data_5CF # _chem_comp.id 5CF _chem_comp.name "5-fluorocytidine 5'-(dihydrogen phosphate)" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H13 F N3 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-10-05 _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 341.187 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 5CF _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 3JXR _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 5CF OP3 OP3 O 0 1 N Y N N N N 17.385 7.462 0.708 -4.850 1.915 -1.416 OP3 5CF 1 5CF P P P 0 1 N N N N N N 16.529 7.170 -0.602 -4.335 1.068 -0.148 P 5CF 2 5CF N1 N1 N 0 1 N N N N N N 12.670 4.555 1.790 2.135 -0.149 -0.239 N1 5CF 3 5CF C2 C2 C 0 1 N N N N N N 11.374 4.310 2.292 2.005 0.724 0.776 C2 5CF 4 5CF O2 O2 O 0 1 N N N N N N 11.051 3.143 2.589 0.985 0.717 1.446 O2 5CF 5 5CF N3 N3 N 0 1 N N N N N N 10.557 5.387 2.402 2.970 1.596 1.062 N3 5CF 6 5CF C4 C4 C 0 1 N N N N N N 10.898 6.610 2.071 4.089 1.626 0.351 C4 5CF 7 5CF N4 N4 N 0 1 N N N N N N 10.027 7.628 2.224 5.080 2.531 0.658 N4 5CF 8 5CF C5 C5 C 0 1 N N N N N N 12.227 6.828 1.557 4.259 0.724 -0.721 C5 5CF 9 5CF F5 F5 F 0 1 N N N N N N 12.539 8.024 1.036 5.392 0.738 -1.457 F5 5CF 10 5CF C6 C6 C 0 1 N N N N N N 13.054 5.801 1.413 3.268 -0.157 -1.000 C6 5CF 11 5CF "C1'" "C1'" C 0 1 N N R N N N 13.606 3.437 1.685 1.059 -1.100 -0.525 "C1'" 5CF 12 5CF "C2'" "C2'" C 0 1 N N R N N N 13.389 2.562 0.489 0.844 -2.059 0.674 "C2'" 5CF 13 5CF "O2'" "O2'" O 0 1 N N N N N N 13.822 1.277 0.789 1.724 -3.182 0.593 "O2'" 5CF 14 5CF "C3'" "C3'" C 0 1 N N S N N N 14.229 3.303 -0.507 -0.629 -2.495 0.480 "C3'" 5CF 15 5CF "O3'" "O3'" O 0 1 N N N N N N 14.461 2.524 -1.601 -0.693 -3.762 -0.178 "O3'" 5CF 16 5CF "C4'" "C4'" C 0 1 N N R N N N 15.469 3.513 0.352 -1.236 -1.393 -0.409 "C4'" 5CF 17 5CF "O4'" "O4'" O 0 1 N N N N N N 14.932 3.917 1.610 -0.207 -0.415 -0.644 "O4'" 5CF 18 5CF "C5'" "C5'" C 0 1 N N N N N N 16.402 4.603 -0.124 -2.422 -0.742 0.305 "C5'" 5CF 19 5CF "O5'" "O5'" O 0 1 N N N N N N 15.731 5.851 -0.307 -3.049 0.196 -0.572 "O5'" 5CF 20 5CF OP1 OP1 O 0 1 N N N N N N 15.474 8.197 -0.722 -3.932 2.075 1.042 OP1 5CF 21 5CF OP2 OP2 O 0 1 N N N N N N 17.493 6.957 -1.674 -5.413 0.165 0.314 OP2 5CF 22 5CF HOP3 HOP3 H 0 0 N Y N N N N 18.310 7.431 0.496 -5.625 2.465 -1.234 HOP3 5CF 23 5CF HN4 HN4 H 0 1 N N N N N N 9.114 7.454 2.592 4.960 3.150 1.395 HN4 5CF 24 5CF HN4A HN4A H 0 0 N N N N N N 10.294 8.557 1.969 5.897 2.551 0.136 HN4A 5CF 25 5CF H6 H6 H 0 1 N N N N N N 14.037 5.957 0.994 3.374 -0.858 -1.814 H6 5CF 26 5CF "H1'" "H1'" H 0 1 N N N N N N 13.428 2.834 2.588 1.277 -1.664 -1.433 "H1'" 5CF 27 5CF "H2'" "H2'" H 0 1 N N N N N N 12.359 2.407 0.135 0.973 -1.533 1.620 "H2'" 5CF 28 5CF "HO2'" "HO2'" H 0 0 N N N N N N 13.689 0.713 0.036 1.627 -3.811 1.321 "HO2'" 5CF 29 5CF "H3'" "H3'" H 0 1 N N N N N N 13.807 4.226 -0.931 -1.143 -2.537 1.440 "H3'" 5CF 30 5CF "HO3'" "HO3'" H 0 0 N N N N N N 14.994 3.004 -2.225 -0.273 -4.482 0.312 "HO3'" 5CF 31 5CF "H4'" "H4'" H 0 1 N N N N N N 16.076 2.596 0.349 -1.561 -1.820 -1.358 "H4'" 5CF 32 5CF "H5'" "H5'" H 0 1 N N N N N N 17.193 4.739 0.628 -3.141 -1.510 0.590 "H5'" 5CF 33 5CF "H5'A" "H5'A" H 0 0 N N N N N N 16.836 4.295 -1.087 -2.069 -0.225 1.198 "H5'A" 5CF 34 5CF HOP1 HOP1 H 0 0 N N N N N N 15.555 8.638 -1.559 -3.229 2.697 0.809 HOP1 5CF 35 # 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 5CF P OP3 SING N N 1 5CF OP3 HOP3 SING N N 2 5CF OP2 P DOUB N N 3 5CF OP1 P SING N N 4 5CF P "O5'" SING N N 5 5CF C6 N1 SING N N 6 5CF "C1'" N1 SING N N 7 5CF N1 C2 SING N N 8 5CF C2 N3 SING N N 9 5CF C2 O2 DOUB N N 10 5CF C4 N3 DOUB N N 11 5CF C5 C4 SING N N 12 5CF C4 N4 SING N N 13 5CF N4 HN4 SING N N 14 5CF N4 HN4A SING N N 15 5CF F5 C5 SING N N 16 5CF C6 C5 DOUB N N 17 5CF C6 H6 SING N N 18 5CF "C2'" "C1'" SING N N 19 5CF "O4'" "C1'" SING N N 20 5CF "C1'" "H1'" SING N N 21 5CF "C3'" "C2'" SING N N 22 5CF "C2'" "O2'" SING N N 23 5CF "C2'" "H2'" SING N N 24 5CF "O2'" "HO2'" SING N N 25 5CF "O3'" "C3'" SING N N 26 5CF "C3'" "C4'" SING N N 27 5CF "C3'" "H3'" SING N N 28 5CF "O3'" "HO3'" SING N N 29 5CF "C5'" "C4'" SING N N 30 5CF "C4'" "O4'" SING N N 31 5CF "C4'" "H4'" SING N N 32 5CF "O5'" "C5'" SING N N 33 5CF "C5'" "H5'" SING N N 34 5CF "C5'" "H5'A" SING N N 35 5CF OP1 HOP1 SING N N 36 # 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 5CF SMILES ACDLabs 11.02 O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C(F)=C1)C(O)C2O 5CF SMILES_CANONICAL CACTVS 3.352 NC1=NC(=O)N(C=C1F)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O 5CF SMILES CACTVS 3.352 NC1=NC(=O)N(C=C1F)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O 5CF SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 C1=C(C(=NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N)F 5CF SMILES "OpenEye OEToolkits" 1.7.0 C1=C(C(=NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)N)F 5CF InChI InChI 1.03 InChI=1S/C9H13FN3O8P/c10-3-1-13(9(16)12-7(3)11)8-6(15)5(14)4(21-8)2-20-22(17,18)19/h1,4-6,8,14-15H,2H2,(H2,11,12,16)(H2,17,18,19)/t4-,5-,6-,8-/m1/s1 5CF InChIKey InChI 1.03 VLZKLBLFWAHHJM-UAKXSSHOSA-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 5CF "SYSTEMATIC NAME" ACDLabs 11.02 "5-fluorocytidine 5'-(dihydrogen phosphate)" 5CF "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,3S,4R,5R)-5-(4-azanyl-5-fluoro-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-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 