data_F2U
#
_chem_comp.id F2U
_chem_comp.name "2'-deoxy-5-ethynyl-2',2'-difluorouridine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H10 F2 N2 O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "2'-deoxy-2',2'-difluoro-5-ethynyluridine"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2014-02-12
_chem_comp.pdbx_modified_date 2021-03-13
_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 288.204
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code F2U
_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 4OQL
_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.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
F2U O01 O01 O 0 1 N N N N N N 51.302 23.306 52.821 -3.825 -2.450 1.396 O01 F2U 1
F2U C03 C03 C 0 1 N N N N N N 50.040 23.932 52.668 -3.735 -1.515 0.319 C03 F2U 2
F2U C06 C06 C 0 1 N N R N N N 50.087 25.259 53.410 -2.799 -0.371 0.713 C06 F2U 3
F2U O08 O08 O 0 1 N N N N N N 48.841 25.927 53.101 -1.435 -0.840 0.787 O08 F2U 4
F2U C09 C09 C 0 1 N N R N N N 50.108 25.160 54.942 -2.784 0.714 -0.387 C09 F2U 5
F2U O11 O11 O 0 1 N N N N N N 50.583 26.356 55.524 -3.657 1.791 -0.039 O11 F2U 6
F2U C13 C13 C 0 1 N N N N N N 48.651 24.899 55.282 -1.316 1.195 -0.419 C13 F2U 7
F2U F14 F14 F 0 1 N N N N N N 48.364 23.578 55.180 -0.749 0.956 -1.675 F14 F2U 8
F2U F15 F15 F 0 1 N N N N N N 48.303 25.311 56.511 -1.239 2.555 -0.099 F15 F2U 9
F2U C16 C16 C 0 1 N N R N N N 47.947 25.755 54.236 -0.618 0.344 0.665 C16 F2U 10
F2U N18 N18 N 0 1 N N N N N N 46.614 25.359 53.765 0.737 -0.013 0.239 N18 F2U 11
F2U C19 C19 C 0 1 N N N N N N 45.536 26.028 54.325 0.904 -0.758 -0.866 C19 F2U 12
F2U O20 O20 O 0 1 N N N N N N 45.648 26.877 55.204 -0.076 -1.120 -1.488 O20 F2U 13
F2U N21 N21 N 0 1 N N N N N N 44.296 25.673 53.822 2.124 -1.115 -1.305 N21 F2U 14
F2U C23 C23 C 0 1 N N N N N N 44.054 24.742 52.833 3.229 -0.727 -0.635 C23 F2U 15
F2U O24 O24 O 0 1 N N N N N N 42.916 24.475 52.430 4.337 -1.046 -1.027 O24 F2U 16
F2U C25 C25 C 0 1 N N N N N N 45.247 24.072 52.283 3.069 0.089 0.578 C25 F2U 17
F2U C26 C26 C 0 1 N N N N N N 46.450 24.422 52.767 1.804 0.423 0.970 C26 F2U 18
F2U C28 C28 C 0 1 N N N N N N 45.102 23.098 51.255 4.210 0.530 1.322 C28 F2U 19
F2U C29 C29 C 0 1 N N N N N N 44.975 22.277 50.389 5.145 0.892 1.933 C29 F2U 20
F2U H1 H1 H 0 1 N N N N N N 51.300 22.472 52.366 -4.404 -3.203 1.216 H1 F2U 21
F2U H2 H2 H 0 1 N N N N N N 49.836 24.107 51.601 -3.343 -2.017 -0.566 H2 F2U 22
F2U H3 H3 H 0 1 N N N N N N 49.251 23.293 53.093 -4.726 -1.116 0.101 H3 F2U 23
F2U H4 H4 H 0 1 N N N N N N 50.947 25.851 53.065 -3.106 0.059 1.666 H4 F2U 24
F2U H5 H5 H 0 1 N N N N N N 50.720 24.298 55.246 -3.067 0.287 -1.349 H5 F2U 25
F2U H6 H6 H 0 1 N N N N N N 50.586 26.269 56.470 -3.686 2.501 -0.695 H6 F2U 26
F2U H7 H7 H 0 1 N N N N N N 47.830 26.748 54.694 -0.589 0.884 1.611 H7 F2U 27
F2U H8 H8 H 0 1 N N N N N N 43.500 26.135 54.213 2.209 -1.653 -2.107 H8 F2U 28
F2U H9 H9 H 0 1 N N N N N N 47.329 23.948 52.356 1.649 1.021 1.855 H9 F2U 29
F2U H10 H10 H 0 1 N N N N N N 44.863 21.552 49.624 5.982 1.215 2.478 H10 F2U 30
#
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
F2U C29 C28 TRIP N N 1
F2U C28 C25 SING N N 2
F2U C25 C26 DOUB N N 3
F2U C25 C23 SING N N 4
