data_F3C
#
_chem_comp.id F3C
_chem_comp.name "2'-deoxy-5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H17 F N3 O12 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-10-26
_chem_comp.pdbx_modified_date 2018-06-15
_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 483.175
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code F3C
_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 6BEL
_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
F3C C4 C1 C 0 1 N N N 9.331 7.582 10.964 -6.745 -2.637 0.403 C4 F3C 1
F3C N4 N1 N 0 1 N N N 10.791 7.604 11.181 -7.519 -3.632 0.952 N4 F3C 2
F3C C5 C2 C 0 1 N N N 8.495 7.186 12.006 -6.571 -2.564 -0.994 C5 F3C 3
F3C C6 C3 C 0 1 N N N 7.120 7.157 11.740 -5.803 -1.574 -1.508 C6 F3C 4
F3C N3 N2 N 0 1 N N N 8.825 7.924 9.777 -6.161 -1.738 1.185 N3 F3C 5
F3C C2 C4 C 0 1 N N N 7.515 7.885 9.585 -5.409 -0.770 0.664 C2 F3C 6
F3C O2 O1 O 0 1 N N N 7.059 8.207 8.509 -4.883 0.045 1.404 O2 F3C 7
F3C N1 N3 N 0 1 N N N 6.682 7.527 10.545 -5.220 -0.677 -0.665 N1 F3C 8
F3C "C1'" C5 C 0 1 N N R 5.222 7.458 10.233 -4.386 0.399 -1.209 "C1'" F3C 9
F3C "C2'" C6 C 0 1 N N N 4.947 6.261 9.820 -4.997 1.776 -0.869 "C2'" F3C 10
F3C "C3'" C7 C 0 1 N N S 4.403 5.489 11.052 -3.771 2.672 -0.586 "C3'" F3C 11
F3C "O3'" O2 O 0 1 N N N 3.608 4.408 10.715 -3.718 3.758 -1.513 "O3'" F3C 12
F3C "O4'" O3 O 0 1 N N N 4.408 7.654 11.576 -3.091 0.403 -0.570 "O4'" F3C 13
F3C "C4'" C8 C 0 1 N N R 3.647 6.614 11.740 -2.563 1.729 -0.787 "C4'" F3C 14
F3C "C5'" C9 C 0 1 N N N 3.471 6.385 13.309 -1.468 2.041 0.235 "C5'" F3C 15
F3C "O5'" O4 O 0 1 N N N 4.748 6.241 13.869 -0.317 1.240 -0.042 "O5'" F3C 16
F3C PA P1 P 0 1 N N N 4.979 4.979 14.875 1.030 1.308 0.838 PA F3C 17
F3C O1A O5 O 0 1 N N N 3.894 4.990 15.918 0.723 0.790 2.331 O1A F3C 18
F3C O2A O6 O 0 1 N N N 6.371 5.041 15.446 1.515 2.705 0.890 O2A F3C 19
F3C O3A O7 O 0 1 N N N 4.947 3.639 13.921 2.156 0.373 0.167 O3A F3C 20
F3C PB P2 P 0 1 N N N 3.808 2.472 13.863 3.750 0.236 0.350 PB F3C 21
F3C O1B O8 O 0 1 N N N 2.480 2.906 14.418 4.454 1.640 -0.007 O1B F3C 22
F3C O2B O9 O 0 1 N N N 3.723 2.121 12.404 4.056 -0.127 1.751 O2B F3C 23
F3C C3B C10 C 0 1 N N R 4.553 0.974 14.756 4.380 -1.061 -0.766 C3B F3C 24
F3C F4B F1 F 0 1 N N N 4.237 -0.142 14.070 3.768 -2.280 -0.456 F4B F3C 25
F3C PG P3 P 0 1 N N N 3.890 0.902 16.471 6.185 -1.216 -0.559 PG F3C 26
F3C O1G O10 O 0 1 N N N 3.652 2.315 16.929 6.741 -2.362 -1.544 O1G F3C 27
F3C O2G O11 O 0 1 N N N 4.893 0.232 17.354 6.889 0.187 -0.915 O2G F3C 28
F3C O3G O12 O 0 1 N N N 2.623 0.123 16.491 6.491 -1.579 0.843 O3G F3C 29
F3C H1 H1 H 0 1 N N N 11.403 7.875 10.438 -7.948 -4.286 0.378 H1 F3C 30
F3C H2 H2 H 0 1 N N N 11.168 7.347 12.071 -7.637 -3.680 1.914 H2 F3C 31
F3C H3 H3 H 0 1 N N N 8.889 6.914 12.974 -7.043 -3.286 -1.644 H3 F3C 32
F3C H4 H4 H 0 1 N N N 6.424 6.836 12.501 -5.655 -1.497 -2.575 H4 F3C 33
F3C H5 H5 H 0 1 N N N 4.943 8.248 9.520 -4.277 0.285 -2.287 H5 F3C 34
F3C H6 H6 H 0 1 N N N 4.186 6.297 9.027 -5.564 2.162 -1.717 H6 F3C 35
F3C H7 H7 H 0 1 N N N 5.855 5.773 9.435 -5.631 1.706 0.015 H7 F3C 36
