data_UFT
#
_chem_comp.id UFT
_chem_comp.name
;2'-deoxy-2'-fluorouridine 5'-(dihydrogen phosphate)
;
_chem_comp.type 'DNA LINKING'
_chem_comp.pdbx_type ATOMN
_chem_comp.formula 'C9 H12 F N2 O8 P'
_chem_comp.mon_nstd_parent_comp_id DU
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2008-07-07
_chem_comp.pdbx_modified_date 2024-09-27
_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 326.172
_chem_comp.one_letter_code U
_chem_comp.three_letter_code UFT
_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 3DD2
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_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
UFT OP3 OP3 O 0 1 N Y N N N N 1.791 -48.091 -34.440 4.622 -2.050 -1.261 OP3 UFT 1
UFT P P P 0 1 N N N N N N 0.500 -47.894 -33.504 4.266 -1.014 -0.082 P UFT 2
UFT OP1 OP1 O 0 1 N N N N N N -0.580 -48.564 -34.236 4.116 -1.750 1.194 OP1 UFT 3
UFT OP2 OP2 O 0 1 N N N N N N 0.338 -46.469 -33.109 5.450 0.068 0.058 OP2 UFT 4
UFT "O5'" "O5'" O 0 1 N N N N N N 0.864 -48.742 -32.203 2.888 -0.258 -0.430 "O5'" UFT 5
UFT N1 N1 N 0 1 N N N N N N 0.588 -52.195 -30.324 -2.364 -0.139 -0.132 N1 UFT 6
UFT C6 C6 C 0 1 N N N N N N -0.041 -51.722 -31.465 -2.320 -0.860 1.031 C6 UFT 7
UFT C2 C2 C 0 1 N N N N N N 0.589 -53.561 -30.030 -3.401 -0.269 -0.979 C2 UFT 8
UFT O2 O2 O 0 1 N N N N N N 1.144 -54.037 -29.042 -3.422 0.385 -2.004 O2 UFT 9
UFT N3 N3 N 0 1 N N N N N N -0.082 -54.350 -30.938 -4.415 -1.112 -0.709 N3 UFT 10
UFT C4 C4 C 0 1 N N N N N N -0.739 -53.936 -32.087 -4.406 -1.843 0.424 C4 UFT 11
UFT O4 O4 O 0 1 N N N N N N -1.351 -54.767 -32.772 -5.323 -2.606 0.670 O4 UFT 12
UFT C5 C5 C 0 1 N N N N N N -0.683 -52.522 -32.330 -3.326 -1.709 1.330 C5 UFT 13
UFT "F2'" "F2'" F 0 1 N N N N N N 3.357 -51.041 -28.359 -1.867 3.074 0.073 "F2'" UFT 14
UFT "C2'" "C2'" C 0 1 N N R N N N 2.793 -51.276 -29.586 -1.226 1.937 0.577 "C2'" UFT 15
UFT "C5'" "C5'" C 0 1 N N N N N N 1.425 -48.104 -31.048 2.249 0.650 0.470 "C5'" UFT 16
UFT "C4'" "C4'" C 0 1 N N R N N N 1.920 -49.126 -30.059 0.967 1.186 -0.170 "C4'" UFT 17
UFT "O4'" "O4'" O 0 1 N N N N N N 0.815 -49.957 -29.612 0.001 0.124 -0.328 "O4'" UFT 18
UFT "C1'" "C1'" C 0 1 N N R N N N 1.276 -51.283 -29.388 -1.276 0.787 -0.453 "C1'" UFT 19
UFT "C3'" "C3'" C 0 1 N N R N N N 2.971 -50.109 -30.558 0.283 2.206 0.767 "C3'" UFT 20
UFT "O3'" "O3'" O 0 1 N N N N N N 4.251 -49.482 -30.526 0.607 3.542 0.376 "O3'" UFT 21
UFT HOP3 HOP3 H 0 0 N Y N N N N 1.520 -48.130 -35.350 5.442 -2.543 -1.118 HOP3 UFT 22
UFT HOP2 HOP2 H 0 0 N N N N N N 0.303 -46.404 -32.162 5.605 0.588 -0.742 HOP2 UFT 23
UFT H6 H6 H 0 1 N N N N N N -0.013 -50.661 -31.667 -1.484 -0.750 1.706 H6 UFT 24
