data_GPD # _chem_comp.id GPD _chem_comp.name "(2R,3S,5S,6R)-5-amino-3-hydroxy-6-methyl-oxan-2-yl" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H26 N6 O13 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-08-12 _chem_comp.pdbx_modified_date 2011-06-04 _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 572.358 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GPD _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 3DR7 _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 GPD N4A N4A N 0 1 N N N 15.953 -2.774 -4.088 -5.754 3.732 -2.372 N4A GPD 1 GPD C4G C4G C 0 1 N N S 17.294 -2.678 -4.620 -6.409 2.794 -1.450 C4G GPD 2 GPD C5G C5G C 0 1 N N R 18.274 -3.343 -3.672 -5.597 2.698 -0.156 C5G GPD 3 GPD C6G C6G C 0 1 N N N 17.968 -4.820 -3.429 -5.565 4.065 0.530 C6G GPD 4 GPD O5G O5G O 0 1 N N N 19.657 -3.158 -3.973 -6.204 1.742 0.715 O5G GPD 5 GPD C3G C3G C 0 1 N N N 17.583 -1.191 -4.782 -6.486 1.409 -2.099 C3G GPD 6 GPD C2G C2G C 0 1 N N S 19.079 -0.962 -4.839 -7.099 0.423 -1.101 C2G GPD 7 GPD O2G O2G O 0 1 N N N 19.434 -0.165 -5.965 -8.437 0.822 -0.795 O2G GPD 8 GPD C1G C1G C 0 1 N N R 19.896 -2.224 -5.008 -6.261 0.418 0.180 C1G GPD 9 GPD O1G O1G O 0 1 N N N 21.181 -1.666 -4.831 -4.938 -0.033 -0.118 O1G GPD 10 GPD P2 P2 P 0 1 N N S 22.474 -1.954 -5.712 -4.018 -0.818 0.945 P2 GPD 11 GPD O3P O3P O 0 1 N N N 22.606 -3.446 -5.825 -4.746 -2.007 1.443 O3P GPD 12 GPD O4P O4P O 0 1 N N N 23.530 -1.153 -4.987 -3.674 0.156 2.179 O4P GPD 13 GPD OPP OPP O 0 1 N N N 22.077 -1.240 -7.102 -2.653 -1.285 0.232 OPP GPD 14 GPD P P P 0 1 N N S 23.091 -1.036 -8.331 -1.542 -2.402 0.564 P GPD 15 GPD O1P O1P O 0 1 N N N 24.484 -1.441 -7.956 -2.071 -3.845 0.083 O1P GPD 16 GPD O2P O2P O 0 1 N N N 22.913 0.366 -8.811 -1.293 -2.430 2.023 O2P GPD 17 GPD "O5'" "O5'" O 0 1 N N N 22.509 -1.992 -9.489 -0.175 -2.046 -0.207 "O5'" GPD 18 GPD "C5'" "C5'" C 0 1 N N N 22.692 -3.401 -9.479 1.033 -2.790 -0.034 "C5'" GPD 19 GPD "C4'" "C4'" C 0 1 N N R 23.214 -3.807 -10.835 2.133 -2.188 -0.910 "C4'" GPD 20 GPD "O4'" "O4'" O 0 1 N N N 22.308 -3.345 -11.854 2.471 -0.874 -0.436 "O4'" GPD 21 GPD "C3'" "C3'" C 0 1 N N S 24.543 -3.109 -11.090 3.406 -3.052 -0.821 "C3'" GPD 22 GPD "O3'" "O3'" O 0 1 N N N 25.396 -4.062 -11.729 3.760 -3.556 -2.110 "O3'" GPD 23 GPD "C2'" "C2'" C 0 1 N N R 24.224 -2.027 -12.110 4.490 -2.078 -0.301 "C2'" GPD 24 GPD "O2'" "O2'" O 0 1 N N N 25.314 -1.866 -13.018 5.732 -2.288 -0.977 "O2'" GPD 25 GPD "C1'" "C1'" C 0 1 N N R 23.017 -2.598 -12.827 3.885 -0.694 -0.665 "C1'" GPD 26 GPD N9 N9 N 0 1 Y N N 22.166 -1.535 -13.392 4.420 0.353 0.209 N9 GPD 27 GPD C8 C8 C 0 1 Y N N 21.343 -0.739 -12.715 3.887 0.765 1.396 C8 GPD 28 GPD N7 N7 N 0 1 Y N N 20.759 0.105 -13.587 4.620 1.711 1.904 N7 GPD 29 GPD C4 C4 C 0 1 Y N N 22.119 -1.212 -14.686 5.550 1.093 -0.013 C4 GPD 30 GPD C5 C5 C 0 1 Y N N 21.223 -0.165 -14.822 