data_CFZ
#
_chem_comp.id CFZ
_chem_comp.name "2'-deoxy-2'-fluorocytidine 5'-(dihydrogen phosphate)"
_chem_comp.type "DNA LINKING"
_chem_comp.pdbx_type ATOMN
_chem_comp.formula "C9 H13 F N3 O7 P"
_chem_comp.mon_nstd_parent_comp_id DC
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2010-04-13
_chem_comp.pdbx_modified_date 2011-06-04
_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 325.188
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code CFZ
_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 3AGV
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
CFZ P P P 0 1 N N N N N N 33.646 15.023 24.064 4.176 1.031 0.067 P CFZ 1
CFZ N1 N1 N 0 1 N N N N N N 33.918 9.728 23.714 -2.467 0.031 0.464 N1 CFZ 2
CFZ C2 C2 C 0 1 N N N N N N 33.873 8.458 23.133 -2.544 0.708 -0.696 C2 CFZ 3
CFZ O2 O2 O 0 1 N N N N N N 34.456 7.519 23.695 -1.667 0.569 -1.532 O2 CFZ 4
CFZ N3 N3 N 0 1 N N N N N N 33.199 8.285 21.974 -3.563 1.528 -0.946 N3 CFZ 5
CFZ C4 C4 C 0 1 N N N N N N 32.595 9.322 21.393 -4.530 1.699 -0.054 C4 CFZ 6
CFZ N4 N4 N 0 1 N N N N N N 31.932 9.101 20.256 -5.578 2.548 -0.324 N4 CFZ 7
CFZ C5 C5 C 0 1 N N N N N N 32.641 10.632 21.953 -4.478 1.004 1.171 C5 CFZ 8
CFZ C6 C6 C 0 1 N N N N N N 33.308 10.788 23.104 -3.439 0.169 1.408 C6 CFZ 9
CFZ "C1'" "C1'" C 0 1 N N R N N N 34.623 9.896 24.995 -1.334 -0.865 0.710 "C1'" CFZ 10
CFZ O1P O1P O 0 1 N N N N N N 34.400 16.152 24.668 4.620 2.004 1.270 O1P CFZ 11
CFZ "C2'" "C2'" C 0 1 N N R N N N 36.139 9.933 24.848 -1.311 -2.003 -0.334 "C2'" CFZ 12
CFZ "F2'" "F2'" F 0 1 N N N N N N 36.798 9.427 25.992 -1.886 -3.164 0.194 "F2'" CFZ 13
CFZ O2P O2P O 0 1 N N N N N N 33.272 15.065 22.626 3.925 1.834 -1.150 O2P CFZ 14
CFZ "C3'" "C3'" C 0 1 N N R N N N 36.390 11.427 24.671 0.192 -2.224 -0.616 "C3'" CFZ 15
CFZ "O3'" "O3'" O 0 1 N N N N N N 37.746 11.809 24.905 0.579 -3.553 -0.259 "O3'" CFZ 16
CFZ O3P O3P O 0 1 N Y N N N N 32.311 14.855 24.934 5.349 -0.033 -0.224 O3P CFZ 17
CFZ "C4'" "C4'" C 0 1 N N R N N N 35.439 11.985 25.716 0.900 -1.193 0.291 "C4'" CFZ 18
CFZ "O4'" "O4'" O 0 1 N N N N N N 34.254 11.152 25.557 -0.086 -0.162 0.517 "O4'" CFZ 19
CFZ "C5'" "C5'" C 0 1 N N N N N N 35.045 13.434 25.589 2.126 -0.614 -0.417 "C5'" CFZ 20
CFZ "O5'" "O5'" O 0 1 N N N N N N 34.447 13.674 24.328 2.831 0.248 0.479 "O5'" CFZ 21
CFZ HN4 HN4 H 0 1 N N N N N N 31.900 8.180 19.867 -5.612 3.025 -1.168 HN4 CFZ 22
CFZ HN4A HN4A H 0 0 N N N N N N 31.467 9.856 19.793 -6.284 2.671 0.330 HN4A CFZ 23
CFZ H5 H5 H 0 1 N N N N N N 32.157 11.467 21.468 -5.258 1.132 1.908 H5 CFZ 24
