data_GKD # _chem_comp.id GKD _chem_comp.name ;GUANOSINE 5'-DIPHOSPHATE-4-KETO-BETA-L-GULOSE ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H23 N5 O16 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2005-10-25 _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 603.325 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GKD _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 2C54 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 GKD N2 N2 N 0 1 N N N 11.512 42.341 9.272 -9.848 0.891 -1.773 N2 GKD 1 GKD C2 C2 C 0 1 Y N N 11.218 43.576 8.853 -8.994 -0.022 -1.208 C2 GKD 2 GKD N1 N1 N 0 1 Y N N 9.930 43.964 8.931 -9.449 -1.280 -0.947 N1 GKD 3 GKD N3 N3 N 0 1 Y N N 12.211 44.338 8.420 -7.762 0.343 -0.931 N3 GKD 4 GKD C4 C4 C 0 1 Y N N 11.889 45.591 8.055 -6.895 -0.514 -0.380 C4 GKD 5 GKD C5 C5 C 0 1 Y N N 10.547 46.097 8.082 -7.300 -1.822 -0.092 C5 GKD 6 GKD C6 C6 C 0 1 Y N N 9.512 45.220 8.581 -8.628 -2.202 -0.396 C6 GKD 7 GKD O6 O6 O 0 1 N N N 8.268 45.520 8.689 -9.024 -3.331 -0.163 O6 GKD 8 GKD N7 N7 N 0 1 Y N N 10.601 47.413 7.681 -6.237 -2.462 0.452 N7 GKD 9 GKD C8 C8 C 0 1 Y N N 11.864 47.649 7.386 -5.227 -1.644 0.515 C8 GKD 10 GKD N9 N9 N 0 1 Y N N 12.641 46.552 7.601 -5.586 -0.427 0.012 N9 GKD 11 GKD "C1'" C1* C 0 1 N N R 14.099 46.560 7.434 -4.728 0.756 -0.091 "C1'" GKD 12 GKD "C2'" C2* C 0 1 N N R 14.837 46.138 8.721 -4.900 1.655 1.153 "C2'" GKD 13 GKD "O2'" O2* O 0 1 N N N 14.816 47.191 9.670 -5.798 2.732 0.879 "O2'" GKD 14 GKD "C3'" C3* C 0 1 N N S 16.237 45.905 8.132 -3.476 2.193 1.425 "C3'" GKD 15 GKD "O3'" O3* O 0 1 N N N 16.958 47.082 7.913 -3.451 3.619 1.325 "O3'" GKD 16 GKD "C4'" C4* C 0 1 N N R 15.917 45.323 6.769 -2.614 1.557 0.311 "C4'" GKD 17 GKD "O4'" O4* O 0 1 N N N 14.543 45.641 6.459 -3.336 0.369 -0.080 "O4'" GKD 18 GKD "C5'" C5* C 0 1 N N N 16.005 43.809 6.696 -1.231 1.187 0.850 "C5'" GKD 19 GKD "O5'" O5* O 0 1 N N N 15.400 43.221 7.828 -0.439 0.642 -0.206 "O5'" GKD 20 GKD PA PA P 0 1 N N R 15.212 41.642 8.028 0.995 0.277 0.429 PA GKD 21 GKD O1A O1A O 0 1 N N N 14.901 40.995 6.696 0.817 -0.894 1.519 O1A GKD 22 GKD O2A O2A O 0 1 N N N 14.283 41.418 9.170 1.566 1.476 1.081 O2A GKD 23 GKD O3A O3A O 0 1 N N N 16.638 41.139 8.542 1.987 -0.223 -0.737 O3A GKD 24 GKD PB PB P 0 1 N N S 18.193 41.355 8.164 3.477 -0.186 -0.128 PB GKD 25 GKD O2B O2B O 0 1 N N N 18.371 41.214 6.684 3.639 1.025 0.707 O2B GKD 26 GKD O3B O3B O 0 1 N N N 18.692 42.656 8.728 3.720 -1.497 0.774 O3B GKD 27 GKD O1B O1B O 0 1 N N N 18.978 40.258 8.990 4.547 -0.156 -1.330 O1B GKD 28 GKD C1G C1G C 0 1 N N R 18.618 38.937 8.834 5.836 -0.006 -0.732 C1G GKD 29 GKD O5G O5G O 0 1 N N N 19.672 38.372 8.010 6.381 -1.293 -0.453 O5G GKD 30 GKD C5G C5G C 0 1 N N S 19.655 36.951 7.773 7.528 -1.109 