F3C H8 H8 H 0 1 N N N 5.250 5.181 11.682 -3.798 3.044 0.438 H8 F3C 37
F3C H9 H9 H 0 1 N N N 3.733 3.712 11.350 -4.483 4.348 -1.471 H9 F3C 38
F3C H10 H10 H 0 1 N N N 2.652 6.727 11.284 -2.175 1.822 -1.801 H10 F3C 39
F3C H11 H11 H 0 1 N N N 2.961 7.250 13.758 -1.201 3.096 0.170 H11 F3C 40
F3C H12 H12 H 0 1 N N N 2.879 5.476 13.490 -1.833 1.819 1.237 H12 F3C 41
F3C H13 H13 H 0 1 N N N 4.285 5.035 16.782 0.400 -0.121 2.373 H13 F3C 42
F3C H14 H14 H 0 1 N N N 1.824 2.877 13.731 4.295 1.940 -0.913 H14 F3C 43
F3C H15 H15 H 0 1 N N N 5.635 1.158 14.833 4.155 -0.793 -1.798 H15 F3C 44
F3C H16 H16 H 0 1 N N N 2.733 2.429 17.141 7.697 -2.499 -1.487 H16 F3C 45
F3C H17 H17 H 0 1 N N N 4.507 -0.547 17.738 6.730 0.488 -1.821 H17 F3C 46
#
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
F3C O2 C2 DOUB N N 1
F3C C2 N3 SING N N 2
F3C C2 N1 SING N N 3
F3C N3 C4 DOUB N N 4
F3C "C2'" "C1'" SING N N 5
F3C "C2'" "C3'" SING N N 6
F3C "C1'" N1 SING N N 7
F3C "C1'" "O4'" SING N N 8
F3C N1 C6 SING N N 9
F3C "O3'" "C3'" SING N N 10
F3C C4 N4 SING N N 11
F3C C4 C5 SING N N 12
F3C "C3'" "C4'" SING N N 13
F3C "O4'" "C4'" SING N N 14
F3C C6 C5 DOUB N N 15
F3C "C4'" "C5'" SING N N 16
F3C O2B PB DOUB N N 17
F3C "C5'" "O5'" SING N N 18
F3C PB O3A SING N N 19
F3C PB O1B SING N N 20
F3C PB C3B SING N N 21
F3C "O5'" PA SING N N 22
F3C O3A PA SING N N 23
F3C F4B C3B SING N N 24
F3C C3B PG SING N N 25
F3C PA O2A DOUB N N 26
F3C PA O1A SING N N 27
F3C PG O3G DOUB N N 28
F3C PG O1G SING N N 29
F3C PG O2G SING N N 30
F3C N4 H1 SING N N 31
F3C N4 H2 SING N N 32
F3C C5 H3 SING N N 33
F3C C6 H4 SING N N 34
F3C "C1'" H5 SING N N 35
F3C "C2'" H6 SING N N 36
F3C "C2'" H7 SING N N 37
F3C "C3'" H8 SING N N 38
F3C "O3'" H9 SING N N 39
F3C "C4'" H10 SING N N 40
F3C "C5'" H11 SING N N 41
F3C "C5'" H12 SING N N 42
F3C O1A H13 SING N N 43
F3C O1B H14 SING N N 44
F3C C3B H15 SING N N 45
F3C O1G H16 SING N N 46
F3C O2G H17 SING N N 47
#
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
F3C SMILES ACDLabs 12.01 "C=1(N)C=CN(C(N=1)=O)C2OC(C(C2)O)COP(=O)(O)OP(O)(C(P(=O)(O)O)F)=O"
F3C InChI InChI 1.03 "InChI=1S/C10H17FN3O12P3/c11-9(27(17,18)19)28(20,21)26-29(22,23)24-4-6-5(15)3-8(25-6)14-2-1-7(12)13-10(14)16/h1-2,5-6,8-9,15H,3-4H2,(H,20,21)(H,22,23)(H2,12,13,16)(H2,17,18,19)/t5-,6+,8+,9+/m0/s1"
F3C InChIKey InChI 1.03 CDDSHZIEMFLZDN-HIORRCEOSA-N
F3C SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)[C@H](F)[P](O)(O)=O)O2"
F3C SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)[CH](F)[P](O)(O)=O)O2"
F3C SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)([C@H](F)P(=O)(O)O)O)O"
F3C SMILES "OpenEye OEToolkits" 2.0.6 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(C(F)P(=O)(O)O)O)O"
#
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
F3C "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine"
F3C "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(~{R})-[[[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]-fluoranyl-methyl]phosphonic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
F3C "Create component" 2017-10-26 RCSB
F3C "Initial release" 2018-06-20 RCSB
#