data_GTF
#
_chem_comp.id GTF
_chem_comp.name "2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate)"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H14 F2 N3 O13 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms Gemcitabine-TRIPHOSPHATE
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2010-04-12
_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 503.138
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GTF
_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 6DW5
_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
GTF F1 F1 F 0 1 N N N -1.180 -0.081 -2.652 -5.424 -1.746 1.484 F1 GTF 1
GTF N1 N1 N 0 1 N N N -3.161 0.808 -0.742 -4.272 1.139 0.501 N1 GTF 2
GTF C2 C1 C 0 1 N N N -3.118 -0.343 0.311 -4.295 1.353 -0.827 C2 GTF 3
GTF F2 F2 F 0 1 N N N -2.860 1.541 -3.292 -5.163 -1.008 -0.677 F2 GTF 4
GTF O2 O1 O 0 1 N N N -2.072 -0.930 0.654 -3.836 0.509 -1.579 O2 GTF 5
GTF N3 N2 N 0 1 N N N -4.459 -0.782 0.890 -4.810 2.471 -1.335 N3 GTF 6
GTF C4 C2 C 0 1 N N N -5.721 -0.088 0.439 -5.316 3.406 -0.540 C4 GTF 7
GTF N4 N3 N 0 1 N N N -6.904 -0.498 1.029 -5.846 4.557 -1.076 N4 GTF 8
GTF C5 C3 C 0 1 N N N -5.793 1.022 -0.569 -5.307 3.212 0.857 C5 GTF 9
GTF C6 C4 C 0 1 N N N -4.487 1.465 -1.164 -4.780 2.070 1.357 C6 GTF 10
GTF PA P1 P 0 1 N N N -3.030 6.733 -1.512 1.662 -1.849 -0.553 PA GTF 11
GTF PB P2 P 0 1 N N N -5.533 7.492 -2.790 4.264 -0.450 -0.313 PB GTF 12
GTF PG P3 P 0 1 N N N -5.857 5.591 -5.270 5.862 1.882 0.579 PG GTF 13
GTF "C1'" C5 C 0 1 N N R -1.791 1.272 -1.247 -3.705 -0.104 1.030 "C1'" GTF 14
GTF O1A O2 O 0 1 N N N -2.054 7.600 -0.604 2.046 -3.409 -0.456 O1A GTF 15
GTF O1B O3 O 0 1 N N N -5.195 8.897 -3.342 4.180 0.088 -1.689 O1B GTF 16
GTF O1G O4 O 0 1 N N N -5.145 4.524 -6.048 5.622 2.952 1.758 O1G GTF 17
GTF "C2'" C6 C 0 1 N N N -1.653 1.218 -2.563 -4.506 -1.321 0.517 "C2'" GTF 18
GTF O2A O5 O 0 1 N N N -2.653 7.293 -2.865 1.541 -1.457 -1.975 O2A GTF 19
GTF O2B O6 O 0 1 N N N -7.019 7.153 -2.385 5.307 -1.675 -0.278 O2B GTF 20
GTF O2G O7 O 0 1 N N N -7.244 5.244 -4.730 7.336 1.251 0.719 O2G GTF 21
GTF "C3'" C7 C 0 1 N N R -0.582 2.316 -2.996 -3.431 -2.405 0.279 "C3'" GTF 22
GTF "O3'" O8 O 0 1 N N N 0.752 2.051 -2.864 -3.671 -3.541 1.111 "O3'" GTF 23
GTF O3A O9 O 0 1 N N N -4.665 7.157 -1.401 2.812 -0.968 0.150 O3A GTF 24
GTF O3B O10 O 0 1 N N N -4.980 6.228 -3.926 4.764 0.709 0.687 O3B GTF 25
GTF O3G O11 O 0 1 N N N -5.888 6.683 -6.305 5.736 2.557 -0.732 O3G GTF 26
GTF "C4'" C8 C 0 1 N N R -1.162 3.541 -2.084 -2.107 -1.714 0.675 "C4'" GTF 27
GTF "O4'" O12 O 0 1 N N N -1.380 2.878 -0.919 -2.368 -0.302 0.521 "O4'" GTF 28
GTF "C5'" C9 C 0 1 N N N -2.454 4.238 -2.704 -0.977 -2.152 -0.259 "C5'" GTF 29
GTF "O5'" O13 O 0 1 N N N -3.135 5.041 -1.730 0.258 -1.594 0.194 "O5'" GTF 30
GTF H1 H1 H 0 1 N N N -6.894 -1.222 1.719 -5.851 4.687 -2.037 H1 GTF 31
GTF H2 H2 H 0 1 N N N -7.769 -0.070 0.766 -6.215 5.238 -0.492 H2 GTF 32
GTF H3 H3 H 0 1 N N N -6.731 1.477 -0.851 -5.714 3.964 1.517 H3 GTF 33
GTF H4 H4 H 0 1 N N N -4.478 2.256 -1.899 -4.762 1.898 2.423 H4 GTF 34
GTF H5 H5 H 0 1 N N N -1.026 0.656 -0.752 -3.697 -0.084 2.119 H5 GTF 35
GTF H6 H6 H 0 1 N N N -1.547 8.186 -1.153 2.142 -3.735 0.449 H6 GTF 36