CFZ H6 H6 H 0 1 N N N N N N 33.365 11.767 23.557 -3.377 -0.375 2.339 H6 CFZ 25
CFZ "H1'" "H1'" H 0 1 N N N N N N 34.343 9.034 25.618 -1.387 -1.274 1.719 "H1'" CFZ 26
CFZ HO1P HO1P H 0 0 N N N N N N 34.563 16.814 24.007 5.425 2.509 1.091 HO1P CFZ 27
CFZ "H2'" "H2'" H 0 1 N N N N N N 36.519 9.310 24.025 -1.831 -1.699 -1.242 "H2'" CFZ 28
CFZ "H3'" "H3'" H 0 1 N N N N N N 36.222 11.792 23.647 0.417 -2.030 -1.665 "H3'" CFZ 29
CFZ "HO3'" "HO3'" H 0 0 N Y N N N N 37.838 12.746 24.780 0.119 -4.243 -0.757 "HO3'" CFZ 30
CFZ HO3P HO3P H 0 0 N Y N N N N 31.558 14.817 24.356 5.566 -0.595 0.533 HO3P CFZ 31
CFZ "H4'" "H4'" H 0 1 N N N N N N 35.938 11.960 26.696 1.190 -1.654 1.235 "H4'" CFZ 32
CFZ "H5'" "H5'" H 0 1 N N N N N N 34.326 13.684 26.383 2.782 -1.426 -0.731 "H5'" CFZ 33
CFZ "H5'A" "H5'A" H 0 0 N N N N N N 35.942 14.062 25.689 1.807 -0.046 -1.291 "H5'A" CFZ 34
#
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
CFZ O2P P DOUB N N 1
CFZ P "O5'" SING N N 2
CFZ P O1P SING N N 3
CFZ P O3P SING N N 4
CFZ C6 N1 SING N N 5
CFZ C2 N1 SING N N 6
CFZ N1 "C1'" SING N N 7
CFZ N3 C2 SING N N 8
CFZ C2 O2 DOUB N N 9
CFZ C4 N3 DOUB N N 10
CFZ N4 C4 SING N N 11
CFZ C4 C5 SING N N 12
CFZ N4 HN4 SING N N 13
CFZ N4 HN4A SING N N 14
CFZ C5 C6 DOUB N N 15
CFZ C5 H5 SING N N 16
CFZ C6 H6 SING N N 17
CFZ "C2'" "C1'" SING N N 18
CFZ "C1'" "O4'" SING N N 19
CFZ "C1'" "H1'" SING N N 20
CFZ O1P HO1P SING N N 21
CFZ "C3'" "C2'" SING N N 22
CFZ "C2'" "F2'" SING N N 23
CFZ "C2'" "H2'" SING N N 24
CFZ "C3'" "O3'" SING N N 25
CFZ "C3'" "C4'" SING N N 26
CFZ "C3'" "H3'" SING N N 27
CFZ "O3'" "HO3'" SING N N 28
CFZ O3P HO3P SING N N 29
CFZ "O4'" "C4'" SING N N 30
CFZ "C5'" "C4'" SING N N 31
CFZ "C4'" "H4'" SING N N 32
CFZ "O5'" "C5'" SING N N 33
CFZ "C5'" "H5'" SING N N 34
CFZ "C5'" "H5'A" SING N N 35
#
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
CFZ SMILES ACDLabs 12.01 O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(F)C2O
CFZ SMILES_CANONICAL CACTVS 3.370 NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2F
CFZ SMILES CACTVS 3.370 NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2F
CFZ SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)F
CFZ SMILES "OpenEye OEToolkits" 1.7.0 C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)F
CFZ InChI InChI 1.03 InChI=1S/C9H13FN3O7P/c10-6-7(14)4(3-19-21(16,17)18)20-8(6)13-2-1-5(11)12-9(13)15/h1-2,4,6-8,14H,3H2,(H2,11,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
CFZ InChIKey InChI 1.03 KTAATIGPZHTGOP-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
