data_6CF
#
_chem_comp.id 6CF
_chem_comp.name "2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H16 F2 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 2011-04-19
_chem_comp.pdbx_modified_date 2012-01-13
_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 501.165
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 6CF
_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 3RJH
_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
6CF N1 N1 N 0 1 N N N 6.721 7.461 10.613 5.396 0.550 -0.612 N1 6CF 1
6CF P1 P1 P 0 1 N N N 5.098 5.378 15.144 -1.016 -1.066 0.623 P1 6CF 2
6CF C2 C2 C 0 1 N N N 7.625 7.861 9.612 5.469 0.882 0.690 C2 6CF 3
6CF O2 O2 O 0 1 N N N 7.186 8.215 8.504 4.855 0.223 1.513 O2 6CF 4
6CF P2 P2 P 0 1 N N N 4.017 2.688 14.103 -3.799 -0.033 0.405 P2 6CF 5
6CF N3 N3 N 0 1 N N N 8.955 7.857 9.881 6.200 1.919 1.095 N3 6CF 6
6CF P3 P3 P 0 1 N N N 3.894 1.277 16.396 -6.376 1.208 -0.375 P3 6CF 7
6CF C4 C4 C 0 1 N N N 9.392 7.483 11.086 6.877 2.652 0.222 C4 6CF 8
6CF N4 N4 N 0 1 N N N 10.709 7.469 11.296 7.630 3.721 0.652 N4 6CF 9
6CF C5 C5 C 0 1 N N N 8.498 7.101 12.127 6.822 2.331 -1.150 C5 6CF 10
6CF C6 C6 C 0 1 N N N 7.185 7.108 11.853 6.074 1.274 -1.546 C6 6CF 11
6CF "C1'" "C1'" C 0 1 N N R 5.275 7.402 10.291 4.588 -0.600 -1.027 "C1'" 6CF 12
6CF F1A F1A F 0 1 N N N 6.221 3.774 13.511 -1.691 1.129 -0.683 F1A 6CF 13
6CF O1A O1A O 0 1 N N N 3.876 5.400 15.997 -0.835 -0.285 2.018 O1A 6CF 14
6CF O1B O1B O 0 1 N N N 4.171 2.244 12.695 -3.633 0.686 1.688 O1B 6CF 15
6CF O1G O1G O 0 1 N N N 3.601 2.642 16.906 -6.731 2.326 -1.478 O1G 6CF 16
6CF "C2'" "C2'" C 0 1 N N N 4.872 6.042 9.707 5.129 -1.897 -0.384 "C2'" 6CF 17
6CF F2A F2A F 0 1 N N N 6.049 3.048 15.538 -2.345 -0.835 -1.649 F2A 6CF 18
6CF O2A O2A O 0 1 N N N 6.351 5.956 15.697 -1.541 -2.426 0.883 O2A 6CF 19
6CF O2B O2B O 0 1 N N N 2.738 3.326 14.520 -4.370 -1.512 0.689 O2B 6CF 20
6CF O2G O2G O 0 1 N N N 4.979 0.484 17.038 -7.321 -0.077 -0.589 O2G 6CF 21
6CF "C3'" "C3'" C 0 1 N N S 4.448 5.299 10.967 3.858 -2.713 -0.060 "C3'" 6CF 22
6CF "O3'" "O3'" O 0 1 N N N 3.562 4.218 10.693 3.863 -3.951 -0.774 "O3'" 6CF 23
6CF C3A C3A C 0 1 N N N 5.411 3.703 14.561 -2.187 -0.156 -0.437 C3A 6CF 24
6CF O3B O3B O 0 1 N N N 4.167 1.406 14.906 -4.834 0.771 -0.530 O3B 6CF 25
6CF O3G O3G O 0 1 N N N 2.647 0.492 16.577 -6.597 1.763 0.979 O3G 6CF 26
6CF "C4'" "C4'" C 0 1 N N R 3.708 6.390 11.715 2.700 -1.813 -0.546 "C4'" 6CF 27
6CF "O4'" "O4'" O 0 1 N N N 4.519 7.570 11.487 3.240 -0.474 -0.525 "O4'" 6CF 28
6CF "C5'" "C5'" C 0 1 N N N 3.494 6.124 13.189 1.507 -1.921 0.406 "C5'" 6CF 29
6CF "O5'" "O5'" O 0 1 N N N 4.691 6.338 13.933 0.408 -1.174 -0.121 "O5'" 6CF 30
6CF HN4 HN4 H 0 1 N N N 11.335 7.733 10.562 7.666 3.939 1.597 HN4 6CF 31
6CF HN4A HN4A H 0 0 N N N 11.070 7.194 12.187 8.124 4.255 0.011 HN4A 6CF 32
6CF H5 H5 H 0 1 N N N 8.864 6.816 13.102 7.367 2.919 -1.873 H5 6CF 33
6CF H6 H6 H 0 1 N N N 6.481 6.830 12.623 6.016 1.007 -2.591 H6 6CF 34
6CF "H1'" "H1'" H 0 1 N N N 5.077 8.195 9.555 4.583 -0.687 -2.113 "H1'" 6CF 35
6CF HO1A HO1A H 0 0 N N N 4.079 5.807 16.831 -0.493 0.615 1.923 HO1A 6CF 36
6CF HO1G HO1G H 0 0 N N N 2.704 2.678 17.217 -7.646 2.636 -1.443 HO1G 6CF 37
6CF "H2'" "H2'" H 0 1 N N N 4.055 6.126 8.975 5.761 -2.437 -1.088 "H2'" 6CF 38