5.664 1.964 1.077 C5 GPD 31 GPD C6 C6 C 0 1 N N N 20.986 0.367 -16.090 6.754 2.864 1.114 C6 GPD 32 GPD O6 O6 O 0 1 N N N 20.186 1.285 -16.316 6.896 3.636 2.046 O6 GPD 33 GPD N3 N3 N 0 1 N N N 22.748 -1.711 -15.773 6.466 1.128 -0.987 N3 GPD 34 GPD C2 C2 C 0 1 N N N 22.512 -1.177 -16.984 7.478 1.966 -0.939 C2 GPD 35 GPD N1 N1 N 0 1 N N N 21.640 -0.162 -17.130 7.636 2.846 0.090 N1 GPD 36 GPD N2 N2 N 0 1 N N N 23.134 -1.643 -18.098 8.393 1.965 -1.962 N2 GPD 37 GPD HN4A HN4A H 0 0 N N N 15.991 -2.796 -3.089 -6.272 3.813 -3.234 HN4A GPD 38 GPD HN4B HN4B H 0 0 N N N 15.420 -1.981 -4.384 -5.629 4.635 -1.940 HN4B GPD 39 GPD H4G H4G H 0 1 N N N 17.394 -3.192 -5.587 -7.415 3.148 -1.224 H4G GPD 40 GPD H5G H5G H 0 1 N N N 18.104 -2.791 -2.736 -4.579 2.384 -0.388 H5G GPD 41 GPD H6G H6G H 0 1 N N N 17.894 -5.343 -4.394 -6.583 4.379 0.762 H6G GPD 42 GPD H6GA H6GA H 0 0 N N N 18.775 -5.268 -2.830 -4.987 3.997 1.451 H6GA GPD 43 GPD H6GB H6GB H 0 0 N N N 17.014 -4.912 -2.888 -5.103 4.795 -0.136 H6GB GPD 44 GPD H3G H3G H 0 1 N N N 17.123 -0.830 -5.714 -7.110 1.459 -2.992 H3G GPD 45 GPD H3GA H3GA H 0 0 N N N 17.164 -0.644 -3.924 -5.485 1.078 -2.373 H3GA GPD 46 GPD H2G H2G H 0 1 N N N 19.301 -0.486 -3.873 -7.108 -0.577 -1.534 H2G GPD 47 GPD HO2G HO2G H 0 0 N N N 19.513 0.743 -5.698 -8.887 0.240 -0.167 HO2G GPD 48 GPD H1G H1G H 0 1 N N N 19.702 -2.772 -5.942 -6.716 -0.250 0.911 H1G GPD 49 GPD HO4P HO4P H 0 0 N N N 24.259 -0.985 -5.573 -3.195 0.958 1.926 HO4P GPD 50 GPD HO1P HO1P H 0 0 N N N 25.012 -1.527 -8.741 -2.256 -3.899 -0.865 HO1P GPD 51 GPD "H5'" "H5'" H 0 1 N N N 23.414 -3.682 -8.698 1.338 -2.750 1.012 "H5'" GPD 52 GPD "H5'A" "H5'A" H 0 0 N N N 21.740 -3.910 -9.266 0.865 -3.828 -0.323 "H5'A" GPD 53 GPD "H4'" "H4'" H 0 1 N N N 23.321 -4.902 -10.860 1.794 -2.133 -1.945 "H4'" GPD 54 GPD "H3'" "H3'" H 0 1 N N N 25.010 -2.712 -10.177 3.261 -3.873 -0.118 "H3'" GPD 55 GPD "HO3'" "HO3'" H 0 0 N N N 25.585 -3.775 -12.615 4.554 -4.108 -2.113 "HO3'" GPD 56 GPD "H2'" "H2'" H 0 1 N N N 24.045 -1.037 -11.665 4.616 -2.176 0.778 "H2'" GPD 57 GPD "HO2'" "HO2'" H 0 0 N N N 24.983 -1.830 -13.908 6.103 -3.172 -0.852 "HO2'" GPD 58 GPD "H1'" "H1'" H 0 1 N N N 23.325 -3.223 -13.678 4.077 -0.457 -1.712 "H1'" GPD 59 GPD H8 H8 H 0 1 N N N 21.172 -0.765 -11.649 2.990 0.364 1.845 H8 GPD 60 GPD HN1 HN1 H 0 1 N N N 21.476 0.208 -18.044 8.392 3.454 0.093 HN1 GPD 61 GPD HN2 HN2 H 0 1 N N N 22.837 -1.129 -18.903 8.288 1.352 -2.706 HN2 GPD 62 GPD HN2A HN2A H 0 0 N N N 23.795 -2.394 -18.112 9.145 2.577 -1.941 HN2A GPD 63 # 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 GPD C4G N4A SING N N 1 GPD N4A HN4A SING N N 2 GPD N4A HN4B SING N N 3 GPD C3G C4G SING N N 4 GPD C4G C5G SING N N 5 GPD C4G H4G SING N N 6 GPD O5G C5G SING N N 7 GPD C5G C6G SING N N 8 GPD C5G H5G SING N N 9 GPD C6G H6G SING N N 10 GPD C6G H6GA SING N N 11 GPD C6G H6GB SING N