data_9S4
#
_chem_comp.id 9S4
_chem_comp.name
"(2~{S},3~{R},4~{R},5~{R})-3-acetamido-2-[(2~{S})-2,3-bis(oxidanyl)propyl]-5-fluoranyl-4-oxidanyl-2,3,4,5-tetrahydropyran-1-ium-6-carboxylic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H17 F N O7"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2017-06-07
_chem_comp.pdbx_modified_date 2018-02-16
_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 294.254
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 9S4
_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 5W2U
_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
9S4 O1B O1 O 0 1 N N N N N N 24.030 20.912 64.877 0.182 -4.248 -0.040 O1B 9S4 1
9S4 C1 C1 C 0 1 N N N N N N 23.463 19.820 64.751 0.835 -3.230 0.050 C1 9S4 2
9S4 O1A O2 O 0 1 N N N N N N 22.267 19.716 65.171 2.179 -3.287 0.016 O1A 9S4 3
9S4 C2 C2 C 0 1 N N N N N N 24.147 18.826 64.130 0.148 -1.914 0.192 C2 9S4 4
9S4 C3 C3 C 0 1 N N R N N N 23.508 17.473 63.901 -1.350 -1.939 0.215 C3 9S4 5
9S4 F1 F1 F 0 1 N N N N N N 23.546 16.790 65.095 -1.832 -2.159 -1.080 F1 9S4 6
9S4 O6 O3 O 1 1 N N N N N N 25.514 19.031 63.664 0.841 -0.964 0.279 O6 9S4 7
9S4 C6 C4 C 0 1 N N S N N N 26.085 18.127 62.667 0.373 0.387 0.443 C6 9S4 8
9S4 C7 C5 C 0 1 N N N N N N 27.606 18.297 62.616 1.221 1.317 -0.427 C7 9S4 9
9S4 C8 C6 C 0 1 N N S N N N 27.941 19.778 62.377 2.672 1.286 0.056 C8 9S4 10
9S4 C9 C7 C 0 1 N N N N N N 29.398 20.112 62.728 3.542 2.118 -0.889 C9 9S4 11
9S4 O9 O4 O 0 1 N N N N N N 30.259 19.487 61.757 4.913 1.995 -0.505 O9 9S4 12
9S4 O8 O5 O 0 1 N N N N N N 27.624 20.146 61.023 2.746 1.831 1.375 O8 9S4 13
9S4 C5 C8 C 0 1 N N R N N N 25.673 16.663 62.880 -1.094 0.518 0.035 C5 9S4 14
9S4 C4 C9 C 0 1 N N R N N N 24.164 16.598 62.822 -1.884 -0.600 0.737 C4 9S4 15
9S4 O4 O6 O 0 1 N N N N N N 23.714 15.273 63.103 -3.274 -0.480 0.427 O4 9S4 16
9S4 N5 N1 N 0 1 N N N N N N 26.151 15.856 61.727 -1.610 1.824 0.452 N5 9S4 17
9S4 C10 C10 C 0 1 N N N N N N 26.963 14.781 61.857 -2.655 2.375 -0.197 C10 9S4 18
9S4 O10 O7 O 0 1 N N N N N N 27.362 14.393 62.949 -3.168 1.790 -1.126 O10 9S4 19
9S4 C11 C11 C 0 1 N N N N N N 27.371 14.047 60.604 -3.184 3.719 0.233 C11 9S4 20
9S4 H1 H1 H 0 1 N N N N N N 21.986 20.547 65.536 2.579 -4.162 -0.082 H1 9S4 21
9S4 H3 H3 H 0 1 N N N N N N 22.463 17.640 63.603 -1.690 -2.742 0.869 H3 9S4 22
9S4 H4 H4 H 0 1 N N N N N N 25.697 18.427 61.682 0.481 0.680 1.487 H4 9S4 23
9S4 H5 H5 H 0 1 N N N N N N 28.017 17.690 61.796 1.176 0.985 -1.464 H5 9S4 24
9S4 H6 H6 H 0 1 N N N N N N 28.045 17.970 63.570 0.835 2.334 -0.355 H6 9S4 25
9S4 H7 H7 H 0 1 N N N N N N 27.303 20.366 63.053 3.030 0.257 0.068 H7 9S4 26
9S4 H8 H8 H 0 1 N N N N N N 29.634 19.731 63.732 3.417 1.757 -1.910 H8 9S4 27
9S4 H9 H9 H 0 1 N N N N N N 29.544 21.202 62.706 3.242 3.164 -0.833 H9 9S4 28
9S4 H10 H10 H 0 1 N N N N N N 31.165 19.686 61.962 5.524 2.497 -1.062 H10 9S4 29
9S4 H11 H11 H 0 1 N N N N N N 27.835 21.062 60.886 2.443 2.747 1.440 H11 9S4 30
9S4 H12 H12 H 0 1 N N N N N N 26.056 16.278 63.837 -1.186 0.414 -1.046 H12 9S4 31