GTF H7 H7 H 0 1 N N N -4.940 4.848 -6.917 6.249 3.688 1.755 H7 GTF 37
GTF H8 H8 H 0 1 N N N -7.571 7.911 -2.541 5.413 -2.077 0.595 H8 GTF 38
GTF H9 H9 H 0 1 N N N -7.895 5.792 -5.153 7.490 0.792 1.556 H9 GTF 39
GTF H10 H10 H 0 1 N N N -0.804 2.578 -4.041 -3.411 -2.699 -0.771 H10 GTF 40
GTF H11 H11 H 0 1 N N N 1.255 2.799 -3.163 -4.518 -3.978 0.946 H11 GTF 41
GTF H12 H12 H 0 1 N N N -0.370 4.298 -1.984 -1.855 -1.943 1.711 H12 GTF 42
GTF H13 H13 H 0 1 N N N -2.147 4.878 -3.544 -0.906 -3.240 -0.258 H13 GTF 43
GTF H14 H14 H 0 1 N N N -3.140 3.459 -3.069 -1.184 -1.801 -1.270 H14 GTF 44
# #
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
GTF O3G PG DOUB N N 1
GTF O1G PG SING N N 2
GTF PG O2G SING N N 3
GTF PG O3B SING N N 4
GTF O3B PB SING N N 5
GTF O1B PB DOUB N N 6
GTF F2 "C2'" SING N N 7
GTF "C3'" "O3'" SING N N 8
GTF "C3'" "C2'" SING N N 9
GTF "C3'" "C4'" SING N N 10
GTF O2A PA DOUB N N 11
GTF PB O2B SING N N 12
GTF PB O3A SING N N 13
GTF "C5'" "C4'" SING N N 14
GTF "C5'" "O5'" SING N N 15
GTF F1 "C2'" SING N N 16
GTF "C2'" "C1'" SING N N 17
GTF "C4'" "O4'" SING N N 18
GTF "O5'" PA SING N N 19
GTF PA O3A SING N N 20
GTF PA O1A SING N N 21
GTF "C1'" "O4'" SING N N 22
GTF "C1'" N1 SING N N 23
GTF C6 N1 SING N N 24
GTF C6 C5 DOUB N N 25
GTF N1 C2 SING N N 26
GTF C5 C4 SING N N 27
GTF C2 O2 DOUB N N 28
GTF C2 N3 SING N N 29
GTF C4 N3 DOUB N N 30
GTF C4 N4 SING N N 31
GTF N4 H1 SING N N 32
GTF N4 H2 SING N N 33
GTF C5 H3 SING N N 34
GTF C6 H4 SING N N 35
GTF "C1'" H5 SING N N 36
GTF O1A H6 SING N N 37
GTF O1G H7 SING N N 38
GTF O2B H8 SING N N 39
GTF O2G H9 SING N N 40
GTF "C3'" H10 SING N N 41
GTF "O3'" H11 SING N N 42
GTF "C4'" H12 SING N N 43
GTF "C5'" H13 SING N N 44
GTF "C5'" H14 SING N N 45
# #
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
GTF SMILES ACDLabs 12.01 "FC2(F)C(N1C(=O)N=C(N)C=C1)OC(C2O)COP(OP(O)(=O)OP(O)(O)=O)(O)=O"
GTF InChI InChI 1.03 "InChI=1S/C9H14F2N3O13P3/c10-9(11)6(15)4(25-7(9)14-2-1-5(12)13-8(14)16)3-24-29(20,21)27-30(22,23)26-28(17,18)19/h1-2,4,6-7,15H,3H2,(H,20,21)(H,22,23)(H2,12,13,16)(H2,17,18,19)/t4-,6-,7-/m1/s1"
GTF InChIKey InChI 1.03 YMOXEIOKAJSRQX-QPPQHZFASA-N
GTF SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)C2(F)F"
GTF SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)C2(F)F"
GTF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1=CN(C(=O)N=C1N)[C@H]2C([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)(F)F"
GTF SMILES "OpenEye OEToolkits" 2.0.6 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)(F)F"
# #
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
GTF "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate)"
GTF "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[(2~{R},3~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4,4-bis(fluoranyl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 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
GTF "Create component" 2010-04-12 RCSB
GTF "Modify descriptor" 2011-06-04 RCSB
GTF "Modify synonyms" 2018-06-27 RCSB
GTF "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id GTF
_pdbx_chem_comp_synonyms.name Gemcitabine-TRIPHOSPHATE
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##