CFZ "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-2'-fluorocytidine 5'-(dihydrogen phosphate)"
CFZ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3R,4R,5R)-5-(4-azanyl-2-oxo-pyrimidin-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
CFZ 'Create component' 2010-04-13 PDBJ
CFZ 'Modify descriptor' 2011-06-04 RCSB
#
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
CFZ P P 9.645 -4.915 1
CFZ N1 N 5.640 1.163 2
CFZ C2 C 6.939 1.914 3
CFZ O2 O 8.238 1.163 4
CFZ N3 N 6.939 3.413 5
CFZ C4 C 5.640 4.163 6
CFZ N4 N 5.640 5.663 7
CFZ C5 C 4.341 3.413 8
CFZ C6 C 4.341 1.914 9
CFZ "C1'" C 5.640 -0.337 10
CFZ O1P O 10.859 -4.033 11
CFZ "C2'" C 4.427 -1.218 12
CFZ "F2'" F 3.000 -0.755 13
CFZ O2P O 10.527 -6.129 14
CFZ "C3'" C 4.890 -2.645 15
CFZ "O3'" O 4.008 -3.858 16
CFZ O3P O 8.432 -5.797 17
CFZ "C4'" C 6.390 -2.645 18
CFZ "O4'" O 6.854 -1.218 19
CFZ "C5'" C 7.272 -3.858 20
CFZ "O5'" O 8.764 -3.701 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
CFZ O2P P DOUBLE NONE 1
CFZ P "O5'" SINGLE NONE 2
CFZ P O1P SINGLE NONE 3
CFZ P O3P SINGLE NONE 4
CFZ C6 N1 SINGLE NONE 5
CFZ C2 N1 SINGLE NONE 6
CFZ "C1'" N1 SINGLE BEGINDASH 7
CFZ N3 C2 SINGLE NONE 8
CFZ C2 O2 DOUBLE NONE 9
CFZ C4 N3 DOUBLE NONE 10
CFZ N4 C4 SINGLE NONE 11
CFZ C4 C5 SINGLE NONE 12
CFZ C5 C6 DOUBLE NONE 13
CFZ "C2'" "C1'" SINGLE NONE 14
CFZ "C1'" "O4'" SINGLE NONE 15
CFZ "C3'" "C2'" SINGLE NONE 16
CFZ "C2'" "F2'" SINGLE BEGINWEDGE 17
CFZ "C3'" "O3'" SINGLE BEGINWEDGE 18
CFZ "C3'" "C4'" SINGLE NONE 19
CFZ "O4'" "C4'" SINGLE NONE 20
CFZ "C4'" "C5'" SINGLE BEGINDASH 21
CFZ "O5'" "C5'" SINGLE NONE 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
CFZ MurckoScaffold S1 scaffold 'O=c1ncccn1[C@H]1CCCO1' InChI=1S/C8H10N2O2/c11-8-9-4-2-5-10(8)7-3-1-6-12-7/h2,4-5,7H,1,3,6H2/t7-/m1/s1 AKXKPKRAUWTVBW-SSDOTTSWSA-N
CFZ 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
CFZ 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
CFZ N1 S1 1
CFZ C2 S1 1
CFZ O2 S1 1
CFZ N3 S1 1
CFZ C4 S1 1
CFZ C5 S1 1
CFZ C6 S1 1
CFZ "C1'" S1 1
CFZ "C2'" S1 1
CFZ "C3'" S1 1
CFZ "C4'" S1 1
CFZ "O4'" S1 1
CFZ O1P F1 1
CFZ P F1 1
CFZ O2P F1 1
CFZ "O5'" F1 1
CFZ O3P F1 1
CFZ C5 F2 1
CFZ C4 F2 1
CFZ N3 F2 1
CFZ C2 F2 1
CFZ N1 F2 1
CFZ C6 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id CFZ
_pdbe_chem_comp_rdkit_properties.exactmw 325.048
_pdbe_chem_comp_rdkit_properties.amw 325.189
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 10
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 10
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 34
