data_GEO # _chem_comp.id GEO _chem_comp.name GEMCITABINE _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H11 F2 N3 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2',2'-DIFLUORODEOXYCYTIDINE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-04-29 _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 263.198 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GEO _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 1P62 _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 GEO "O5'" "O5'" O 0 1 N N N 69.971 38.095 20.611 -3.334 2.813 -0.531 "O5'" GEO 1 GEO "C5'" "C5'" C 0 1 N N N 70.268 37.346 21.792 -3.226 1.662 0.310 "C5'" GEO 2 GEO "C4'" "C4'" C 0 1 N N R 70.467 35.860 21.371 -2.441 0.570 -0.419 "C4'" GEO 3 GEO "O4'" "O4'" O 0 1 N N N 69.149 35.328 21.046 -1.070 0.980 -0.614 "O4'" GEO 4 GEO "C1'" "C1'" C 0 1 N N R 69.210 34.473 19.901 -0.334 -0.243 -0.834 "C1'" GEO 5 GEO N1 N1 N 0 1 Y N N 67.922 34.422 19.161 1.090 -0.036 -0.561 N1 GEO 6 GEO C6 C6 C 0 1 Y N N 67.146 35.472 18.997 2.017 -0.395 -1.493 C6 GEO 7 GEO C5 C5 C 0 1 Y N N 65.911 35.351 18.582 3.331 -0.194 -1.232 C5 GEO 8 GEO C4 C4 C 0 1 Y N N 65.456 34.201 18.160 3.703 0.371 0.005 C4 GEO 9 GEO N3 N3 N 0 1 Y N N 66.250 33.126 18.194 2.765 0.704 0.882 N3 GEO 10 GEO C2 C2 C 0 1 Y N N 67.498 33.222 18.696 1.476 0.506 0.608 C2 GEO 11 GEO O2 O2 O 0 1 N N N 68.273 32.128 18.727 0.633 0.821 1.431 O2 GEO 12 GEO N4 N4 N 0 1 N N N 64.225 34.032 17.639 5.030 0.582 0.298 N4 GEO 13 GEO "C2'" "C2'" C 0 1 N N N 70.386 35.084 19.098 -0.933 -1.252 0.171 "C2'" GEO 14 GEO F1 F1 F 0 1 N N N 69.943 36.062 18.337 -0.176 -1.279 1.347 F1 GEO 15 GEO F2 F2 F 0 1 N N N 70.869 34.206 18.263 -1.005 -2.529 -0.396 F2 GEO 16 GEO "C3'" "C3'" C 0 1 N N R 71.368 35.602 20.169 -2.352 -0.703 0.451 "C3'" GEO 17 GEO "O3'" "O3'" O 0 1 N N N 72.407 34.586 20.411 -3.344 -1.652 0.055 "O3'" GEO 18 GEO "H5'" "H5'" H 0 1 N N N 69.849 39.001 20.867 -3.834 3.475 -0.035 "H5'" GEO 19 GEO "H5'1" "1H5'" H 0 0 N N N 71.136 37.756 22.358 -4.223 1.294 0.551 "H5'1" GEO 20 GEO "H5'2" "2H5'" H 0 0 N N N 69.499 37.471 22.589 -2.706 1.931 1.229 "H5'2" GEO 21 GEO "H4'" "H4'" H 0 1 N N N 70.979 35.371 22.232 -2.909 0.342 -1.377 "H4'" GEO 22 GEO "H1'" "H1'" H 0 1 N N N 69.378 33.397 20.143 -0.478 -0.594 -1.856 "H1'" GEO 23 GEO H6 H6 H 0 1 N N N 67.540 36.479 19.212 1.708 -0.831 -2.432 H6 GEO 24 GEO H5 H5 H 0 1 N N N 65.244 36.230 18.588 4.082 -0.471 -1.957 H5 GEO 25 GEO HN41 1HN4 H 0 0 N N N 63.869 33.134 17.309 5.282 0.975 1.148 HN41 GEO 26 GEO HN42 2HN4 H 0 0 N N N 64.129 34.694 16.869 5.714 0.334 -0.344 HN42 GEO 27 GEO "H3'" "H3'" H 0 1 N N N 71.930 36.523 19.890 -2.464 -0.453 1.506 "H3'" GEO 28 GEO H1 H1 H 0 1 N N N 72.968 34.425 19.661 -3.240 -2.422 0.630 H1 GEO 29 # # 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 GEO "O5'" "C5'" SING N N 1 GEO "O5'" "H5'" SING N N 2 GEO "C5'" "C4'" SING N N 3 GEO "C5'" "H5'1" SING N N 4 GEO "C5'" "H5'2" SING N N 5 GEO "C4'" "O4'" SING N N 6 GEO "C4'" "C3'" SING N N 7 GEO "C4'" "H4'" SING N N 8 GEO "O4'" "C1'" SING N N 9 GEO "C1'" N1 SING N N 10 GEO "C1'" "C2'" SING N N 11 GEO "C1'" "H1'" SING N N 12 GEO N1 C6 SING Y N 13 GEO N1 C2 SING Y N 14 GEO C6 C5 DOUB Y N 15 GEO C6 H6 SING N N 16 GEO C5 C4 SING Y N 17 GEO C5 H5 SING N N 18 GEO C4 N3 DOUB Y N 19 GEO C4 N4 SING N N 20 GEO N3 C2 SING Y N 21 GEO C2 O2 DOUB N N 22 GEO N4 HN41 SING N N 23 GEO N4 HN42 SING N N 24 GEO "C2'" F1 SING N N 25 GEO "C2'" F2 SING N N 26 GEO "C2'" "C3'" SING N N 27 GEO "C3'" "O3'" SING N N 28 GEO "C3'" "H3'" SING N N 29 GEO "O3'" H1 SING N N 30 # # 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 GEO SMILES ACDLabs 10.04 "O=C1N=C(N)C=CN1C2OC(C(O)C2(F)F)CO" GEO SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO)[C@@H](O)C2(F)F" GEO SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO)[CH](O)C2(F)F" GEO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)[C@H]2C([C@@H]([C@H](O2)CO)O)(F)F" GEO SMILES "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)CO)O)(F)F" GEO InChI InChI 1.03 "InChI=1S/C9H11F2N3O4/c10-9(11)6(16)4(3-15)18-7(9)14-2-1-5(12)13-8(14)17/h1-2,4,6-7,15-16H,3H2,(H2,12,13,17)/t4-,6-,7-/m1/s1" GEO InChIKey InChI 1.03 SDUQYLNIPVEERB-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 GEO "SYSTEMATIC NAME" ACDLabs 10.04 "2'-deoxy-2',2'-difluorocytidine" GEO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "4-amino-1-[(2R,4R,5R)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site GEO "Create component" 2003-04-29 RCSB GEO "Modify descriptor" 2011-06-04 RCSB GEO "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id GEO _pdbx_chem_comp_synonyms.name "2',2'-DIFLUORODEOXYCYTIDINE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##