UFT H5 H5 H 0 1 N N N N N N -1.156 -52.104 -33.206 -3.304 -2.284 2.243 H5 UFT 25
UFT "H2'" "H2'" H 0 1 N N N N N N 3.253 -52.198 -29.972 -1.683 1.628 1.517 "H2'" UFT 26
UFT "H5'" "H5'" H 0 1 N N N N N N 2.268 -47.471 -31.362 2.002 0.130 1.396 "H5'" UFT 27
UFT "H5'A" "H5'A" H 0 0 N N N N N N 0.645 -47.496 -30.567 2.922 1.480 0.688 "H5'A" UFT 28
UFT "H4'" "H4'" H 0 1 N N N N N N 2.381 -48.504 -29.278 1.189 1.644 -1.134 "H4'" UFT 29
UFT "H1'" "H1'" H 0 1 N N N N N N 1.053 -51.636 -28.370 -1.402 1.185 -1.460 "H1'" UFT 30
UFT "H3'" "H3'" H 0 1 N N N N N N 2.874 -50.449 -31.600 0.575 2.029 1.802 "H3'" UFT 31
UFT "HO3'" "HO3'" H 0 0 N Y N N N N 4.558 -49.343 -31.414 0.157 4.223 0.894 "HO3'" UFT 32
UFT HN3 HN3 H 0 1 N N N N N N -0.097 -55.332 -30.747 -5.155 -1.193 -1.331 HN3 UFT 33
#
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
UFT OP3 P SING N N 1
UFT OP1 P DOUB N N 2
UFT P OP2 SING N N 3
UFT P "O5'" SING N N 4
UFT OP3 HOP3 SING N N 5
UFT OP2 HOP2 SING N N 6
UFT "O5'" "C5'" SING N N 7
UFT C6 N1 SING N N 8
UFT N1 C2 SING N N 9
UFT N1 "C1'" SING N N 10
UFT C5 C6 DOUB N N 11
UFT C6 H6 SING N N 12
UFT N3 C2 SING N N 13
UFT C2 O2 DOUB N N 14
UFT C4 N3 SING N N 15
UFT O4 C4 DOUB N N 16
UFT C5 C4 SING N N 17
UFT C5 H5 SING N N 18
UFT "C2'" "F2'" SING N N 19
UFT "C3'" "C2'" SING N N 20
UFT "C2'" "C1'" SING N N 21
UFT "C2'" "H2'" SING N N 22
UFT "C5'" "C4'" SING N N 23
UFT "C5'" "H5'" SING N N 24
UFT "C5'" "H5'A" SING N N 25
UFT "C3'" "C4'" SING N N 26
UFT "C4'" "O4'" SING N N 27
UFT "C4'" "H4'" SING N N 28
UFT "O4'" "C1'" SING N N 29
UFT "C1'" "H1'" SING N N 30
UFT "C3'" "O3'" SING N N 31
UFT "C3'" "H3'" SING N N 32
UFT "O3'" "HO3'" SING N N 33
UFT N3 HN3 SING N N 34
#
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
UFT SMILES ACDLabs 10.04 'O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(F)C2O'
UFT SMILES_CANONICAL CACTVS 3.341 'O[C@H]1[C@@H](F)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O'
UFT SMILES CACTVS 3.341 'O[CH]1[CH](F)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O'
UFT SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)F'
UFT SMILES 'OpenEye OEToolkits' 1.5.0 'C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)F'
UFT InChI InChI 1.03 'InChI=1S/C9H12FN2O8P/c10-6-7(14)4(3-19-21(16,17)18)20-8(6)12-2-1-5(13)11-9(12)15/h1-2,4,6-8,14H,3H2,(H,11,13,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1'
UFT InChIKey InChI 1.03 RTGGYPQTXNSBPD-XVFCMESISA-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
UFT 'SYSTEMATIC NAME' ACDLabs 10.04
;2'-deoxy-2'-fluorouridine 5'-(dihydrogen phosphate)
;
UFT 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '[(2R,3R,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-4-fluoro-3-hydroxy-oxolan-2-yl]methyl dihydrogen 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
