data_60F
#
_chem_comp.id 60F
_chem_comp.name "(2~{R})-2-azanyl-3-[(~{E})-3-(4-hydroxyphenyl)prop-2-enoyl]sulfanyl-propanoic acid"
_chem_comp.type "L-peptide linking"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C12 H13 N O4 S"
_chem_comp.mon_nstd_parent_comp_id CYS
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2016-01-07
_chem_comp.pdbx_modified_date 2023-11-03
_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 267.301
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 60F
_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 5HD3
_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
60F C1 C1 C 0 1 N N N N N N 12.115 2.916 -19.805 0.443 -0.355 -0.008 C1 60F 1
60F C2 C2 C 0 1 N N N N N N 13.030 1.973 -19.080 -0.962 0.045 0.053 C2 60F 2
60F C3 C3 C 0 1 N N N N N N 13.830 1.157 -19.727 -1.934 -0.868 -0.152 C3 60F 3
60F O1 O1 O 0 1 N N N N N N 12.333 3.143 -20.995 0.737 -1.512 -0.249 O1 60F 4
60F "C1'" "C1'" C 0 1 Y N N N N N 14.855 0.349 -19.011 -3.346 -0.466 -0.090 "C1'" 60F 5
60F "C6'" "C6'" C 0 1 Y N N N N N 15.163 0.469 -17.623 -4.356 -1.412 -0.302 "C6'" 60F 6
60F "C5'" "C5'" C 0 1 Y N N N N N 16.233 -0.223 -17.089 -5.677 -1.029 -0.242 "C5'" 60F 7
60F "C4'" "C4'" C 0 1 Y N N N N N 17.019 -1.055 -17.871 -6.009 0.293 0.027 "C4'" 60F 8
60F "O4'" "O4'" O 0 1 N N N N N N 17.987 -1.777 -17.265 -7.314 0.665 0.084 "O4'" 60F 9
60F "C3'" "C3'" C 0 1 Y N N N N N 16.742 -1.205 -19.199 -5.010 1.237 0.238 "C3'" 60F 10
60F "C2'" "C2'" C 0 1 Y N N N N N 15.718 -0.460 -19.807 -3.686 0.864 0.186 "C2'" 60F 11
60F N N N 0 1 N N N Y Y N 12.042 5.865 -21.383 4.466 1.708 -0.743 N 60F 12
60F CA CA C 0 1 N N R Y N N 11.021 6.138 -20.379 4.436 0.634 0.259 CA 60F 13
60F CB CB C 0 1 N N N N N N 10.191 4.896 -19.952 3.175 -0.210 0.064 CB 60F 14
60F SG SG S 0 1 N N N N N N 11.008 3.791 -18.811 1.712 0.838 0.259 SG 60F 15
60F C C C 0 1 N N N Y N Y 11.537 6.850 -19.133 5.654 -0.239 0.097 C 60F 16
60F O O O 0 1 N N N Y N Y 10.739 7.397 -18.347 6.265 -0.236 -0.946 O 60F 17
60F H1 H1 H 0 1 N N N N N N 13.031 1.965 -18.000 -1.222 1.073 0.262 H1 60F 18
60F H10 H2 H 0 1 N N N N N N 13.743 1.070 -20.800 -1.674 -1.896 -0.360 H2 60F 19
60F H3 H3 H 0 1 N N N N N N 14.559 1.101 -16.989 -4.099 -2.439 -0.512 H3 60F 20
60F H4 H4 H 0 1 N N N N N N 16.462 -0.113 -16.039 -6.457 -1.758 -0.406 H4 60F 21
60F H5 H5 H 0 1 N N N N N N 18.034 -1.537 -16.347 -7.705 0.594 0.965 H5 60F 22
60F H6 H6 H 0 1 N N N N N N 17.316 -1.904 -19.789 -5.273 2.263 0.447 H6 60F 23
60F H7 H7 H 0 1 N N N N N N 15.584 -0.500 -20.878 -2.911 1.597 0.351 H7 60F 24
60F H H8 H 0 1 N N N Y Y N 12.529 6.710 -21.602 5.256 2.318 -0.596 H8 60F 25
60F H2 H9 H 0 1 N Y N Y Y N 12.689 5.191 -21.026 4.471 1.329 -1.679 H9 60F 26
60F HA H11 H 0 1 N N N Y N N 10.301 6.828 -20.843 4.432 1.069 1.258 H11 60F 27
60F H12 H12 H 0 1 N N N N N N 9.265 5.252 -19.477 3.180 -0.646 -0.935 H12 60F 28
60F H13 H13 H 0 1 N N N N N N 9.941 4.325 -20.859 3.153 -1.007 0.808 H13 60F 29
