data_GDD # _chem_comp.id GDD _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H25 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 2005-10-26 _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 605.341 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GDD _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 2C59 _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 GDD N2 N2 N 0 1 N N N 11.769 42.380 9.080 9.181 -1.062 1.800 N2 GDD 1 GDD C2 C2 C 0 1 N N N 11.482 43.658 8.685 8.118 -1.486 1.044 C2 GDD 2 GDD N1 N1 N 0 1 N N N 10.209 44.069 8.708 8.190 -2.696 0.421 N1 GDD 3 GDD N3 N3 N 0 1 N N N 12.502 44.495 8.321 7.062 -0.711 0.937 N3 GDD 4 GDD C4 C4 C 0 1 Y N N 12.259 45.777 7.929 6.002 -1.083 0.210 C4 GDD 5 GDD C5 C5 C 0 1 Y N N 10.894 46.282 7.964 6.012 -2.317 -0.450 C5 GDD 6 GDD C6 C6 C 0 1 N N N 9.854 45.342 8.372 7.155 -3.141 -0.326 C6 GDD 7 GDD O6 O6 O 0 1 N N N 8.667 45.748 8.359 7.207 -4.224 -0.883 O6 GDD 8 GDD N7 N7 N 0 1 Y N N 10.919 47.567 7.572 4.829 -2.435 -1.101 N7 GDD 9 GDD C8 C8 C 0 1 Y N N 12.195 47.882 7.301 4.111 -1.372 -0.885 C8 GDD 10 GDD N9 N9 N 0 1 Y N N 12.987 46.836 7.555 4.794 -0.508 -0.080 N9 GDD 11 GDD "C1'" C1* C 0 1 N N R 14.434 46.879 7.368 4.321 0.797 0.389 "C1'" GDD 12 GDD "C2'" C2* C 0 1 N N R 15.131 46.363 8.606 4.802 1.916 -0.561 "C2'" GDD 13 GDD "O2'" O2* O 0 1 N N N 15.058 47.274 9.683 5.967 2.558 -0.041 "O2'" GDD 14 GDD "C3'" C3* C 0 1 N N S 16.515 46.030 8.065 3.613 2.905 -0.606 "C3'" GDD 15 GDD "O3'" O3* O 0 1 N N N 17.327 47.193 7.901 4.007 4.186 -0.111 "O3'" GDD 16 GDD "C4'" C4* C 0 1 N N R 16.174 45.530 6.665 2.558 2.266 0.325 "C4'" GDD 17 GDD "O4'" O4* O 0 1 N N N 14.860 46.014 6.300 2.879 0.858 0.336 "O4'" GDD 18 GDD "C5'" C5* C 0 1 N N N 16.246 44.035 6.536 1.150 2.488 -0.230 "C5'" GDD 19 GDD "O5'" O5* O 0 1 N N N 15.600 43.517 7.694 0.190 1.928 0.668 "O5'" GDD 20 GDD PA PA P 0 1 N N S 15.425 41.946 7.955 -1.261 2.195 0.025 PA GDD 21 GDD O1A O1A O 0 1 N N N 15.091 41.324 6.650 -1.300 1.647 -1.350 O1A GDD 22 GDD O2A O2A O 0 1 N N N 14.439 41.676 9.078 -1.544 3.780 -0.021 O2A GDD 23 GDD O3A O3A O 0 1 N N N 16.818 41.332 8.557 -2.387 1.475 0.922 O3A GDD 24 GDD PB PB P 0 1 N N R 18.393 41.382 8.172 -3.691 1.314 -0.009 PB GDD 25 GDD O2B O2B O 0 1 N N N 18.640 41.169 6.700 -4.416 2.742 -0.168 O2B GDD 26 GDD O3B O3B O 0 1 N N N 19.021 42.676 8.610 -3.287 0.814 -1.342 O3B GDD 27 GDD O1B O1B O 0 1 N N N 19.027 40.193 9.091 -4.709 0.267 0.670 O1B GDD 28 GDD C11 C11 C 0 1 N N R 18.351 38.959 8.826 -5.783 0.078 -0.253 C11 GDD 29 GDD O51 O51 O 0 1 N N N 19.184 38.157 7.957 -5.470 -1.002 -1.130 O51 GDD 30 GDD C51 C51 C 0 1 N N R 20.387 37.627 8.547 -5.118 -2.125 -0.324 C51 GDD 31 GDD C61 C61 C 0 1 N N N 21.163 