UFT 'Create component' 2008-07-07 RCSB
UFT 'Modify descriptor' 2011-06-04 RCSB
UFT 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id UFT
_pdbx_chem_comp_pcm.modified_residue_id LYS
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Covalent chemical modification'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom C6
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom NZ
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
UFT OP3 O 10.527 -5.896 1
UFT P P 9.645 -4.683 2
UFT OP1 O 10.859 -3.801 3
UFT OP2 O 8.432 -5.564 4
UFT "O5'" O 8.764 -3.469 5
UFT N1 N 5.640 1.396 6
UFT C6 C 4.341 2.146 7
UFT C2 C 6.939 2.146 8
UFT O2 O 8.238 1.396 9
UFT N3 N 6.939 3.646 10
UFT C4 C 5.640 4.396 11
UFT O4 O 5.640 5.896 12
UFT C5 C 4.341 3.646 13
UFT "F2'" F 3.000 -0.522 14
UFT "C2'" C 4.427 -0.986 15
UFT "C5'" C 7.272 -3.626 16
UFT "C4'" C 6.390 -2.412 17
UFT "O4'" O 6.854 -0.986 18
UFT "C1'" C 5.640 -0.104 19
UFT "C3'" C 4.890 -2.412 20
UFT "O3'" O 4.008 -3.626 21
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
UFT OP3 P SINGLE NONE 1
UFT OP1 P DOUBLE NONE 2
UFT P OP2 SINGLE NONE 3
UFT P "O5'" SINGLE NONE 4
UFT "O5'" "C5'" SINGLE NONE 5
UFT C6 N1 SINGLE NONE 6
UFT N1 C2 SINGLE NONE 7
UFT "C1'" N1 SINGLE BEGINDASH 8
UFT C5 C6 DOUBLE NONE 9
UFT N3 C2 SINGLE NONE 10
UFT C2 O2 DOUBLE NONE 11
UFT C4 N3 SINGLE NONE 12
UFT O4 C4 DOUBLE NONE 13
UFT C5 C4 SINGLE NONE 14
UFT "C2'" "F2'" SINGLE BEGINWEDGE 15
UFT "C3'" "C2'" SINGLE NONE 16
UFT "C2'" "C1'" SINGLE NONE 17
UFT "C4'" "C5'" SINGLE BEGINDASH 18
UFT "C3'" "C4'" SINGLE NONE 19
UFT "C4'" "O4'" SINGLE NONE 20
UFT "O4'" "C1'" SINGLE NONE 21
UFT "C3'" "O3'" SINGLE BEGINWEDGE 22
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
UFT MurckoScaffold S1 scaffold 'O=c1ccn([C@H]2CCCO2)c(=O)[nH]1' InChI=1S/C8H10N2O3/c11-6-3-4-10(8(12)9-6)7-2-1-5-13-7/h3-4,7H,1-2,5H2,(H,9,11,12)/t7-/m1/s1 CWWIKVUHBBTKHC-SSDOTTSWSA-N
UFT phosphate F1 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
UFT pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
UFT N1 S1 1
UFT C6 S1 1
UFT C2 S1 1
UFT O2 S1 1
UFT N3 S1 1
UFT C4 S1 1
UFT O4 S1 1
UFT C5 S1 1
UFT "C2'" S1 1
UFT "C4'" S1 1
UFT "O4'" S1 1
UFT "C1'" S1 1
UFT "C3'" S1 1
UFT OP3 F1 1
UFT P F1 1
UFT OP1 F1 1
UFT OP2 F1 1
UFT "O5'" F1 1
UFT C5 F2 1
UFT C6 F2 1
UFT N1 F2 1
UFT C2 F2 1
UFT N3 F2 1
UFT C4 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id UFT
_pdbe_chem_comp_rdkit_properties.exactmw 326.032
_pdbe_chem_comp_rdkit_properties.amw 326.173
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 10
