data_YGP # _chem_comp.id YGP _chem_comp.name "5'-O-[(R)-[(3,6-dimethyl-2-oxo-1,2-dihydropyridin-4-yl)oxy](hydroxy)phosphoryl]guanosine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H21 N6 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-05-30 _chem_comp.pdbx_modified_date 2014-01-31 _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 484.357 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YGP _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 3WB2 _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 YGP C2 C2 C 0 1 N N N 24.457 -49.407 10.945 6.996 -0.232 1.306 C2 YGP 1 YGP N2 N2 N 0 1 N N N 24.788 -50.456 11.691 7.821 0.552 2.072 N2 YGP 2 YGP C4 C4 C 0 1 Y N N 24.306 -48.319 8.866 4.947 -0.532 0.282 C4 YGP 3 YGP C5 C5 C 0 1 Y N N 23.716 -47.225 9.415 5.354 -1.782 -0.197 C5 YGP 4 YGP C6 C6 C 0 1 N N N 23.499 -47.192 10.737 6.659 -2.234 0.112 C6 YGP 5 YGP O6 O6 O 0 1 N N N 22.991 -46.211 11.259 7.056 -3.316 -0.284 O6 YGP 6 YGP N1 N1 N 0 1 N N N 23.843 -48.301 11.559 7.450 -1.440 0.868 N1 YGP 7 YGP N3 N3 N 0 1 N N N 24.660 -49.382 9.600 5.788 0.201 1.021 N3 YGP 8 YGP N7 N7 N 0 1 Y N N 23.488 -46.309 8.454 4.320 -2.298 -0.905 N7 YGP 9 YGP C8 C8 C 0 1 Y N N 23.903 -46.871 7.317 3.326 -1.459 -0.888 C8 YGP 10 YGP N9 N9 N 0 1 Y N N 24.401 -48.101 7.572 3.664 -0.355 -0.162 N9 YGP 11 YGP "C1'" C1* C 0 1 N N R 24.973 -49.102 6.599 2.814 0.811 0.090 "C1'" YGP 12 YGP "O4'" O4* O 0 1 N N N 25.176 -48.541 5.243 1.422 0.463 -0.074 "O4'" YGP 13 YGP "C2'" C2* C 0 1 N N R 23.956 -50.235 6.454 3.076 1.906 -0.967 "C2'" YGP 14 YGP "O2'" O2* O 0 1 N N N 24.626 -51.424 6.160 3.969 2.896 -0.452 "O2'" YGP 15 YGP "C3'" C3* C 0 1 N N S 23.151 -49.781 5.266 1.681 2.516 -1.231 "C3'" YGP 16 YGP "O3'" O3* O 0 1 N N N 22.482 -50.879 4.623 1.669 3.904 -0.888 "O3'" YGP 17 YGP "C4'" C4* C 0 1 N N R 24.219 -49.183 4.343 0.740 1.716 -0.299 "C4'" YGP 18 YGP "C5'" C5* C 0 1 N N N 23.557 -48.099 3.524 -0.608 1.474 -0.982 "C5'" YGP 19 YGP "O5'" O5* O 0 1 N N N 22.742 -47.252 4.377 -1.475 0.772 -0.088 "O5'" YGP 20 YGP PBG PBG P 0 1 N N N 21.932 -46.049 3.674 -2.979 0.350 -0.477 PBG YGP 21 YGP OAI OAI O 0 1 N N N 21.332 -45.117 4.751 -2.941 -0.724 -1.677 OAI YGP 22 YGP OAF OAF O 0 1 N N N 20.877 -46.525 2.771 -3.732 1.548 -0.911 OAF YGP 23 YGP OAR OAR O 0 1 N N N 23.074 -45.177 2.855 -3.701 -0.303 0.805 OAR YGP 24 YGP CAW CAW C 0 1 N N N 24.302 -44.766 3.306 -5.013 -0.583 0.615 CAW YGP 25 YGP CAK CAK C 0 1 N N N 24.523 -44.167 4.559 -5.407 -1.567 -0.314 