data_GCQ # _chem_comp.id GCQ _chem_comp.name "GEMCITABINE DIPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H13 F2 N3 O10 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;((2R,3R,5R)-5-(4-AMINO-2-OXOPYRIMIDIN-1(2H)-YL)-4,4-DIFLUORO-3-HYDROXYTETRAHYDROFURAN-2-YL)METHYL TRIHYDROGEN DIPHOSPHATE ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2005-11-22 _chem_comp.pdbx_modified_date 2020-06-17 _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 423.158 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GCQ _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 2EUD _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 GCQ O3B O3B O 0 1 N N N 27.556 53.497 17.439 -5.866 2.345 -0.831 O3B GCQ 1 GCQ PB PB P 0 1 N N N 27.583 53.005 16.010 -5.131 1.131 -0.070 PB GCQ 2 GCQ O1B O1B O 0 1 N N N 28.940 52.871 15.396 -6.212 -0.005 0.295 O1B GCQ 3 GCQ O2B O2B O 0 1 N N N 26.730 53.765 15.013 -4.506 1.635 1.174 O2B GCQ 4 GCQ O3A O3A O 0 1 N N N 27.176 51.456 16.177 -3.997 0.506 -1.026 O3A GCQ 5 GCQ PA PA P 0 1 N N S 26.062 50.482 15.517 -3.053 -0.405 -0.093 PA GCQ 6 GCQ O1A O1A O 0 1 N N N 26.561 49.141 15.957 -3.761 -1.828 0.160 O1A GCQ 7 GCQ O2A O2A O 0 1 N N N 25.907 50.681 13.982 -2.835 0.275 1.203 O2A GCQ 8 GCQ "O5'" O5* O 0 1 N N N 24.769 50.856 16.376 -1.636 -0.633 -0.824 "O5'" GCQ 9 GCQ "C5'" C5* C 0 1 N N N 23.540 50.189 16.173 -0.806 -1.343 0.097 "C5'" GCQ 10 GCQ "C4'" C4* C 0 1 N N R 22.393 50.855 16.925 0.563 -1.594 -0.539 "C4'" GCQ 11 GCQ "C3'" C3* C 0 1 N N R 21.191 51.143 16.069 1.464 -2.403 0.420 "C3'" GCQ 12 GCQ "O3'" O3* O 0 1 N N N 20.149 50.235 16.467 1.449 -3.789 0.072 "O3'" GCQ 13 GCQ "C2'" C2* C 0 1 N N N 20.842 52.604 16.294 2.875 -1.805 0.205 "C2'" GCQ 14 GCQ F1 F1 F 0 1 N N N 19.506 52.698 16.786 3.754 -2.783 -0.273 F1 GCQ 15 GCQ "O4'" O4* O 0 1 N N N 22.772 52.068 17.632 1.261 -0.345 -0.737 "O4'" GCQ 16 GCQ "C1'" C1* C 0 1 N N R 21.848 53.147 17.321 2.655 -0.704 -0.857 "C1'" GCQ 17 GCQ N1 N1 N 0 1 Y N N 22.510 54.423 16.806 3.506 0.454 -0.573 N1 GCQ 18 GCQ C6 C6 C 0 1 Y N N 23.651 54.422 16.019 4.474 0.818 -1.460 C6 GCQ 19 GCQ C5 C5 C 0 1 Y N N 24.237 55.616 15.553 5.251 1.894 -1.190 C5 GCQ 20 GCQ C4 C4 C 0 1 Y N N 23.633 56.848 15.907 5.041 2.602 0.011 C4 GCQ 21 GCQ N4 N4 N 0 1 N N N 24.187 58.015 15.464 5.819 3.696 0.314 N4 GCQ 22 GCQ N3 N3 N 0 1 Y N N 22.500 56.865 16.690 4.087 2.211 0.845 N3 GCQ 23 GCQ C2 C2 C 0 1 Y N N 21.916 55.703 17.152 3.327 1.154 0.563 C2 GCQ 24 GCQ O2 O2 O 0 1 N N N 20.874 55.747 17.868 2.456 0.815 1.346 O2 GCQ 25 GCQ F2 F2 F 0 1 N N N 20.837 53.254 15.141 3.358 -1.248 1.394 F2 GCQ 26 GCQ H3B H3B H 0 1 N N N 27.550 52.753 18.030 -6.536 2.690 -0.225 H3B GCQ 27 GCQ H1B H1B H 0 1 N N N 28.859 52.843 14.450 -6.595 -0.306 -0.540 H1B GCQ 28 GCQ H1A H1A H 0 1 N N N 26.667 48.578 15.199 -3.885 -2.237 -0.708 H1A GCQ 29 GCQ "H5'1" 1H5* H 0 0 N N N 23.644 49.162 16.553 -1.272 -2.297 0.345 "H5'1" GCQ 30 GCQ "H5'2" 2H5* H 0 0 N N N 23.308 50.201 15.098 -0.682 -0.753 1.005 "H5'2" GCQ 31 GCQ "H4'" H4* H 0 1 N N N 22.117 50.094 17.670 0.450 -2.120 -1.487 "H4'" GCQ 32 GCQ "H3'" H3* H 0 1 N N N 21.359 50.992 14.992 1.143 -2.265 1.453 "H3'" GCQ 33 GCQ H1 H1 H 0 1 N N N 20.239 50.035 17.391 2.026 -4.241 0.702 H1 GCQ 34 GCQ "H1'" H1* H 0 1 N N N 21.358 53.454 18.257 2.863 -1.092 -1.854 "H1'" GCQ 35 GCQ H6 H6 H 0 1 N N N 24.105 53.478 15.755 4.618 0.256 -2.371 H6 GCQ 36 GCQ H5 H5 H 0 1 N N N 25.126 55.593 14.940 6.024 2.199 -1.879 H5 GCQ 37 GCQ HN41 1HN4 H 0 0 N N N 25.005 58.091 14.894 5.670 4.184 1.139 HN41 GCQ 38 GCQ HN42 2HN4 H 0 0 N N N 23.641 58.781 15.802 6.519 3.977 -0.296 HN42 GCQ 39 # # 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 GCQ O3B PB SING N N 1 GCQ O3B H3B SING N N 2 GCQ PB O1B SING N N 3 GCQ PB O2B DOUB N N 4 GCQ PB O3A SING N N 5 GCQ O1B H1B SING N N 6 GCQ O3A PA SING N N 7 GCQ PA O1A SING N N 8 GCQ PA O2A DOUB N N 9 GCQ PA "O5'" SING N N 10 GCQ O1A H1A SING N N 11 GCQ "O5'" "C5'" SING N N 12 GCQ "C5'" "C4'" SING N N 13 GCQ "C5'" "H5'1" SING N N 14 GCQ "C5'" "H5'2" SING N N 15 GCQ "C4'" "C3'" SING N N 16 GCQ "C4'" "O4'" SING N N 17 GCQ "C4'" "H4'" SING N N 18 GCQ "C3'" "O3'" SING N N 19 GCQ "C3'" "C2'" SING N N 20 GCQ "C3'" "H3'" SING N N 21 GCQ "O3'" H1 SING N N 22 GCQ "C2'" F1 SING N N 23 GCQ "C2'" "C1'" SING N N 24 GCQ "C2'" F2 SING N N 25 GCQ "O4'" "C1'" SING N N 26 GCQ "C1'" N1 SING N N 27 GCQ "C1'" "H1'" SING N N 28 GCQ N1 C6 SING Y N 29 GCQ N1 C2 SING Y N 30 GCQ C6 C5 DOUB Y N 31 GCQ C6 H6 SING N N 32 GCQ C5 C4 SING Y N 33 GCQ C5 H5 SING N N 34 GCQ C4 N4 SING N N 35 GCQ C4 N3 DOUB Y N 36 GCQ N4 HN41 SING N N 37 GCQ N4 HN42 SING N N 38 GCQ N3 C2 SING Y N 39 GCQ C2 O2 DOUB N N 40 # # 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 GCQ SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(F)(F)C2O" GCQ SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)C2(F)F" GCQ SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)C2(F)F" GCQ SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)[C@H]2C([C@@H]([C@H](O2)CO[P@](=O)(O)OP(=O)(O)O)O)(F)F" GCQ SMILES "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)(F)F" GCQ InChI InChI 1.03 "InChI=1S/C9H13F2N3O10P2/c10-9(11)6(15)4(3-22-26(20,21)24-25(17,18)19)23-7(9)14-2-1-5(12)13-8(14)16/h1-2,4,6-7,15H,3H2,(H,20,21)(H2,12,13,16)(H2,17,18,19)/t4-,6-,7-/m1/s1" GCQ InChIKey InChI 1.03 FRQISCZGNNXEMD-QPPQHZFASA-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 GCQ "SYSTEMATIC NAME" ACDLabs 10.04 "2'-deoxy-2',2'-difluorocytidine 5'-(trihydrogen diphosphate)" GCQ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-4,4-difluoro-3-hydroxy-oxolan-2-yl]methyl phosphono 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 GCQ "Create component" 2005-11-22 RCSB GCQ "Modify descriptor" 2011-06-04 RCSB GCQ "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id GCQ _pdbx_chem_comp_synonyms.name "((2R,3R,5R)-5-(4-AMINO-2-OXOPYRIMIDIN-1(2H)-YL)-4,4-DIFLUORO-3-HYDROXYTETRAHYDROFURAN-2-YL)METHYL TRIHYDROGEN DIPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##