_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 135.367
_pdbe_chem_comp_rdkit_properties.tpsa 157.130
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.950
_pdbe_chem_comp_rdkit_properties.CrippenMR 65.002
_pdbe_chem_comp_rdkit_properties.chi0v 10.419
_pdbe_chem_comp_rdkit_properties.chi1v 6.242
_pdbe_chem_comp_rdkit_properties.chi2v 2.233
_pdbe_chem_comp_rdkit_properties.chi3v 2.233
_pdbe_chem_comp_rdkit_properties.chi4v 1.348
_pdbe_chem_comp_rdkit_properties.chi0n 22.525
_pdbe_chem_comp_rdkit_properties.chi1n 10.901
_pdbe_chem_comp_rdkit_properties.chi2n 1.918
_pdbe_chem_comp_rdkit_properties.chi3n 1.918
_pdbe_chem_comp_rdkit_properties.chi4n 1.153
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.360
_pdbe_chem_comp_rdkit_properties.kappa1 6.030
_pdbe_chem_comp_rdkit_properties.kappa2 5.794
_pdbe_chem_comp_rdkit_properties.kappa3 3.643
_pdbe_chem_comp_rdkit_properties.Phi 1.664
#
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
CFZ UniChem ChEMBL CHEMBL1231760
CFZ UniChem PDBe CFZ
CFZ UniChem ZINC ZINC000058633383
CFZ UniChem SureChEMBL SCHEMBL599385
CFZ UniChem Nikkaji J2.387.035E
CFZ UniChem PubChem 49866784
#
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
CFZ P 3.443 1.913 0.399 ETKDGv3 1
CFZ N1 -1.765 -0.503 0.470 ETKDGv3 2
CFZ C2 -3.167 -0.833 0.490 ETKDGv3 3
CFZ O2 -3.552 -2.020 0.658 ETKDGv3 4
CFZ N3 -4.134 0.206 0.313 ETKDGv3 5
CFZ C4 -3.774 1.439 0.109 ETKDGv3 6
CFZ N4 -4.770 2.447 -0.063 ETKDGv3 7
CFZ C5 -2.341 1.801 0.047 ETKDGv3 8
CFZ C6 -1.400 0.868 0.214 ETKDGv3 9
CFZ "C1'" -0.737 -1.550 0.574 ETKDGv3 10
CFZ O1P 4.783 1.472 -0.537 ETKDGv3 11
CFZ "C2'" -0.359 -2.074 -0.802 ETKDGv3 12
CFZ "F2'" -1.140 -3.160 -1.166 ETKDGv3 13
CFZ O2P 3.902 2.789 1.543 ETKDGv3 14
CFZ "C3'" 1.091 -2.446 -0.631 ETKDGv3 15
CFZ "O3'" 1.246 -3.802 -0.281 ETKDGv3 16
CFZ O3P 2.339 2.775 -0.553 ETKDGv3 17
CFZ "C4'" 1.552 -1.520 0.503 ETKDGv3 18
CFZ "O4'" 0.420 -1.050 1.210 ETKDGv3 19
CFZ "C5'" 2.344 -0.322 -0.036 ETKDGv3 20
CFZ "O5'" 2.691 0.523 1.036 ETKDGv3 21
CFZ HN4 -5.784 2.200 -0.023 ETKDGv3 22
CFZ HN4A -4.499 3.441 -0.230 ETKDGv3 23
CFZ H5 -2.051 2.828 -0.139 ETKDGv3 24
CFZ H6 -0.359 1.157 0.155 ETKDGv3 25
CFZ "H1'" -1.118 -2.390 1.197 ETKDGv3 26
CFZ HO1P 5.146 2.327 -0.881 ETKDGv3 27
CFZ "H2'" -0.452 -1.273 -1.570 ETKDGv3 28
CFZ "H3'" 1.648 -2.267 -1.578 ETKDGv3 29
CFZ "HO3'" 0.764 -3.961 0.573 ETKDGv3 30
CFZ HO3P 2.849 3.553 -0.892 ETKDGv3 31
CFZ "H4'" 2.208 -2.077 1.208 ETKDGv3 32
CFZ "H5'" 1.712 0.213 -0.782 ETKDGv3 33
CFZ "H5'A" 3.264 -0.704 -0.535 ETKDGv3 34
#