60F OXT O2 O 0 1 N Y N Y N Y 12.848 6.846 -18.950 6.061 -1.019 1.110 O2 60F 30
60F HXT H10 H 0 1 N Y N Y N Y 13.058 7.313 -18.150 6.847 -1.561 0.959 H10 60F 31
#
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
60F N CA SING N N 1
60F O1 C1 DOUB N N 2
60F CA CB SING N N 3
60F CA C SING N N 4
60F CB SG SING N N 5
60F "C2'" "C3'" DOUB Y N 6
60F "C2'" "C1'" SING Y N 7
60F C1 C2 SING N N 8
60F C1 SG SING N N 9
60F C3 C2 DOUB N E 10
60F C3 "C1'" SING N N 11
60F "C3'" "C4'" SING Y N 12
60F C O DOUB N N 13
60F "C1'" "C6'" DOUB Y N 14
60F "C4'" "O4'" SING N N 15
60F "C4'" "C5'" DOUB Y N 16
60F "C6'" "C5'" SING Y N 17
60F C2 H1 SING N N 18
60F C3 H10 SING N N 19
60F "C6'" H3 SING N N 20
60F "C5'" H4 SING N N 21
60F "O4'" H5 SING N N 22
60F "C3'" H6 SING N N 23
60F "C2'" H7 SING N N 24
60F N H SING N N 25
60F N H2 SING N N 26
60F CA HA SING N N 27
60F CB H12 SING N N 28
60F CB H13 SING N N 29
60F C OXT SING N N 30
60F OXT HXT 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
60F InChI InChI 1.03 InChI=1S/C12H13NO4S/c13-10(12(16)17)7-18-11(15)6-3-8-1-4-9(14)5-2-8/h1-6,10,14H,7,13H2,(H,16,17)/b6-3+/t10-/m0/s1
60F InChIKey InChI 1.03 RIXZOZKLGOTDHO-YVGDHZEHSA-N
60F SMILES_CANONICAL CACTVS 3.385 N[C@@H](CSC(=O)/C=C/c1ccc(O)cc1)C(O)=O
60F SMILES CACTVS 3.385 N[CH](CSC(=O)C=Cc1ccc(O)cc1)C(O)=O
60F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 c1cc(ccc1/C=C/C(=O)SC[C@@H](C(=O)O)N)O
60F SMILES "OpenEye OEToolkits" 2.0.4 c1cc(ccc1C=CC(=O)SCC(C(=O)O)N)O
#
_pdbx_chem_comp_identifier.comp_id 60F
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.4
_pdbx_chem_comp_identifier.identifier
"(2~{R})-2-azanyl-3-[(~{E})-3-(4-hydroxyphenyl)prop-2-enoyl]sulfanyl-propanoic 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
60F 'Create component' 2016-01-07 RCSB
60F 'Initial release' 2016-05-18 RCSB
60F 'Modify backbone' 2023-11-03 PDBE
#
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
60F C1 C 5.598 1.268 1
60F C2 C 5.598 -0.233 2
60F C3 C 4.299 -0.983 3
60F O1 O 4.299 2.018 4
60F "C1'" C 4.299 -2.482 5
60F "C6'" C 5.598 -3.232 6
60F "C5'" C 5.598 -4.732 7
60F "C4'" C 4.299 -5.482 8
60F "O4'" O 4.299 -6.982 9
60F "C3'" C 3.000 -4.732 10
60F "C2'" C 3.000 -3.232 11
60F N N 9.495 3.518 12
60F CA C 8.196 4.268 13
60F CB C 6.897 3.518 14
60F SG S 6.897 2.018 15
60F C C 8.196 5.768 16
60F O O 9.495 6.518 17
60F OXT O 6.897 6.518 18
#
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
60F CA N SINGLE BEGINWEDGE 1
60F O1 C1 DOUBLE NONE 2
60F CA CB SINGLE NONE 3
60F CA C SINGLE NONE 4
60F CB SG SINGLE NONE 5
60F "C2'" "C3'" SINGLE NONE 6
60F "C2'" "C1'" DOUBLE NONE 7
60F C1 C2 SINGLE ENDDOWNRIGHT 8
60F C1 SG SINGLE NONE 9
60F C3 C2 DOUBLE NONE 10
60F C3 "C1'" SINGLE ENDDOWNRIGHT 11
60F "C3'" "C4'" DOUBLE NONE 12
60F C O DOUBLE NONE 13
60F "C1'" "C6'" SINGLE NONE 14
60F "C4'" "O4'" SINGLE NONE 15
60F "C4'" "C5'" SINGLE NONE 16
60F "C6'" "C5'" DOUBLE NONE 17
60F C OXT SINGLE NONE 18
#
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