0.379 C5G GKD 31 GKD C6G C6G C 0 1 N N N 20.955 36.550 7.053 8.125 -2.472 0.737 C6G GKD 32 GKD O6A O6A O 0 1 N N N 21.214 37.440 5.960 7.194 -3.205 1.536 O6A GKD 33 GKD C2G C2G C 0 1 N N S 18.493 38.220 10.192 6.755 0.756 -1.690 C2G GKD 34 GKD O2G O2G O 0 1 N N N 17.371 38.734 10.900 6.147 1.998 -2.051 O2G GKD 35 GKD C3G C3G C 0 1 N N R 18.407 36.684 10.071 8.091 1.024 -0.981 C3G GKD 36 GKD O3G O3G O 0 1 N N N 17.152 36.312 9.537 7.913 2.000 0.047 O3G GKD 37 GKD C4G C4G C 0 1 N N N 19.486 36.180 9.099 8.551 -0.287 -0.373 C4G GKD 38 GKD O4G O4G O 0 1 N N N 20.079 35.129 9.330 9.694 -0.661 -0.486 O4G GKD 39 GKD H2N1 1H2N H 0 0 N N N 12.487 42.047 9.213 -9.540 1.792 -1.962 H2N1 GKD 40 GKD H2N2 2H2N H 0 0 N N N 10.747 41.754 9.606 -10.759 0.635 -1.988 H2N2 GKD 41 GKD H1 H1 H 0 1 N N N 9.237 43.294 9.265 -10.364 -1.517 -1.164 H1 GKD 42 GKD H8 H8 H 0 1 N N N 12.244 48.615 7.012 -4.251 -1.890 0.906 H8 GKD 43 GKD "H1'" H1* H 0 1 N N N 14.427 47.586 7.145 -4.959 1.314 -0.998 "H1'" GKD 44 GKD "H2'" H2* H 0 1 N N N 14.412 45.199 9.145 -5.255 1.069 2.000 "H2'" GKD 45 GKD HA HA H 0 1 N N N 15.271 46.931 10.463 -5.816 3.289 1.670 HA GKD 46 GKD "H3'" H3* H 0 1 N N N 16.820 45.184 8.751 -3.127 1.874 2.407 "H3'" GKD 47 GKD HB HB H 0 1 N N N 17.823 46.938 7.549 -4.003 3.959 2.043 HB GKD 48 GKD "H4'" H4* H 0 1 N N N 16.588 45.775 6.002 -2.521 2.241 -0.533 "H4'" GKD 49 GKD "H5'1" 1H5* H 0 0 N N N 17.056 43.461 6.561 -0.745 2.079 1.247 "H5'1" GKD 50 GKD "H5'2" 2H5* H 0 0 N N N 15.575 43.415 5.746 -1.337 0.448 1.644 "H5'2" GKD 51 GKD H1A H1A H 0 1 N N N 14.790 40.059 6.815 0.443 -1.655 1.054 H1A GKD 52 GKD H3B H3B H 0 1 N N N 19.607 42.783 8.506 3.605 -2.262 0.193 H3B GKD 53 GKD H1G H1G H 0 1 N N N 17.647 38.877 8.290 5.740 0.554 0.198 H1G GKD 54 GKD H5G H5G H 0 1 N N N 18.792 36.711 7.109 7.238 -0.587 1.290 H5G GKD 55 GKD H6G1 1H6G H 0 0 N N N 20.937 35.484 6.726 8.337 -3.027 -0.176 H6G1 GKD 56 GKD H6G2 2H6G H 0 0 N N N 21.819 36.493 7.756 9.049 -2.327 1.297 H6G2 GKD 57 GKD H6A H6A H 0 1 N N N 22.016 37.193 5.516 7.608 -4.054 1.739 H6A GKD 58 GKD H2G H2G H 0 1 N N N 19.406 38.461 10.786 6.929 0.160 -2.586 H2G GKD 59 GKD HC HC H 0 1 N N N 17.294 38.292 11.737 6.763 2.450 -2.643 HC GKD 60 GKD H3G H3G H 0 1 N N N 18.548 36.215 11.073 8.829 1.376 -1.703 H3G GKD 61 GKD HD HD H 0 1 N N N 17.099 35.366 9.462 8.771 2.108 0.481 HD GKD 62 # 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 GKD N2 C2 SING N N 1 GKD N2 H2N1 SING N N 2 GKD N2 H2N2 SING N N 3 GKD C2 N1 SING Y N 4 GKD C2 N3 DOUB Y N 5 GKD N1 C6 SING Y N 6 GKD N1 H1 SING N N 7 GKD N3 C4 SING Y N 8 GKD C4 C5 DOUB Y N 9 GKD C4 N9 SING Y N 10 GKD C5 C6 SING Y N 11 GKD C5 N7 SING Y N 12 GKD C6 O6 DOUB N N 13 GKD N7 C8 DOUB Y N 14 GKD C8 N9 SING Y N 15 GKD C8 