CAK YGP 26 YGP CAT CAT C 0 1 N N N 25.818 -43.778 4.938 -6.719 -1.835 -0.492 CAT YGP 27 YGP CAA CAA C 0 1 N N N 26.078 -43.204 6.191 -7.134 -2.888 -1.487 CAA YGP 28 YGP NAO NAO N 0 1 N N N 26.885 -43.961 3.997 -7.669 -1.168 0.215 NAO YGP 29 YGP CAX CAX C 0 1 N N N 26.657 -44.547 2.743 -7.332 -0.222 1.111 CAX YGP 30 YGP OAD OAD O 0 1 N N N 27.631 -44.670 1.983 -8.203 0.364 1.735 OAD YGP 31 YGP CAV CAV C 0 1 N N N 25.339 -44.955 2.385 -5.985 0.087 1.334 CAV YGP 32 YGP CAB CAB C 0 1 N N N 25.013 -45.565 1.125 -5.600 1.145 2.336 CAB YGP 33 YGP H1 H1 H 0 1 N N N 25.201 -51.262 11.266 8.714 0.244 2.294 H1 YGP 34 YGP H2 H2 H 0 1 N N N 24.624 -50.440 12.677 7.512 1.415 2.391 H2 YGP 35 YGP H3 H3 H 0 1 N N N 23.654 -48.294 12.541 8.345 -1.732 1.100 H3 YGP 36 YGP H4 H4 H 0 1 N N N 23.849 -46.412 6.341 2.373 -1.617 -1.371 H4 YGP 37 YGP H5 H5 H 0 1 N N N 25.919 -49.504 6.990 2.992 1.201 1.092 H5 YGP 38 YGP H6 H6 H 0 1 N N N 23.327 -50.311 7.353 3.480 1.467 -1.880 H6 YGP 39 YGP H7 H7 H 0 1 N N N 25.130 -51.700 6.917 4.169 3.608 -1.075 H7 YGP 40 YGP H8 H8 H 0 1 N N N 22.437 -49.000 5.566 1.395 2.379 -2.274 H8 YGP 41 YGP H9 H9 H 0 1 N N N 21.825 -51.237 5.208 2.286 4.441 -1.403 H9 YGP 42 YGP H10 H10 H 0 1 N N N 24.683 -49.952 3.708 0.600 2.246 0.642 H10 YGP 43 YGP H11 H11 H 0 1 N N N 24.331 -47.487 3.038 -1.057 2.431 -1.248 H11 YGP 44 YGP H12 H12 H 0 1 N N N 22.920 -48.562 2.756 -0.457 0.880 -1.883 H12 YGP 45 YGP H13 H13 H 0 1 N N N 20.395 -45.037 4.615 -2.397 -1.501 -1.492 H13 YGP 46 YGP H14 H14 H 0 1 N N N 23.694 -44.006 5.232 -4.663 -2.104 -0.882 H14 YGP 47 YGP H16 H16 H 0 1 N N N 25.144 -43.146 6.769 -7.188 -3.856 -0.989 H16 YGP 48 YGP H17 H17 H 0 1 N N N 26.807 -43.823 6.734 -8.112 -2.635 -1.896 H17 YGP 49 YGP H18 H18 H 0 1 N N N 26.487 -42.192 6.053 -6.403 -2.934 -2.293 H18 YGP 50 YGP H19 H19 H 0 1 N N N 23.936 -45.786 1.092 -6.500 1.623 2.724 H19 YGP 51 YGP H20 H20 H 0 1 N N N 25.272 -44.877 0.307 -5.051 0.685 3.157 H20 YGP 52 YGP H21 H21 H 0 1 N N N 25.582 -46.499 1.012 -4.972 1.893 1.852 H21 YGP 53 YGP H15 H15 H 0 1 N N N 27.809 -43.665 4.239 -8.605 -1.377 0.071 H15 YGP 54 # 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 YGP CAB CAV SING N N 1 YGP OAD CAX DOUB N N 2 YGP CAV CAX SING N N 3 YGP CAV CAW DOUB N N 4 YGP CAX NAO SING N N 5 YGP OAF PBG DOUB N N 6 YGP OAR CAW SING N N 7 YGP OAR PBG SING N N 8 YGP CAW CAK SING N N 9 YGP "C5'" "C4'" SING N N 10 YGP "C5'" "O5'" SING N N 11 YGP PBG "O5'" SING N N 12 YGP PBG OAI SING N N 13 YGP