97.404 0.165 0.082 -1.032 "C2'" P1D 9 P1D "C3'" "C3'" C 0 1 N N R 65.548 -45.129 98.894 1.242 1.174 -1.314 "C3'" P1D 10 P1D "C4'" "C4'" C 0 1 N N R 66.899 -45.269 99.587 1.438 1.807 0.084 "C4'" P1D 11 P1D "C5'" "C5'" C 0 1 N N N 67.007 -46.598 100.351 1.931 3.250 -0.044 "C5'" P1D 12 P1D "O5'" "O5'" O 0 1 N N N 68.339 -46.808 100.827 2.171 3.789 1.257 "O5'" P1D 13 P1D "O4'" "O4'" O 0 1 N N N 67.854 -45.049 98.522 0.120 1.773 0.670 "O4'" P1D 14 P1D "C1'" "C1'" C 0 1 N N S 67.310 -45.546 97.278 -0.469 0.515 0.303 "C1'" P1D 15 P1D C9 C9 C 0 1 Y N N 67.848 -46.939 96.900 -1.958 0.676 0.137 C9 P1D 16 P1D C8 C8 C 0 1 Y N N 69.111 -47.316 97.103 -2.607 1.826 -0.140 C8 P1D 17 P1D N7 N7 N 0 1 Y N N 69.255 -48.597 96.767 -3.944 1.584 -0.217 N7 P1D 18 P1D C5 C5 C 0 1 Y N N 68.084 -49.071 96.347 -4.167 0.247 0.016 C5 P1D 19 P1D C4 C4 C 0 1 Y N N 67.145 -48.037 96.404 -2.921 -0.350 0.237 C4 P1D 20 P1D N3 N3 N 0 1 Y N N 65.842 -48.212 96.066 -2.858 -1.678 0.500 N3 P1D 21 P1D C2 C2 C 0 1 Y N N 65.356 -49.383 95.660 -3.936 -2.405 0.538 C2 P1D 22 P1D N1 N1 N 0 1 Y N N 66.257 -50.467 95.574 -5.170 -1.880 0.326 N1 P1D 23 P1D C6 C6 C 0 1 Y N N 67.618 -50.322 95.920 -5.320 -0.563 0.063 C6 P1D 24 P1D O6 O6 O 0 1 N N N 68.350 -51.314 95.901 -6.426 -0.086 -0.128 O6 P1D 25 P1D HO3 HO3 H 0 1 N N N 68.613 -41.266 96.150 5.078 0.172 -0.210 HO3 P1D 26 P1D HO4 HO4 H 0 1 N N N 64.854 -39.849 97.246 5.121 -2.006 1.873 HO4 P1D 27 P1D H1P1 1H1P H 0 0 N N N 67.389 -42.765 97.980 2.929 -2.878 -1.214 H1P1 P1D 28 P1D H1P2 2H1P H 0 0 N N N 66.484 -41.689 98.939 4.075 -1.713 -1.919 H1P2 P1D 29 P1D H1 H1 H 0 1 N N N 64.399 -42.363 97.478 1.775 -1.246 -2.715 H1 P1D 30 P1D "H2'" "H2'" H 0 1 N N N 65.282 -46.174 96.912 -0.562 -0.028 -1.836 "H2'" P1D 31 P1D "H3'" "H3'" H 0 1 N N N 64.837 -45.859 99.347 0.957 1.896 -2.080 "H3'" P1D 32 P1D "H4'" "H4'" H 0 1 N N N 67.083 -44.535 100.406 2.136 1.216 0.677 "H4'" P1D 33 P1D "H5'1" "1H5'" H 0 0 N N N 66.260 -46.659 101.176 1.175 3.849 -0.552 "H5'1" P1D 34 P1D "H5'2" "2H5'" H 0 0 N N N 66.649 -47.456 99.735 2.856 3.268 -0.621 "H5'2" P1D 35 P1D "H5'" "H5'" H 0 1 N N N 68.405 -47.629 101.299 2.480 4.696 1.132 "H5'" P1D 36 P1D "H1'" "H1'" H 0 1 N N N 67.650 -45.006 96.363 -0.261 -0.230 1.071 "H1'" P1D 37 P1D H8 H8 H 0 1 N N N 69.914 -46.666 97.490 -2.138 2.789 -0.279 H8 P1D 38 P1D HN7 HN7 H 0 1 N N N 70.123 -49.129 96.822 -4.628 2.247 -0.405 HN7 P1D 39 P1D H2 H2 H 0 1 N N N 64.283 -49.450 95.412 -3.847 -3.462 0.746 H2 P1D 40 P1D HN1 HN1 H 0 1 N N N 65.917 -51.374 95.255 -5.951 -2.454 0.363 HN1 P1D 41 # # 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 P1D O3 P SING N N 