N 12 GPD C1G O5G SING N N 13 GPD C2G C3G SING N N 14 GPD C3G H3G SING N N 15 GPD C3G H3GA SING N N 16 GPD O2G C2G SING N N 17 GPD C1G C2G SING N N 18 GPD C2G H2G SING N N 19 GPD O2G HO2G SING N N 20 GPD C1G O1G SING N N 21 GPD C1G H1G SING N N 22 GPD P2 O1G SING N N 23 GPD OPP P2 SING N N 24 GPD O3P P2 DOUB N N 25 GPD P2 O4P SING N N 26 GPD O4P HO4P SING N N 27 GPD P OPP SING N N 28 GPD "O5'" P SING N N 29 GPD O2P P DOUB N N 30 GPD P O1P SING N N 31 GPD O1P HO1P SING N N 32 GPD "O5'" "C5'" SING N N 33 GPD "C4'" "C5'" SING N N 34 GPD "C5'" "H5'" SING N N 35 GPD "C5'" "H5'A" SING N N 36 GPD "O4'" "C4'" SING N N 37 GPD "C3'" "C4'" SING N N 38 GPD "C4'" "H4'" SING N N 39 GPD "C1'" "O4'" SING N N 40 GPD "C2'" "C3'" SING N N 41 GPD "O3'" "C3'" SING N N 42 GPD "C3'" "H3'" SING N N 43 GPD "O3'" "HO3'" SING N N 44 GPD "O2'" "C2'" SING N N 45 GPD "C1'" "C2'" SING N N 46 GPD "C2'" "H2'" SING N N 47 GPD "O2'" "HO2'" SING N N 48 GPD N9 "C1'" SING N N 49 GPD "C1'" "H1'" SING N N 50 GPD C4 N9 SING Y N 51 GPD N9 C8 SING Y N 52 GPD N7 C8 DOUB Y N 53 GPD C8 H8 SING N N 54 GPD C5 N7 SING Y N 55 GPD N3 C4 SING N N 56 GPD C5 C4 DOUB Y N 57 GPD C6 C5 SING N N 58 GPD N1 C6 SING N N 59 GPD O6 C6 DOUB N N 60 GPD C2 N3 DOUB N N 61 GPD N2 C2 SING N N 62 GPD N1 C2 SING N N 63 GPD N1 HN1 SING N N 64 GPD N2 HN2 SING N N 65 GPD N2 HN2A SING N N 66 # 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 GPD SMILES ACDLabs 10.04 "O=P(OC1OC(C(N)CC1O)C)(O)OP(=O)(O)OCC4OC(n2c3N=C(N)NC(=O)c3nc2)C(O)C4O" GPD SMILES_CANONICAL CACTVS 3.341 "C[C@H]1O[C@H](O[P@@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC(=Nc34)N)[C@@H](O)C[C@@H]1N" GPD SMILES CACTVS 3.341 "C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4C(=O)NC(=Nc34)N)[CH](O)C[CH]1N" GPD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@@H]1[C@H](C[C@@H]([C@H](O1)O[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3N=C(NC4=O)N)O)O)O)N" GPD SMILES "OpenEye OEToolkits" 1.5.0 "CC1C(CC(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3N=C(NC4=O)N)O)O)O)N" GPD InChI InChI 1.03 "InChI=1S/C16H26N6O13P2/c1-5-6(17)2-7(23)15(32-5)34-37(29,30)35-36(27,28)31-3-8-10(24)11(25)14(33-8)22-4-19-9-12(22)20-16(18)21-13(9)26/h4-8,10-11,14-15,23-25H,2-3,17H2,1H3,(H,27,28)(H,29,30)(H3,18,20,21,26)/t5-,6+,7+,8-,10-,11-,14-,15-/m1/s1" GPD InChIKey InChI 1.03 DRNSMVBRYJDNAT-CYCRINRGSA-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 GPD "SYSTEMATIC NAME" ACDLabs 10.04 "(2R,3S,5S,6R)-5-amino-3-hydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)" GPD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5S,6R)-5-amino-3-hydroxy-6-methyl-oxan-2-yl] [[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] 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 GPD "Create component" 2008-08-12 RCSB GPD "Modify aromatic_flag" 2011-06-04 RCSB GPD "Modify descriptor" 2011-06-04 RCSB #