NAO CAT SING N N 14 YGP "C4'" "O4'" SING N N 15 YGP "C4'" "C3'" SING N N 16 YGP CAK CAT DOUB N N 17 YGP "O3'" "C3'" SING N N 18 YGP CAT CAA SING N N 19 YGP "O4'" "C1'" SING N N 20 YGP "C3'" "C2'" SING N N 21 YGP "O2'" "C2'" SING N N 22 YGP "C2'" "C1'" SING N N 23 YGP "C1'" N9 SING N N 24 YGP C8 N9 SING Y N 25 YGP C8 N7 DOUB Y N 26 YGP N9 C4 SING Y N 27 YGP N7 C5 SING Y N 28 YGP C4 C5 DOUB Y N 29 YGP C4 N3 SING N N 30 YGP C5 C6 SING N N 31 YGP N3 C2 DOUB N N 32 YGP C6 O6 DOUB N N 33 YGP C6 N1 SING N N 34 YGP C2 N1 SING N N 35 YGP C2 N2 SING N N 36 YGP N2 H1 SING N N 37 YGP N2 H2 SING N N 38 YGP N1 H3 SING N N 39 YGP C8 H4 SING N N 40 YGP "C1'" H5 SING N N 41 YGP "C2'" H6 SING N N 42 YGP "O2'" H7 SING N N 43 YGP "C3'" H8 SING N N 44 YGP "O3'" H9 SING N N 45 YGP "C4'" H10 SING N N 46 YGP "C5'" H11 SING N N 47 YGP "C5'" H12 SING N N 48 YGP OAI H13 SING N N 49 YGP CAK H14 SING N N 50 YGP CAA H16 SING N N 51 YGP CAA H17 SING N N 52 YGP CAA H18 SING N N 53 YGP CAB H19 SING N N 54 YGP CAB H20 SING N N 55 YGP CAB H21 SING N N 56 YGP NAO H15 SING N N 57 # 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 YGP SMILES ACDLabs 12.01 "O=C4NC(=CC(OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O)=C4C)C" YGP InChI InChI 1.03 "InChI=1S/C17H21N6O9P/c1-6-3-8(7(2)14(26)20-6)32-33(28,29)30-4-9-11(24)12(25)16(31-9)23-5-19-10-13(23)21-17(18)22-15(10)27/h3,5,9,11-12,16,24-25H,4H2,1-2H3,(H,20,26)(H,28,29)(H3,18,21,22,27)/t9-,11-,12-,16-/m1/s1" YGP InChIKey InChI 1.03 SHYVQHDJQQBUQP-UBEDBUPSSA-N YGP SMILES_CANONICAL CACTVS 3.385 "CC1=CC(=C(C)C(=O)N1)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC(=Nc34)N" YGP SMILES CACTVS 3.385 "CC1=CC(=C(C)C(=O)N1)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4C(=O)NC(=Nc34)N" YGP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1=CC(=C(C(=O)N1)C)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3N=C(NC4=O)N)O)O" YGP SMILES "OpenEye OEToolkits" 1.7.6 "CC1=CC(=C(C(=O)N1)C)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3N=C(NC4=O)N)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 YGP "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(R)-[(3,6-dimethyl-2-oxo-1,2-dihydropyridin-4-yl)oxy](hydroxy)phosphoryl]guanosine" YGP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl (3,6-dimethyl-2-oxidanylidene-1H-pyridin-4-yl) 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 YGP "Create component" 2013-05-30 PDBJ YGP "Modify atom id" 2013-06-24 PDBJ YGP "Initial release" 2014-02-05 RCSB #