data_YC9 # _chem_comp.id YC9 _chem_comp.name "[(3R)-4-hydroxy-3-{[(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}butyl]phosphonic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H17 N4 O5 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-01-24 _chem_comp.pdbx_modified_date 2023-07-14 _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 316.250 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YC9 _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 8FX0 _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 YC9 C10 C1 C 0 1 N N N 0.484 108.965 102.697 2.646 1.043 -0.155 C10 YC9 1 YC9 C01 C2 C 0 1 N N N -2.668 104.425 106.127 -4.950 -0.830 0.661 C01 YC9 2 YC9 C02 C3 C 0 1 Y N N -2.341 105.673 105.367 -3.799 -0.976 -0.140 C02 YC9 3 YC9 C03 C4 C 0 1 Y N N -1.709 106.707 106.005 -2.957 0.129 -0.307 C03 YC9 4 YC9 C04 C5 C 0 1 Y N N -1.549 107.708 105.049 -1.900 -0.292 -1.143 C04 YC9 5 YC9 C05 C6 C 0 1 Y N N -2.106 107.181 103.888 -2.111 -1.588 -1.454 C05 YC9 6 YC9 C07 C7 C 0 1 N N N -0.901 109.092 105.248 -0.743 0.555 -1.605 C07 YC9 7 YC9 C09 C8 C 0 1 N N R 1.324 109.264 103.957 1.407 1.457 -0.951 C09 YC9 8 YC9 C11 C9 C 0 1 N N N 1.304 108.676 101.448 3.026 -0.395 -0.514 C11 YC9 9 YC9 C16 C10 C 0 1 N N N 2.704 108.547 103.951 1.101 2.933 -0.688 C16 YC9 10 YC9 C19 C11 C 0 1 N N N -1.696 105.355 108.153 -4.334 1.410 1.036 C19 YC9 11 YC9 N06 N1 N 0 1 Y N N -2.554 105.977 104.112 -3.256 -2.017 -0.856 N06 YC9 12 YC9 N08 N2 N 0 1 N N N 0.571 109.062 105.212 0.261 0.637 -0.536 N08 YC9 13 YC9 N18 N3 N 0 1 N N N -1.371 106.567 107.423 -3.266 1.299 0.301 N18 YC9 14 YC9 N20 N4 N 0 1 N N N -2.348 104.276 107.475 -5.187 0.371 1.232 N20 YC9 15 YC9 O13 O1 O 0 1 N N N 0.920 108.277 98.968 4.250 -0.687 1.880 O13 YC9 16 YC9 O14 O2 O 0 1 N N N 0.407 110.473 99.671 4.825 -2.441 0.158 O14 YC9 17 YC9 O15 O3 O 0 1 N N N -1.131 108.876 100.237 5.758 0.011 -0.021 O15 YC9 18 YC9 O17 O4 O 0 1 N N N 3.242 108.645 105.253 0.972 3.148 0.719 O17 YC9 19 YC9 O21 O5 O 0 1 N N N -3.189 103.571 105.588 -5.716 -1.764 0.831 O21 YC9 20 YC9 P12 P1 P 0 1 N N N 0.286 109.056 99.974 4.503 -0.888 0.435 P12 YC9 21 YC9 H101 H1 H 0 0 N N N -0.155 109.837 102.495 3.474 1.709 -0.399 H101 YC9 22 YC9 H102 H2 H 0 0 N N N -0.147 108.088 102.905 2.431 1.107 0.911 H102 YC9 23 YC9 H051 H3 H 0 0 N N N -2.160 107.694 102.939 -1.471 -2.190 -2.082 H051 YC9 24 YC9 H072 H4 H 0 0 N N N -1.255 109.760 104.449 -0.294 0.105 -2.490 H072 YC9 25 YC9 H071 H5 H 0 0 N N N -1.217 109.487 106.224 -1.099 1.556 -1.847 H071 YC9 26 YC9 H091 H6 H 0 0 N N N 1.554 110.339 103.908 1.593 1.309 -2.015 H091 YC9 27 YC9 H112 H7 H 0 0 N N N 1.594 107.615 101.433 2.198 -1.061 -0.270 H112 YC9 28 YC9 H111 H8 H 0 0 N N N 2.207 109.304 101.445 3.242 -0.458 -1.580 H111 YC9 29 YC9 H162 H9 H 0 0 N N N 2.576 107.489 103.677 