1 P1D O3 HO3 SING N N 2 P1D P O4 SING N N 3 P1D P O2 DOUB N N 4 P1D P C1P SING N N 5 P1D O4 HO4 SING N N 6 P1D C1P C1 SING N N 7 P1D C1P H1P1 SING N N 8 P1D C1P H1P2 SING N N 9 P1D C1 "O3'" SING N N 10 P1D C1 "O2'" SING N N 11 P1D C1 H1 SING N N 12 P1D "O3'" "C3'" SING N N 13 P1D "O2'" "C2'" SING N N 14 P1D "C2'" "C3'" SING N N 15 P1D "C2'" "C1'" SING N N 16 P1D "C2'" "H2'" SING N N 17 P1D "C3'" "C4'" SING N N 18 P1D "C3'" "H3'" SING N N 19 P1D "C4'" "C5'" SING N N 20 P1D "C4'" "O4'" SING N N 21 P1D "C4'" "H4'" SING N N 22 P1D "C5'" "O5'" SING N N 23 P1D "C5'" "H5'1" SING N N 24 P1D "C5'" "H5'2" SING N N 25 P1D "O5'" "H5'" SING N N 26 P1D "O4'" "C1'" SING N N 27 P1D "C1'" C9 SING N N 28 P1D "C1'" "H1'" SING N N 29 P1D C9 C8 DOUB Y N 30 P1D C9 C4 SING Y N 31 P1D C8 N7 SING Y N 32 P1D C8 H8 SING N N 33 P1D N7 C5 SING Y N 34 P1D N7 HN7 SING N N 35 P1D C5 C4 DOUB Y N 36 P1D C5 C6 SING Y N 37 P1D C4 N3 SING Y N 38 P1D N3 C2 DOUB Y N 39 P1D C2 N1 SING Y N 40 P1D C2 H2 SING N N 41 P1D N1 C6 SING Y N 42 P1D N1 HN1 SING N N 43 P1D C6 O6 DOUB N N 44 # # 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 P1D SMILES ACDLabs 10.04 "O=C1NC=Nc2c1ncc2C3OC(C4OC(OC34)CP(=O)(O)O)CO" P1D SMILES_CANONICAL CACTVS 3.341 "OC[C@H]1O[C@H]([C@@H]2O[C@H](C[P](O)(O)=O)O[C@H]12)c3c[nH]c4C(=O)NC=Nc34" P1D SMILES CACTVS 3.341 "OC[CH]1O[CH]([CH]2O[CH](C[P](O)(O)=O)O[CH]12)c3c[nH]c4C(=O)NC=Nc34" P1D SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1c(c2c([nH]1)C(=O)NC=N2)[C@H]3[C@H]4[C@@H]([C@H](O3)CO)O[C@H](O4)CP(=O)(O)O" P1D SMILES "OpenEye OEToolkits" 1.5.0 "c1c(c2c([nH]1)C(=O)NC=N2)C3C4C(C(O3)CO)OC(O4)CP(=O)(O)O" P1D InChI InChI 1.03 "InChI=1S/C13H16N3O8P/c17-2-6-11-12(24-7(23-11)3-25(19,20)21)10(22-6)5-1-14-9-8(5)15-4-16-13(9)18/h1,4,6-7,10-12,14,17H,2-3H2,(H,15,16,18)(H2,19,20,21)/t6-,7-,10+,11-,12+/m1/s1" P1D InChIKey InChI 1.03 ZOEDLCUBOBTIHG-USQSKNHBSA-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 P1D "SYSTEMATIC NAME" ACDLabs 10.04 "(1S)-1,4-anhydro-1-(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)-2,3-O-[(1S)-2-phosphonoethylidene]-D-ribitol" P1D "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S,3aS,4S,6R,6aR)-6-(hydroxymethyl)-4-(4-oxo-3,5-dihydropyrrolo[4,5-d]pyrimidin-7-yl)-3a,4,6,6a-tetrahydrofuro[4,3-d][1,3]dioxol-2-yl]methylphosphonic 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 P1D "Create component" 2005-08-04 RCSB P1D "Modify descriptor" 2011-06-04 RCSB P1D "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id P1D _pdbx_chem_comp_synonyms.name "9-DEAZAINOSINE-2',3'-O-ETHYLIDENEPHOSPHONATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##