36.807 7.509 -4.592 -3.249 -1.218 C61 GDD 32 GDD O6A O6A O 0 1 N N N 21.497 37.642 6.400 -3.374 -2.833 -1.839 O6A GDD 33 GDD C21 C21 C 0 1 N N S 17.953 38.163 10.100 -7.067 -0.237 0.518 C21 GDD 34 GDD O21 O21 O 0 1 N N N 17.140 37.023 9.757 -8.138 -0.457 -0.403 O21 GDD 35 GDD C31 C31 C 0 1 N N S 19.196 37.621 10.781 -6.849 -1.498 1.360 C31 GDD 36 GDD O31 O31 O 0 1 N N N 18.841 36.881 11.956 -8.080 -1.891 1.969 O31 GDD 37 GDD C41 C41 C 0 1 N N S 20.058 36.780 9.800 -6.348 -2.619 0.442 C41 GDD 38 GDD O41 O41 O 0 1 N N N 21.285 36.350 10.424 -5.996 -3.760 1.226 O41 GDD 39 GDD H2N1 1H2N H 0 0 N N N 12.684 41.976 9.100 9.147 -0.201 2.247 H2N1 GDD 40 GDD H2N2 2H2N H 0 0 N N N 10.927 41.910 9.346 9.966 -1.625 1.892 H2N2 GDD 41 GDD H1 H1 H 0 1 N N N 9.496 43.423 8.980 8.984 -3.244 0.520 H1 GDD 42 GDD H8 H8 H 0 1 N N N 12.532 48.839 6.932 3.122 -1.200 -1.283 H8 GDD 43 GDD "H1'" H1* H 0 1 N N N 14.686 47.927 7.147 4.672 0.985 1.404 "H1'" GDD 44 GDD "H2'" H2* H 0 1 N N N 14.676 45.481 9.079 5.000 1.513 -1.554 "H2'" GDD 45 GDD HA HA H 0 1 N N N 15.935 47.479 9.985 6.181 3.283 -0.644 HA GDD 46 GDD "H3'" H3* H 0 1 N N N 17.064 45.343 8.725 3.224 2.991 -1.620 "H3'" GDD 47 GDD HB HB H 0 1 N N N 16.773 47.964 7.865 4.663 4.535 -0.730 HB GDD 48 GDD "H4'" H4* H 0 1 N N N 16.932 45.927 5.974 2.639 2.681 1.330 "H4'" GDD 49 GDD "H5'1" 1H5* H 0 0 N N N 17.286 43.685 6.463 0.966 3.556 -0.339 "H5'1" GDD 50 GDD "H5'2" 2H5* H 0 0 N N N 15.736 43.698 5.622 1.063 2.003 -1.203 "H5'2" GDD 51 GDD HO2A HO2A H 0 0 N N N 14.906 41.620 9.903 -1.510 4.096 0.892 HO2A GDD 52 GDD HO2B HO2B H 0 0 N N N 17.809 41.124 6.242 -4.663 3.031 0.721 HO2B GDD 53 GDD H11 H11 H 0 1 N N N 17.396 39.206 8.339 -5.925 0.988 -0.836 H11 GDD 54 GDD H51 H51 H 0 1 N N N 21.022 38.464 8.872 -4.343 -1.833 0.385 H51 GDD 55 GDD H611 1H61 H 0 0 N N N 20.541 35.968 7.164 -4.406 -4.137 -0.614 H611 GDD 56 GDD H612 2H61 H 0 0 N N N 22.084 36.415 7.965 -5.331 -3.479 -1.985 H612 GDD 57 GDD H6A H6A H 0 1 N N N 20.714 37.827 5.895 -3.077 -3.568 -2.393 H6A GDD 58 GDD H21 H21 H 0 1 N N N 17.401 38.850 10.758 -7.313 0.599 1.171 H21 GDD 59 GDD HC HC H 0 1 N N N 17.690 36.252 9.682 -8.241 0.359 -0.911 HC GDD 60 GDD H31 H31 H 0 1 N N N 19.818 38.472 11.097 -6.106 -1.298 2.132 H31 GDD 61 GDD HD HD H 0 1 N N N 19.620 36.717 12.475 -8.358 -1.159 2.536 HD GDD 62 GDD H41 H41 H 0 1 N N N 19.484 35.887 9.512 -7.133 -2.890 -0.265 H41 GDD 63 GDD HE HE H 0 1 N N N 21.961 36.255 9.763 -6.797 -4.038 1.690 HE GDD 64 # 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 GDD N2 C2 SING N N 1 GDD N2 H2N1 SING N N 2 GDD N2 H2N2 SING N N 3 GDD C2 N1 SING N N 4 GDD C2 N3 DOUB N N 5 GDD N1 C6 SING N N 6 GDD N1 H1 SING N N 7 GDD N3 C4 SING N N 8 GDD C4 C5 DOUB