60F MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
60F peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
60F phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-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
60F "C1'" S1 1
60F "C6'" S1 1
60F "C5'" S1 1
60F "C4'" S1 1
60F "C3'" S1 1
60F "C2'" S1 1
60F O F1 1
60F C F1 1
60F CA F1 1
60F N F1 1
60F "C1'" F2 1
60F "C2'" F2 1
60F "C3'" F2 1
60F "C4'" F2 1
60F "C5'" F2 1
60F "C6'" F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 60F
_pdbe_chem_comp_rdkit_properties.exactmw 267.057
_pdbe_chem_comp_rdkit_properties.amw 267.306
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.167
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 126.860
_pdbe_chem_comp_rdkit_properties.tpsa 100.620
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.560
_pdbe_chem_comp_rdkit_properties.CrippenMR 69.341
_pdbe_chem_comp_rdkit_properties.chi0v 9.305
_pdbe_chem_comp_rdkit_properties.chi1v 5.015
_pdbe_chem_comp_rdkit_properties.chi2v 1.908
_pdbe_chem_comp_rdkit_properties.chi3v 1.908
_pdbe_chem_comp_rdkit_properties.chi4v 1.014
_pdbe_chem_comp_rdkit_properties.chi0n 21.488
_pdbe_chem_comp_rdkit_properties.chi1n 10.409
_pdbe_chem_comp_rdkit_properties.chi2n 1.325
_pdbe_chem_comp_rdkit_properties.chi3n 1.325
_pdbe_chem_comp_rdkit_properties.chi4n 0.639
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.790
_pdbe_chem_comp_rdkit_properties.kappa1 4.395
_pdbe_chem_comp_rdkit_properties.kappa2 6.827
_pdbe_chem_comp_rdkit_properties.kappa3 5.027
_pdbe_chem_comp_rdkit_properties.Phi 1.667
#
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
60F UniChem PDBe 60F
60F UniChem PubChem 101030914
60F UniChem Nikkaji J1.525.874H
#
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
60F C1 1.116 2.528 -0.839 ETKDGv3 1
60F C2 -0.109 1.733 -1.056 ETKDGv3 2
60F C3 -0.745 1.088 -0.069 ETKDGv3 3
60F O1 1.579 3.205 -1.793 ETKDGv3 4
60F "C1'" -1.971 0.280 -0.278 ETKDGv3 5
60F "C6'" -2.342 -0.268 -1.614 ETKDGv3 6
60F "C5'" -3.453 -1.001 -1.759 ETKDGv3 7
60F "C4'" -4.319 -1.282 -0.594 ETKDGv3 8
60F "O4'" -5.478 -2.039 -0.741 ETKDGv3 9
60F "C3'" -3.982 -0.809 0.612 ETKDGv3 10
60F "C2'" -2.756 -0.002 0.779 ETKDGv3 11
60F N 2.130 -0.361 1.786 ETKDGv3 12
60F CA 2.636 -0.118 0.433 ETKDGv3 13
60F CB 3.209 1.303 0.319 ETKDGv3 14
60F SG 1.968 2.580 0.746 ETKDGv3 15
60F C 3.686 -1.134 0.068 ETKDGv3 16
60F O 3.513 -1.890 -0.925 ETKDGv3 17
60F H1 -0.506 1.715 -2.062 ETKDGv3 18
60F H10 -0.376 1.176 0.946 ETKDGv3 19
60F H3 -1.712 -0.108 -2.477 ETKDGv3 20
60F H4 -3.711 -1.401 -2.732 ETKDGv3 21
60F H5 -5.752 -2.408 -1.644 ETKDGv3 22
60F H6 -4.608 -1.012 1.472 ETKDGv3 23
60F H7 -2.509 0.368 1.767 ETKDGv3 24
60F H 1.703 -1.316 1.817 ETKDGv3 25
60F H2 2.926 -0.350 2.466 ETKDGv3 26
60F HA 1.792 -0.216 -0.282 ETKDGv3 27
60F H12 4.064 1.417 1.018 ETKDGv3 28
60F H13 3.591 1.480 -0.710 ETKDGv3 29
60F OXT 4.850 -1.240 0.824 ETKDGv3 30
60F HXT 5.564 -1.918 0.587 ETKDGv3 31
#