1.912 3.547 -1.077 H162 YC9 30 YC9 H161 H10 H 0 0 N N N 3.377 109.034 103.230 0.169 3.204 -1.184 H161 YC9 31 YC9 H191 H11 H 0 0 N N N -1.448 105.268 109.200 -4.549 2.359 1.505 H191 YC9 32 YC9 H1 H12 H 0 1 N N N -2.989 105.383 103.435 -3.628 -2.911 -0.924 H1 YC9 33 YC9 H2 H13 H 0 1 N N N 0.842 108.165 105.561 0.560 -0.283 -0.249 H2 YC9 34 YC9 H201 H15 H 0 0 N N N -2.570 103.430 107.960 -5.973 0.493 1.788 H201 YC9 35 YC9 H3 H16 H 0 1 N N N 0.887 110.584 98.859 5.600 -2.772 0.632 H3 YC9 36 YC9 H4 H17 H 0 1 N N N -1.479 108.209 99.657 5.981 -0.071 -0.958 H4 YC9 37 YC9 H171 H18 H 0 0 N N N 4.088 108.214 105.280 0.777 4.064 0.960 H171 YC9 38 # 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 YC9 O13 P12 DOUB N N 1 YC9 O14 P12 SING N N 2 YC9 P12 O15 SING N N 3 YC9 P12 C11 SING N N 4 YC9 C11 C10 SING N N 5 YC9 C10 C09 SING N N 6 YC9 C05 N06 SING Y N 7 YC9 C05 C04 DOUB Y N 8 YC9 C16 C09 SING N N 9 YC9 C16 O17 SING N N 10 YC9 C09 N08 SING N N 11 YC9 N06 C02 SING Y N 12 YC9 C04 C07 SING N N 13 YC9 C04 C03 SING Y N 14 YC9 N08 C07 SING N N 15 YC9 C02 C03 DOUB Y N 16 YC9 C02 C01 SING N N 17 YC9 O21 C01 DOUB N N 18 YC9 C03 N18 SING N N 19 YC9 C01 N20 SING N N 20 YC9 N18 C19 DOUB N N 21 YC9 N20 C19 SING N N 22 YC9 C10 H101 SING N N 23 YC9 C10 H102 SING N N 24 YC9 C05 H051 SING N N 25 YC9 C07 H072 SING N N 26 YC9 C07 H071 SING N N 27 YC9 C09 H091 SING N N 28 YC9 C11 H112 SING N N 29 YC9 C11 H111 SING N N 30 YC9 C16 H162 SING N N 31 YC9 C16 H161 SING N N 32 YC9 C19 H191 SING N N 33 YC9 N06 H1 SING N N 34 YC9 N08 H2 SING N N 35 YC9 N20 H201 SING N N 36 YC9 O14 H3 SING N N 37 YC9 O15 H4 SING N N 38 YC9 O17 H171 SING N N 39 # 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 YC9 SMILES ACDLabs 12.01 "O=P(O)(O)CCC(CO)NCc1c[NH]c2c1N=CNC2=O" YC9 InChI InChI 1.06 "InChI=1S/C11H17N4O5P/c16-5-8(1-2-21(18,19)20)12-3-7-4-13-10-9(7)14-6-15-11(10)17/h4,6,8,12-13,16H,1-3,5H2,(H,14,15,17)(H2,18,19,20)/t8-/m1/s1" YC9 InChIKey InChI 1.06 YYXVNWBGVIIBOW-MRVPVSSYSA-N YC9 SMILES_CANONICAL CACTVS 3.385 "OC[C@@H](CC[P](O)(O)=O)NCc1c[nH]c2C(=O)NC=Nc12" YC9 SMILES CACTVS 3.385 "OC[CH](CC[P](O)(O)=O)NCc1c[nH]c2C(=O)NC=Nc12" YC9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1c(c2c([nH]1)C(=O)NC=N2)CN[C@H](CCP(=O)(O)O)CO" YC9 SMILES "OpenEye OEToolkits" 2.0.7 "c1c(c2c([nH]1)C(=O)NC=N2)CNC(CCP(=O)(O)O)CO" # 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 YC9 "SYSTEMATIC NAME" ACDLabs 12.01 "[(3R)-4-hydroxy-3-{[(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}butyl]phosphonic acid" YC9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(3~{R})-4-oxidanyl-3-[(4-oxidanylidene-3,5-dihydropyrrolo[3,2-d]pyrimidin-7-yl)methylamino]butyl]phosphonic 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 YC9 "Create component" 2023-01-24 RCSB YC9 "Initial release" 2023-07-19 RCSB #