data_FF4
#
_chem_comp.id FF4
_chem_comp.name "2'-deoxy-5'-O-[(R)-{[(R)-[(S)-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 2018-03-27
_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 FF4
_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 6CTR
_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
FF4 C4 C1 C 0 1 N N N 9.325 7.550 10.995 -6.792 -2.615 0.416 C4 FF4 1
FF4 N4 N1 N 0 1 N N N 10.781 7.567 11.249 -7.584 -3.595 0.969 N4 FF4 2
FF4 C5 C2 C 0 1 N N N 8.464 7.156 12.016 -6.600 -2.562 -0.980 C5 FF4 3
FF4 C6 C3 C 0 1 N N N 7.091 7.133 11.732 -5.815 -1.588 -1.497 C6 FF4 4
FF4 N3 N2 N 0 1 N N N 8.846 7.907 9.800 -6.208 -1.712 1.193 N3 FF4 5
FF4 C2 C4 C 0 1 N N N 7.534 7.862 9.579 -5.439 -0.760 0.669 C2 FF4 6
FF4 O2 O1 O 0 1 N N N 7.108 8.178 8.488 -4.912 0.059 1.404 O2 FF4 7
FF4 N1 N3 N 0 1 N N N 6.676 7.489 10.523 -5.232 -0.686 -0.659 N1 FF4 8
FF4 "C1'" C5 C 0 1 N N R 5.218 7.427 10.207 -4.380 0.373 -1.206 "C1'" FF4 9
FF4 "C2'" C6 C 0 1 N N N 4.937 6.237 9.794 -4.980 1.761 -0.893 "C2'" FF4 10
FF4 "C3'" C7 C 0 1 N N S 4.412 5.485 11.041 -3.747 2.647 -0.606 "C3'" FF4 11
FF4 "O3'" O2 O 0 1 N N N 3.623 4.397 10.750 -3.671 3.720 -1.547 "O3'" FF4 12
FF4 "O4'" O3 O 0 1 N N N 4.429 7.634 11.566 -3.092 0.371 -0.552 "O4'" FF4 13
FF4 "C4'" C8 C 0 1 N N R 3.648 6.608 11.711 -2.548 1.689 -0.780 "C4'" FF4 14
FF4 "C5'" C9 C 0 1 N N N 3.425 6.333 13.268 -1.462 2.002 0.251 "C5'" FF4 15
FF4 "O5'" O4 O 0 1 N N N 4.688 6.221 13.879 -0.316 1.185 0.000 "O5'" FF4 16
FF4 PA P1 P 0 1 N N N 4.948 4.962 14.898 1.020 1.250 0.895 PA FF4 17
FF4 O1A O5 O 0 1 N N N 3.872 4.932 15.962 0.689 0.755 2.391 O1A FF4 18
FF4 O2A O6 O 0 1 N N N 6.352 5.046 15.430 1.520 2.642 0.935 O2A FF4 19
FF4 O3A O7 O 0 1 N N N 4.887 3.621 13.919 2.145 0.294 0.251 O3A FF4 20
FF4 PB P2 P 0 1 N N N 3.771 2.446 13.858 3.734 0.142 0.455 PB FF4 21
FF4 O1B O8 O 0 1 N N N 2.440 2.881 14.412 4.458 1.532 0.089 O1B FF4 22
FF4 O2B O9 O 0 1 N N N 3.707 2.106 12.398 4.019 -0.206 1.865 O2B FF4 23
FF4 C3B C10 C 0 1 N N S 4.469 0.925 14.747 4.364 -1.177 -0.635 C3B FF4 24
FF4 F4B F1 F 0 1 N N N 5.795 1.138 14.839 4.094 -0.848 -1.968 F4B FF4 25
FF4 PG P3 P 0 1 N N N 3.787 0.806 16.450 6.163 -1.349 -0.403 PG FF4 26
FF4 O1G O10 O 0 1 N N N 4.788 0.111 17.311 6.720 -2.514 -1.366 O1G FF4 27
FF4 O2G O11 O 0 1 N N N 3.537 2.218 16.947 6.887 0.041 -0.770 O2G FF4 28
FF4 O3G O12 O 0 1 N N N 2.509 0.050 16.449 6.448 -1.697 1.007 O3G FF4 29
FF4 H1 H1 H 0 1 N N N 11.412 7.846 10.525 -8.013 -4.251 0.398 H1 FF4 30
FF4 H2 H2 H 0 1 N N N 11.135 7.299 12.145 -7.714 -3.628 1.929 H2 FF4 31
FF4 H3 H3 H 0 1 N N N 8.840 6.879 12.990 -7.071 -3.288 -1.626 H3 FF4 32
FF4 H4 H4 H 0 1 N N N 6.381 6.830 12.487 -5.652 -1.527 -2.563 H4 FF4 33
FF4 H5 H5 H 0 1 N N N 4.941 8.223 9.500 -4.259 0.244 -2.282 H5 FF4 34
FF4 H6 H6 H 0 1 N N N 4.164 6.273 9.012 -5.532 2.142 -1.752 H6 FF4 35