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 9
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 33
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 12
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.556
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 132.725
_pdbe_chem_comp_rdkit_properties.tpsa 151.080
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.042
_pdbe_chem_comp_rdkit_properties.CrippenMR 64.348
_pdbe_chem_comp_rdkit_properties.chi0v 10.380
_pdbe_chem_comp_rdkit_properties.chi1v 6.223
_pdbe_chem_comp_rdkit_properties.chi2v 2.223
_pdbe_chem_comp_rdkit_properties.chi3v 2.223
_pdbe_chem_comp_rdkit_properties.chi4v 1.342
_pdbe_chem_comp_rdkit_properties.chi0n 21.486
_pdbe_chem_comp_rdkit_properties.chi1n 10.434
_pdbe_chem_comp_rdkit_properties.chi2n 1.908
_pdbe_chem_comp_rdkit_properties.chi3n 1.908
_pdbe_chem_comp_rdkit_properties.chi4n 1.147
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.360
_pdbe_chem_comp_rdkit_properties.kappa1 6.405
_pdbe_chem_comp_rdkit_properties.kappa2 5.794
_pdbe_chem_comp_rdkit_properties.kappa3 3.643
_pdbe_chem_comp_rdkit_properties.Phi 1.767
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
UFT UniChem ZINC ZINC000013604346
UFT UniChem SureChEMBL SCHEMBL600756
UFT UniChem BRENDA 41264
UFT UniChem PubChem 44448730
UFT UniChem Nikkaji J2.014.161A
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
UFT OP3 3.551 2.649 1.099 ETKDGv3 1
UFT P 3.750 1.083 0.491 ETKDGv3 2
UFT OP1 4.619 1.144 -0.746 ETKDGv3 3
UFT OP2 4.507 0.125 1.664 ETKDGv3 4
UFT "O5'" 2.220 0.443 0.098 ETKDGv3 5
UFT N1 -1.959 -0.280 0.476 ETKDGv3 6
UFT C6 -1.355 1.001 0.762 ETKDGv3 7
UFT C2 -3.365 -0.470 0.739 ETKDGv3 8
UFT O2 -3.940 -1.549 0.433 ETKDGv3 9
UFT N3 -4.116 0.580 1.352 ETKDGv3 10
UFT C4 -3.469 1.817 1.655 ETKDGv3 11
UFT O4 -4.115 2.752 2.198 ETKDGv3 12
UFT C5 -2.050 1.995 1.324 ETKDGv3 13
UFT "F2'" -1.496 -2.170 -2.404 ETKDGv3 14
UFT "C2'" -1.071 -1.057 -1.694 ETKDGv3 15
UFT "C5'" 2.388 -0.889 -0.331 ETKDGv3 16
UFT "C4'" 1.031 -1.491 -0.711 ETKDGv3 17
UFT "O4'" 0.130 -1.385 0.365 ETKDGv3 18
UFT "C1'" -1.169 -1.329 -0.190 ETKDGv3 19
UFT "C3'" 0.401 -0.805 -1.914 ETKDGv3 20
UFT "O3'" 0.863 -1.371 -3.113 ETKDGv3 21
UFT HOP3 2.907 2.549 1.844 ETKDGv3 22
UFT HOP2 3.873 0.111 2.425 ETKDGv3 23
UFT H6 -0.316 1.175 0.519 ETKDGv3 24
UFT H5 -1.565 2.941 1.530 ETKDGv3 25
UFT "H2'" -1.673 -0.176 -2.010 ETKDGv3 26
UFT "H5'" 3.058 -0.943 -1.219 ETKDGv3 27
UFT "H5'A" 2.817 -1.510 0.488 ETKDGv3 28
UFT "H4'" 1.181 -2.573 -0.936 ETKDGv3 29
UFT "H1'" -1.641 -2.322 -0.020 ETKDGv3 30
UFT "H3'" 0.600 0.292 -1.893 ETKDGv3 31
UFT "HO3'" 0.535 -0.785 -3.843 ETKDGv3 32
UFT HN3 -5.130 0.449 1.566 ETKDGv3 33
#