H8 SING N N 16 GKD N9 "C1'" SING N N 17 GKD "C1'" "C2'" SING N N 18 GKD "C1'" "O4'" SING N N 19 GKD "C1'" "H1'" SING N N 20 GKD "C2'" "O2'" SING N N 21 GKD "C2'" "C3'" SING N N 22 GKD "C2'" "H2'" SING N N 23 GKD "O2'" HA SING N N 24 GKD "C3'" "O3'" SING N N 25 GKD "C3'" "C4'" SING N N 26 GKD "C3'" "H3'" SING N N 27 GKD "O3'" HB SING N N 28 GKD "C4'" "O4'" SING N N 29 GKD "C4'" "C5'" SING N N 30 GKD "C4'" "H4'" SING N N 31 GKD "C5'" "O5'" SING N N 32 GKD "C5'" "H5'1" SING N N 33 GKD "C5'" "H5'2" SING N N 34 GKD "O5'" PA SING N N 35 GKD PA O1A SING N N 36 GKD PA O2A DOUB N N 37 GKD PA O3A SING N N 38 GKD O1A H1A SING N N 39 GKD O3A PB SING N N 40 GKD PB O2B DOUB N N 41 GKD PB O3B SING N N 42 GKD PB O1B SING N N 43 GKD O3B H3B SING N N 44 GKD O1B C1G SING N N 45 GKD C1G O5G SING N N 46 GKD C1G C2G SING N N 47 GKD C1G H1G SING N N 48 GKD O5G C5G SING N N 49 GKD C5G C6G SING N N 50 GKD C5G C4G SING N N 51 GKD C5G H5G SING N N 52 GKD C6G O6A SING N N 53 GKD C6G H6G1 SING N N 54 GKD C6G H6G2 SING N N 55 GKD O6A H6A SING N N 56 GKD C2G O2G SING N N 57 GKD C2G C3G SING N N 58 GKD C2G H2G SING N N 59 GKD O2G HC SING N N 60 GKD C3G O3G SING N N 61 GKD C3G C4G SING N N 62 GKD C3G H3G SING N N 63 GKD O3G HD SING N N 64 GKD C4G O4G DOUB N N 65 # 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 GKD SMILES ACDLabs 10.04 "O=C1C(O)C(O)C(OC1CO)OP(=O)(O)OP(=O)(O)OCC4OC(n3cnc2c3N=C(N)NC2=O)C(O)C4O" GKD SMILES_CANONICAL CACTVS 3.341 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)O[C@H]4O[C@@H](CO)C(=O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O" GKD SMILES CACTVS 3.341 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]4O[CH](CO)C(=O)[CH](O)[CH]4O)[CH](O)[CH]3O" GKD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)O[C@@H]4[C@H]([C@H](C(=O)[C@@H](O4)CO)O)O)O)O)N=C(NC2=O)N" GKD SMILES "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4C(C(C(=O)C(O4)CO)O)O)O)O)N=C(NC2=O)N" GKD InChI InChI 1.03 "InChI=1S/C16H23N5O16P2/c17-16-19-12-6(13(28)20-16)18-3-21(12)14-10(26)8(24)5(34-14)2-33-38(29,30)37-39(31,32)36-15-11(27)9(25)7(23)4(1-22)35-15/h3-5,8-11,14-15,22,24-27H,1-2H2,(H,29,30)(H,31,32)(H3,17,19,20,28)/t4-,5+,8+,9-,10+,11-,14+,15+/m0/s1" GKD InChIKey InChI 1.03 QZZKIVADHWVJFF-UFFCYROPSA-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 GKD "SYSTEMATIC NAME" ACDLabs 10.04 "[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4R,6S)-3,4-dihydroxy-6-(hydroxymethyl)-5-oxotetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)" GKD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [[(2R,3S,4R,6S)-3,4-dihydroxy-6-(hydroxymethyl)-5-oxo-oxan-2-yl]oxy-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 GKD "Create component" 2005-10-25 EBI GKD "Modify descriptor" 2011-06-04 RCSB #