5CF 'Create component' 2009-10-05 RCSB 5CF '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 5CF OP3 O 11.218 -6.129 1 5CF P P 10.336 -4.915 2 5CF N1 N 6.331 1.163 3 5CF C2 C 7.630 1.914 4 5CF O2 O 8.929 1.163 5 5CF N3 N 7.630 3.413 6 5CF C4 C 6.331 4.163 7 5CF N4 N 6.331 5.663 8 5CF C5 C 5.032 3.413 9 5CF F5 F 3.733 4.163 10 5CF C6 C 5.032 1.914 11 5CF "C1'" C 6.331 -0.337 12 5CF "C2'" C 5.118 -1.218 13 5CF "O2'" O 3.691 -0.755 14 5CF "C3'" C 5.581 -2.645 15 5CF "O3'" O 4.699 -3.858 16 5CF "C4'" C 7.081 -2.645 17 5CF "O4'" O 7.545 -1.218 18 5CF "C5'" C 7.963 -3.858 19 5CF "O5'" O 9.455 -3.701 20 5CF OP1 O 9.123 -5.797 21 5CF OP2 O 11.550 -4.033 22 # 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 5CF P OP3 SINGLE NONE 1 5CF OP2 P DOUBLE NONE 2 5CF OP1 P SINGLE NONE 3 5CF P "O5'" SINGLE NONE 4 5CF C6 N1 SINGLE NONE 5 5CF "C1'" N1 SINGLE BEGINDASH 6 5CF N1 C2 SINGLE NONE 7 5CF C2 N3 SINGLE NONE 8 5CF C2 O2 DOUBLE NONE 9 5CF C4 N3 DOUBLE NONE 10 5CF C5 C4 SINGLE NONE 11 5CF C4 N4 SINGLE NONE 12 5CF F5 C5 SINGLE NONE 13 5CF C6 C5 DOUBLE NONE 14 5CF "C2'" "C1'" SINGLE NONE 15 5CF "O4'" "C1'" SINGLE NONE 16 5CF "C3'" "C2'" SINGLE NONE 17 5CF "C2'" "O2'" SINGLE BEGINWEDGE 18 5CF "C3'" "O3'" SINGLE BEGINWEDGE 19 5CF "C3'" "C4'" SINGLE NONE 20 5CF "C4'" "C5'" SINGLE BEGINDASH 21 5CF "C4'" "O4'" SINGLE NONE 22 5CF "O5'" "C5'" SINGLE NONE 23 # 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 5CF 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 5CF 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 5CF pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N 5CF ribose F3 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-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 5CF N1 S1 1 5CF C2 S1 1 5CF O2 S1 1 5CF N3 S1 1 5CF C4 S1 1 5CF C5 S1 1 5CF C6 S1 1 5CF "C1'" S1 1 5CF "C2'" S1 1 5CF "C3'" S1 1 5CF "C4'" S1 1 5CF "O4'" S1 1 5CF OP3 F1 1 5CF P F1 1 5CF OP2 F1 1 5CF OP1 F1 1 5CF "O5'" F1 1 5CF C5 F2 1 5CF C4 F2 1 5CF N3 F2 1 5CF C2 F2 1 5CF N1 F2 1 5CF C6 F2 1 5CF "C2'" F3 1 5CF "C3'" F3 1 5CF "C4'" F3 1 5CF "O4'" F3 1 5CF "C1'" F3 1 5CF "C5'" F3 1 5CF "O5'" F3 1 5CF "O3'" F3 1 5CF "O2'" F3 1 # _pdbe_chem_comp_rdkit_properties.comp_id 5CF _pdbe_chem_comp_rdkit_properties.exactmw 341.042 _pdbe_chem_comp_rdkit_properties.amw 341.188 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 11 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 6 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9 _pdbe_chem_comp_rdkit_properties.NumHBD 5 _pdbe_chem_comp_rdkit_properties.NumHBA 11 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 22 _pdbe_chem_comp_rdkit_properties.NumAtoms 35 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 13 _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 140.248 _pdbe_chem_comp_rdkit_properties.tpsa 177.360 _pdbe_chem_comp_rdkit_properties.CrippenClogP -1.788 _pdbe_chem_comp_rdkit_properties.CrippenMR 66.071 _pdbe_chem_comp_rdkit_properties.chi0v 10.827 _pdbe_chem_comp_rdkit_properties.chi1v 6.446 _pdbe_chem_comp_rdkit_properties.chi2v 2.373 _pdbe_chem_comp_rdkit_properties.chi3v 2.373 _pdbe_chem_comp_rdkit_properties.chi4v 1.419 _pdbe_chem_comp_rdkit_properties.chi0n 22.933 _pdbe_chem_comp_rdkit_properties.chi1n 11.013 _pdbe_chem_comp_rdkit_properties.chi2n 2.058 _pdbe_chem_comp_rdkit_properties.chi3n 2.058 _pdbe_chem_comp_rdkit_properties.chi4n 1.225 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.400 _pdbe_chem_comp_rdkit_properties.kappa1 6.610 _pdbe_chem_comp_rdkit_properties.kappa2 6.006 _pdbe_chem_comp_rdkit_properties.kappa3 3.495 _pdbe_chem_comp_rdkit_properties.Phi 1.805 # 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 5CF UniChem ChEMBL CHEMBL1230391 5CF UniChem PDBe 5CF 5CF UniChem SureChEMBL SCHEMBL677085 5CF UniChem ACTor 51960-70-4 5CF UniChem Nikkaji J2.318.932A 5CF UniChem BRENDA 51427 5CF UniChem PubChem 191215 # 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 5CF OP3 4.807 -1.993 1.662 ETKDGv3 1 5CF P 4.650 -0.311 1.525 ETKDGv3 2 5CF N1 -1.987 -0.317 -0.502 ETKDGv3 3 5CF C2 -2.026 -0.285 0.939 ETKDGv3 4 5CF O2 -0.977 -0.120 1.616 ETKDGv3 5 5CF N3 -3.282 -0.437 1.608 ETKDGv3 6 5CF C4 -4.392 -0.577 0.944 ETKDGv3 7 5CF N4 -5.621 -0.725 1.655 ETKDGv3 8 5CF C5 -4.385 -0.575 -0.538 ETKDGv3 9 5CF F5 -5.548 -0.700 -1.225 ETKDGv3 10 5CF C6 -3.235 -0.445 -1.206 ETKDGv3 11 5CF "C1'" -0.740 -0.119 -1.257 ETKDGv3 12 5CF "C2'" -0.319 1.358 -1.239 ETKDGv3 13 5CF "O2'" -0.310 1.881 -2.543 ETKDGv3 14 5CF "C3'" 1.077 1.325 -0.653 ETKDGv3 15 5CF "O3'" 1.961 2.153 -1.367 ETKDGv3 16 5CF "C4'" 1.470 -0.145 -0.775 ETKDGv3 17 5CF "O4'" 0.291 -0.909 -0.706 ETKDGv3 18 5CF "C5'" 2.431 -0.592 0.331 ETKDGv3 19 5CF "O5'" 3.654 0.094 0.200 ETKDGv3 20 5CF OP1 6.182 0.363 1.280 ETKDGv3 21 5CF OP2 4.066 0.256 2.800 ETKDGv3 22 5CF HOP3 4.031 -2.283 2.204 ETKDGv3 23 5CF HN4 -5.630 -0.724 2.699 ETKDGv3 24 5CF HN4A -6.526 -0.837 1.147 ETKDGv3 25 5CF H6 -3.251 -0.438 -2.290 ETKDGv3 26 5CF "H1'" -0.885 -0.458 -2.308 ETKDGv3 27 5CF "H2'" -0.981 1.976 -0.588 ETKDGv3 28 5CF "HO2'" -1.260 2.032 -2.791 ETKDGv3 29 5CF "H3'" 1.022 1.635 0.419 ETKDGv3 30 5CF "HO3'" 2.715 2.361 -0.757 ETKDGv3 31 5CF "H4'" 1.951 -0.330 -1.764 ETKDGv3 32 5CF "H5'" 2.597 -1.687 0.216 ETKDGv3 33 5CF "H5'A" 1.955 -0.397 1.320 ETKDGv3 34 5CF HOP1 6.496 -0.033 0.428 ETKDGv3 35 #