FF4 H7 H7 H 0 1 N N N 5.837 5.744 9.398 -5.625 1.709 -0.016 H7 FF4 36
FF4 H8 H8 H 0 1 N N N 5.268 5.201 11.671 -3.783 3.033 0.413 H8 FF4 37
FF4 H9 H9 H 0 1 N N N 3.770 3.717 11.397 -4.430 4.319 -1.522 H9 FF4 38
FF4 H10 H10 H 0 1 N N N 2.667 6.734 11.229 -2.146 1.764 -1.790 H10 FF4 39
FF4 H11 H11 H 0 1 N N N 2.866 7.167 13.717 -1.182 3.053 0.176 H11 FF4 40
FF4 H12 H12 H 0 1 N N N 2.861 5.398 13.404 -1.841 1.798 1.253 H12 FF4 41
FF4 H13 H13 H 0 1 N N N 4.275 4.973 16.821 0.356 -0.151 2.441 H13 FF4 42
FF4 H14 H14 H 0 1 N N N 1.787 2.861 13.722 4.314 1.822 -0.822 H14 FF4 43
FF4 H15 H15 H 0 1 N N N 4.164 0.031 14.183 3.874 -2.118 -0.387 H15 FF4 44
FF4 H16 H16 H 0 1 N N N 4.399 -0.673 17.681 7.673 -2.661 -1.295 H16 FF4 45
FF4 H17 H17 H 0 1 N N N 2.616 2.323 17.153 6.744 0.331 -1.681 H17 FF4 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
FF4 O2 C2 DOUB N N 1
FF4 C2 N3 SING N N 2
FF4 C2 N1 SING N N 3
FF4 "C2'" "C1'" SING N N 4
FF4 "C2'" "C3'" SING N N 5
FF4 N3 C4 DOUB N N 6
FF4 "C1'" N1 SING N N 7
FF4 "C1'" "O4'" SING N N 8
FF4 N1 C6 SING N N 9
FF4 "O3'" "C3'" SING N N 10
FF4 C4 N4 SING N N 11
FF4 C4 C5 SING N N 12
FF4 "C3'" "C4'" SING N N 13
FF4 "O4'" "C4'" SING N N 14
FF4 "C4'" "C5'" SING N N 15
FF4 C6 C5 DOUB N N 16
FF4 O2B PB DOUB N N 17
FF4 "C5'" "O5'" SING N N 18
FF4 PB O3A SING N N 19
FF4 PB O1B SING N N 20
FF4 PB C3B SING N N 21
FF4 "O5'" PA SING N N 22
FF4 O3A PA SING N N 23
FF4 C3B F4B SING N N 24
FF4 C3B PG SING N N 25
FF4 PA O2A DOUB N N 26
FF4 PA O1A SING N N 27
FF4 O3G PG DOUB N N 28
FF4 PG O2G SING N N 29
FF4 PG O1G SING N N 30
FF4 N4 H1 SING N N 31
FF4 N4 H2 SING N N 32
FF4 C5 H3 SING N N 33
FF4 C6 H4 SING N N 34
FF4 "C1'" H5 SING N N 35
FF4 "C2'" H6 SING N N 36
FF4 "C2'" H7 SING N N 37
FF4 "C3'" H8 SING N N 38
FF4 "O3'" H9 SING N N 39
FF4 "C4'" H10 SING N N 40
FF4 "C5'" H11 SING N N 41
FF4 "C5'" H12 SING N N 42
FF4 O1A H13 SING N N 43
FF4 O1B H14 SING N N 44
FF4 C3B H15 SING N N 45
FF4 O1G H16 SING N N 46
FF4 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
FF4 SMILES ACDLabs 12.01 "C=1(N)C=CN(C(N=1)=O)C2OC(C(C2)O)COP(=O)(O)OP(O)(C(F)P(O)(O)=O)=O"
FF4 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"
FF4 InChIKey InChI 1.03 CDDSHZIEMFLZDN-LWIVVEGESA-N
FF4 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"
FF4 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"
FF4 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"
FF4 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
FF4 "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5'-O-[(R)-{[(R)-[(S)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine"
FF4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(~{S})-[[[(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
FF4 "Create component" 2018-03-27 RCSB
FF4 "Initial release" 2018-06-20 RCSB
#