F2U O24 C23 DOUB N N 5
F2U C03 O01 SING N N 6
F2U C03 C06 SING N N 7
F2U C26 N18 SING N N 8
F2U C23 N21 SING N N 9
F2U O08 C06 SING N N 10
F2U O08 C16 SING N N 11
F2U C06 C09 SING N N 12
F2U N18 C16 SING N N 13
F2U N18 C19 SING N N 14
F2U N21 C19 SING N N 15
F2U C16 C13 SING N N 16
F2U C19 O20 DOUB N N 17
F2U C09 C13 SING N N 18
F2U C09 O11 SING N N 19
F2U F14 C13 SING N N 20
F2U C13 F15 SING N N 21
F2U O01 H1 SING N N 22
F2U C03 H2 SING N N 23
F2U C03 H3 SING N N 24
F2U C06 H4 SING N N 25
F2U C09 H5 SING N N 26
F2U O11 H6 SING N N 27
F2U C16 H7 SING N N 28
F2U N21 H8 SING N N 29
F2U C26 H9 SING N N 30
F2U C29 H10 SING N N 31
#
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
F2U SMILES ACDLabs 12.01 "O=C1NC(=O)N(C=C1C#C)C2OC(C(O)C2(F)F)CO"
F2U InChI InChI 1.03 InChI=1S/C11H10F2N2O5/c1-2-5-3-15(10(19)14-8(5)18)9-11(12,13)7(17)6(4-16)20-9/h1,3,6-7,9,16-17H,4H2,(H,14,18,19)/t6-,7-,9-/m1/s1
F2U InChIKey InChI 1.03 JFVJRPYRLUHQTG-ZXFLCMHBSA-N
F2U SMILES_CANONICAL CACTVS 3.370 "OC[C@H]1O[C@@H](N2C=C(C#C)C(=O)NC2=O)C(F)(F)[C@@H]1O"
F2U SMILES CACTVS 3.370 "OC[CH]1O[CH](N2C=C(C#C)C(=O)NC2=O)C(F)(F)[CH]1O"
F2U SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C#CC1=CN(C(=O)NC1=O)[C@H]2C([C@@H]([C@H](O2)CO)O)(F)F"
F2U SMILES "OpenEye OEToolkits" 1.7.6 "C#CC1=CN(C(=O)NC1=O)C2C(C(C(O2)CO)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
F2U "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5-ethynyl-2',2'-difluorouridine"
F2U "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 1-[(2R,4R,5R)-3,3-bis(fluoranyl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-5-ethynyl-pyrimidine-2,4-dione
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
F2U 'Create component' 2014-02-12 RCSB
F2U 'Modify synonyms' 2014-02-17 RCSB
F2U 'Initial release' 2014-08-13 RCSB
F2U 'Modify synonyms' 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id F2U
_pdbx_chem_comp_synonyms.name "2'-deoxy-2',2'-difluoro-5-ethynyluridine"
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id F2U
_pdbe_chem_comp_synonyms.name "2'-deoxy-2',2'-difluoro-5-ethynyluridine"
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 '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
F2U O01 O 4.579 -4.179 1
F2U C03 C 6.071 -4.336 2
F2U C06 C 6.952 -3.123 3
F2U O08 O 6.489 -1.696 4
F2U C09 C 8.453 -3.123 5
F2U O11 O 9.334 -4.336 6
F2U C13 C 8.916 -1.696 7
F2U F14 F 10.343 -2.159 8
F2U F15 F 9.798 -0.482 9
F2U C16 C 7.702 -0.814 10
F2U N18 N 7.702 0.686 11
F2U C19 C 9.002 1.436 12
F2U O20 O 10.301 0.686 13
F2U N21 N 9.002 2.936 14
F2U C23 C 7.702 3.686 15
F2U O24 O 7.702 5.186 16
F2U C25 C 6.404 2.936 17
F2U C26 C 6.404 1.436 18
F2U C28 C 5.104 3.686 19
F2U C29 C 3.805 4.436 20
#
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
F2U C29 C28 TRIPLE NONE 1
F2U C28 C25 SINGLE NONE 2
F2U C25 C26 DOUBLE NONE 3
F2U C25 C23 SINGLE NONE 4
F2U O24 C23 DOUBLE NONE 5
F2U C03 O01 SINGLE NONE 6
F2U C06 C03 SINGLE BEGINWEDGE 7
F2U C26 N18 SINGLE NONE 8
F2U C23 N21 SINGLE NONE 9
F2U O08 C06 SINGLE NONE 10
F2U O08 C16 SINGLE NONE 11
F2U C06 C09 SINGLE NONE 12
F2U C16 N18 SINGLE BEGINWEDGE 13
F2U N18 C19 SINGLE NONE 14
F2U N21 C19 SINGLE NONE 15
F2U C16 C13 SINGLE NONE 16