6CF "H2'A" "H2'A" H 0 0 N N N 5.705 5.545 9.188 5.680 -1.670 0.529 "H2'A" 6CF 39
6CF HO2B HO2B H 0 0 N N N 2.147 3.368 13.777 -4.505 -2.041 -0.109 HO2B 6CF 40
6CF HO2G HO2G H 0 0 N N N 4.616 -0.316 17.400 -7.229 -0.493 -1.457 HO2G 6CF 41
6CF "H3'" "H3'" H 0 1 N N N 5.294 4.843 11.502 3.780 -2.890 1.013 "H3'" 6CF 42
6CF "HO3'" "HO3'" H 0 0 N N N 3.708 3.521 11.322 4.604 -4.530 -0.551 "HO3'" 6CF 43
6CF "H4'" "H4'" H 0 1 N N N 2.676 6.483 11.347 2.403 -2.089 -1.557 "H4'" 6CF 44
6CF "H5'" "H5'" H 0 1 N N N 2.716 6.805 13.564 1.218 -2.967 0.511 "H5'" 6CF 45
6CF "H5'A" "H5'A" H 0 0 N N N 3.176 5.079 13.319 1.783 -1.521 1.382 "H5'A" 6CF 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
6CF C2 N1 SING N N 1
6CF "C1'" N1 SING N N 2
6CF N1 C6 SING N N 3
6CF "O5'" P1 SING N N 4
6CF C3A P1 SING N N 5
6CF P1 O2A DOUB N N 6
6CF P1 O1A SING N N 7
6CF O2 C2 DOUB N N 8
6CF C2 N3 SING N N 9
6CF O1B P2 DOUB N N 10
6CF P2 O2B SING N N 11
6CF P2 C3A SING N N 12
6CF P2 O3B SING N N 13
6CF N3 C4 DOUB N N 14
6CF O3B P3 SING N N 15
6CF P3 O3G DOUB N N 16
6CF P3 O1G SING N N 17
6CF P3 O2G SING N N 18
6CF C4 N4 SING N N 19
6CF C4 C5 SING N N 20
6CF N4 HN4 SING N N 21
6CF N4 HN4A SING N N 22
6CF C6 C5 DOUB N N 23
6CF C5 H5 SING N N 24
6CF C6 H6 SING N N 25
6CF "C2'" "C1'" SING N N 26
6CF "C1'" "O4'" SING N N 27
6CF "C1'" "H1'" SING N N 28
6CF F1A C3A SING N N 29
6CF O1A HO1A SING N N 30
6CF O1G HO1G SING N N 31
6CF "C2'" "C3'" SING N N 32
6CF "C2'" "H2'" SING N N 33
6CF "C2'" "H2'A" SING N N 34
6CF C3A F2A SING N N 35
6CF O2B HO2B SING N N 36
6CF O2G HO2G SING N N 37
6CF "O3'" "C3'" SING N N 38
6CF "C3'" "C4'" SING N N 39
6CF "C3'" "H3'" SING N N 40
6CF "O3'" "HO3'" SING N N 41
6CF "O4'" "C4'" SING N N 42
6CF "C4'" "C5'" SING N N 43
6CF "C4'" "H4'" SING N N 44
6CF "C5'" "O5'" SING N N 45
6CF "C5'" "H5'" SING N N 46
6CF "C5'" "H5'A" 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
6CF SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)C(F)(F)P(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2O"
6CF SMILES_CANONICAL CACTVS 3.370 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)C(F)(F)[P](O)(=O)O[P](O)(O)=O)O2"
6CF SMILES CACTVS 3.370 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)C(F)(F)[P](O)(=O)O[P](O)(O)=O)O2"
6CF SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@](=O)(C(F)(F)[P@](=O)(O)OP(=O)(O)O)O)O"
6CF SMILES "OpenEye OEToolkits" 1.7.2 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(C(F)(F)P(=O)(O)OP(=O)(O)O)O)O"
6CF InChI InChI 1.03 "InChI=1S/C10H16F2N3O12P3/c11-10(12,29(20,21)27-30(22,23)24)28(18,19)25-4-6-5(16)3-8(26-6)15-2-1-7(13)14-9(15)17/h1-2,5-6,8,16H,3-4H2,(H,18,19)(H,20,21)(H2,13,14,17)(H2,22,23,24)/t5-,6+,8+/m0/s1"
6CF InChIKey InChI 1.03 NCCTXZHZERSHKT-SHYZEUOFSA-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
6CF "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine"
6CF "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "[(2R,3S,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-[bis(fluoranyl)-[oxidanyl(phosphonooxy)phosphoryl]methyl]phosphinic 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
6CF "Create component" 2011-04-19 RCSB
6CF "Modify descriptor" 2011-06-04 RCSB
#