Y N 9 GDD C4 N9 SING Y N 10 GDD C5 C6 SING N N 11 GDD C5 N7 SING Y N 12 GDD C6 O6 DOUB N N 13 GDD N7 C8 DOUB Y N 14 GDD C8 N9 SING Y N 15 GDD C8 H8 SING N N 16 GDD N9 "C1'" SING N N 17 GDD "C1'" "C2'" SING N N 18 GDD "C1'" "O4'" SING N N 19 GDD "C1'" "H1'" SING N N 20 GDD "C2'" "O2'" SING N N 21 GDD "C2'" "C3'" SING N N 22 GDD "C2'" "H2'" SING N N 23 GDD "O2'" HA SING N N 24 GDD "C3'" "O3'" SING N N 25 GDD "C3'" "C4'" SING N N 26 GDD "C3'" "H3'" SING N N 27 GDD "O3'" HB SING N N 28 GDD "C4'" "O4'" SING N N 29 GDD "C4'" "C5'" SING N N 30 GDD "C4'" "H4'" SING N N 31 GDD "C5'" "O5'" SING N N 32 GDD "C5'" "H5'1" SING N N 33 GDD "C5'" "H5'2" SING N N 34 GDD "O5'" PA SING N N 35 GDD PA O1A DOUB N N 36 GDD PA O2A SING N N 37 GDD PA O3A SING N N 38 GDD O2A HO2A SING N N 39 GDD O3A PB SING N N 40 GDD PB O2B SING N N 41 GDD PB O3B DOUB N N 42 GDD PB O1B SING N N 43 GDD O2B HO2B SING N N 44 GDD O1B C11 SING N N 45 GDD C11 O51 SING N N 46 GDD C11 C21 SING N N 47 GDD C11 H11 SING N N 48 GDD O51 C51 SING N N 49 GDD C51 C61 SING N N 50 GDD C51 C41 SING N N 51 GDD C51 H51 SING N N 52 GDD C61 O6A SING N N 53 GDD C61 H611 SING N N 54 GDD C61 H612 SING N N 55 GDD O6A H6A SING N N 56 GDD C21 O21 SING N N 57 GDD C21 C31 SING N N 58 GDD C21 H21 SING N N 59 GDD O21 HC SING N N 60 GDD C31 O31 SING N N 61 GDD C31 C41 SING N N 62 GDD C31 H31 SING N N 63 GDD O31 HD SING N N 64 GDD C41 O41 SING N N 65 GDD C41 H41 SING N N 66 GDD O41 HE SING N N 67 # 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 GDD SMILES ACDLabs 10.04 "O=P(OC1OC(C(O)C(O)C1O)CO)(O)OP(=O)(O)OCC4OC(n2c3N=C(N)NC(=O)c3nc2)C(O)C4O" GDD 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@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O" GDD 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)[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O" GDD 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@@H]([C@H](O4)CO)O)O)O)O)O)N=C(NC2=O)N" GDD SMILES "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4C(C(C(C(O4)CO)O)O)O)O)O)N=C(NC2=O)N" GDD InChI InChI 1.03 "InChI=1S/C16H25N5O16P2/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/h3-5,7-11,14-15,22-27H,1-2H2,(H,29,30)(H,31,32)(H3,17,19,20,28)/t4-,5-,7-,8-,9+,10-,11+,14-,15-/m1/s1" GDD InChIKey InChI 1.03 MVMSCBBUIHUTGJ-GDJBGNAASA-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 GDD "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,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)" GDD "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 [hydroxy-[(2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-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 GDD "Create component" 2005-10-26 EBI GDD "Modify descriptor" 2011-06-04 RCSB #