F2U C19 O20 DOUBLE NONE 17
F2U C09 C13 SINGLE NONE 18
F2U C09 O11 SINGLE BEGINDASH 19
F2U F14 C13 SINGLE NONE 20
F2U C13 F15 SINGLE NONE 21
#
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
F2U 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
F2U pyrimidine F1 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
F2U C06 S1 1
F2U O08 S1 1
F2U C09 S1 1
F2U C13 S1 1
F2U C16 S1 1
F2U N18 S1 1
F2U C19 S1 1
F2U O20 S1 1
F2U N21 S1 1
F2U C23 S1 1
F2U O24 S1 1
F2U C25 S1 1
F2U C26 S1 1
F2U C25 F1 1
F2U C26 F1 1
F2U N18 F1 1
F2U C19 F1 1
F2U N21 F1 1
F2U C23 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id F2U
_pdbe_chem_comp_rdkit_properties.exactmw 288.056
_pdbe_chem_comp_rdkit_properties.amw 288.206
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 30
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 9
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.455
_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 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 124.266
_pdbe_chem_comp_rdkit_properties.tpsa 104.550
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.149
_pdbe_chem_comp_rdkit_properties.CrippenMR 61.157
_pdbe_chem_comp_rdkit_properties.chi0v 9.192
_pdbe_chem_comp_rdkit_properties.chi1v 4.721
_pdbe_chem_comp_rdkit_properties.chi2v 2.205
_pdbe_chem_comp_rdkit_properties.chi3v 2.205
_pdbe_chem_comp_rdkit_properties.chi4v 1.319
_pdbe_chem_comp_rdkit_properties.chi0n 19.192
_pdbe_chem_comp_rdkit_properties.chi1n 9.484
_pdbe_chem_comp_rdkit_properties.chi2n 2.205
_pdbe_chem_comp_rdkit_properties.chi3n 2.205
_pdbe_chem_comp_rdkit_properties.chi4n 1.319
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.020
_pdbe_chem_comp_rdkit_properties.kappa1 6.173
_pdbe_chem_comp_rdkit_properties.kappa2 4.824
_pdbe_chem_comp_rdkit_properties.kappa3 2.035
_pdbe_chem_comp_rdkit_properties.Phi 1.489
#
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
F2U UniChem PDBe F2U
F2U UniChem ZINC ZINC000098208851
F2U UniChem PubChem 76871912
#
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
F2U O01 -3.648 -2.844 1.293 ETKDGv3 1
F2U C03 -2.321 -2.582 0.919 ETKDGv3 2
F2U C06 -1.869 -1.218 1.459 ETKDGv3 3
F2U O08 -0.470 -1.101 1.293 ETKDGv3 4
F2U C09 -2.568 -0.046 0.743 ETKDGv3 5
F2U O11 -3.158 0.839 1.667 ETKDGv3 6
F2U C13 -1.451 0.613 -0.033 ETKDGv3 7
F2U F14 -1.561 1.995 -0.045 ETKDGv3 8
F2U F15 -1.441 0.141 -1.336 ETKDGv3 9
F2U C16 -0.213 0.164 0.727 ETKDGv3 10
F2U N18 0.976 0.125 -0.143 ETKDGv3 11
F2U C19 1.275 -1.009 -0.988 ETKDGv3 12
F2U O20 0.525 -2.022 -1.005 ETKDGv3 13
F2U N21 2.432 -0.979 -1.824 ETKDGv3 14
F2U C23 3.255 0.188 -1.844 ETKDGv3 15
F2U O24 4.278 0.220 -2.578 ETKDGv3 16
F2U C25 2.894 1.348 -1.007 ETKDGv3 17
F2U C26 1.812 1.299 -0.217 ETKDGv3 18
F2U C28 3.703 2.542 -1.040 ETKDGv3 19
F2U C29 4.378 3.540 -1.069 ETKDGv3 20
F2U H1 -4.226 -2.555 0.539 ETKDGv3 21
F2U H2 -2.192 -2.627 -0.188 ETKDGv3 22
F2U H3 -1.677 -3.373 1.359 ETKDGv3 23
F2U H4 -2.091 -1.193 2.550 ETKDGv3 24
F2U H5 -3.362 -0.387 0.043 ETKDGv3 25
F2U H6 -2.451 1.157 2.288 ETKDGv3 26
F2U H7 -0.030 0.869 1.570 ETKDGv3 27
F2U H8 2.668 -1.799 -2.425 ETKDGv3 28
F2U H9 1.560 2.165 0.385 ETKDGv3 29
F2U H10 4.972 4.416 -1.093 ETKDGv3 30
#