9S4 H13 H13 H 0 1 N N N N N N 23.819 16.925 61.830 -1.738 -0.535 1.815 H13 9S4 32
9S4 H14 H14 H 0 1 N N N N N N 22.765 15.245 63.064 -3.828 -1.156 0.840 H14 9S4 33
9S4 H15 H15 H 0 1 N N N N N N 25.858 16.121 60.808 -1.199 2.292 1.196 H15 9S4 34
9S4 H16 H16 H 0 1 N N N N N N 28.021 13.200 60.870 -2.601 4.087 1.077 H16 9S4 35
9S4 H17 H17 H 0 1 N N N N N N 26.473 13.673 60.089 -3.107 4.422 -0.596 H17 9S4 36
9S4 H18 H18 H 0 1 N N N N N N 27.916 14.733 59.939 -4.229 3.620 0.529 H18 9S4 37
#
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
9S4 C11 C10 SING N N 1
9S4 O8 C8 SING N N 2
9S4 N5 C10 SING N N 3
9S4 N5 C5 SING N N 4
9S4 O9 C9 SING N N 5
9S4 C10 O10 DOUB N N 6
9S4 C8 C7 SING N N 7
9S4 C8 C9 SING N N 8
9S4 C7 C6 SING N N 9
9S4 C6 C5 SING N N 10
9S4 C6 O6 SING N N 11
9S4 C4 C5 SING N N 12
9S4 C4 O4 SING N N 13
9S4 C4 C3 SING N N 14
9S4 O6 C2 DOUB N N 15
9S4 C3 C2 SING N N 16
9S4 C3 F1 SING N N 17
9S4 C2 C1 SING N N 18
9S4 C1 O1B DOUB N N 19
9S4 C1 O1A SING N N 20
9S4 O1A H1 SING N N 21
9S4 C3 H3 SING N N 22
9S4 C6 H4 SING N N 23
9S4 C7 H5 SING N N 24
9S4 C7 H6 SING N N 25
9S4 C8 H7 SING N N 26
9S4 C9 H8 SING N N 27
9S4 C9 H9 SING N N 28
9S4 O9 H10 SING N N 29
9S4 O8 H11 SING N N 30
9S4 C5 H12 SING N N 31
9S4 C4 H13 SING N N 32
9S4 O4 H14 SING N N 33
9S4 N5 H15 SING N N 34
9S4 C11 H16 SING N N 35
9S4 C11 H17 SING N N 36
9S4 C11 H18 SING N N 37
#
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
9S4 SMILES ACDLabs 12.01 O=C(O)C=1C(F)C(C(C([O+]=1)CC(CO)O)NC(=O)C)O
9S4 InChI InChI 1.03 InChI=1S/C11H16FNO7/c1-4(15)13-8-6(2-5(16)3-14)20-10(11(18)19)7(12)9(8)17/h5-9,14,16-17H,2-3H2,1H3,(H-,13,15,18,19)/p+1/t5-,6-,7+,8-,9-/m0/s1
9S4 InChIKey InChI 1.03 DFROFKMCNZKOFD-PQFOHKHZSA-O
9S4 SMILES_CANONICAL CACTVS 3.385 CC(=O)N[C@@H]1[C@@H](O)[C@@H](F)C(=[O+][C@H]1C[C@H](O)CO)C(O)=O
9S4 SMILES CACTVS 3.385 CC(=O)N[CH]1[CH](O)[CH](F)C(=[O+][CH]1C[CH](O)CO)C(O)=O
9S4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 CC(=O)N[C@H]1[C@@H]([O+]=C([C@@H]([C@@H]1O)F)C(=O)O)C[C@@H](CO)O
9S4 SMILES "OpenEye OEToolkits" 2.0.6 CC(=O)NC1C([O+]=C(C(C1O)F)C(=O)O)CC(CO)O
#
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
9S4 "SYSTEMATIC NAME" ACDLabs 12.01 "(2S,3R,4R,5R)-3-(acetylamino)-6-carboxy-2-[(2S)-2,3-dihydroxypropyl]-5-fluoro-4-hydroxy-2,3,4,5-tetrahydropyranium (non-preferred name)"
9S4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(2~{S},3~{R},4~{R},5~{R})-3-acetamido-2-[(2~{S})-2,3-bis(oxidanyl)propyl]-5-fluoranyl-4-oxidanyl-2,3,4,5-tetrahydropyran-1-ium-6-carboxylic 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
9S4 'Create component' 2017-06-07 RCSB
9S4 'Modify formula' 2017-06-13 RCSB
9S4 'Initial release' 2018-02-21 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
9S4 O1B O 7.702 -4.035 1
9S4 C1 C 6.404 -3.285 2
9S4 O1A O 5.104 -4.035 3
9S4 C2 C 6.404 -1.785 4
9S4 C3 C 5.104 -1.035 5
9S4 F1 F 3.805 -1.785 6
9S4 O6 O 7.702 -1.035 7
9S4 C6 C 7.702 0.465 8
9S4 C7 C 9.002 1.215 9
9S4 C8 C 10.301 0.465 10
9S4 C9 C 11.600 1.215 11
9S4 O9 O 12.899 0.465 12
9S4 O8 O 10.301 -1.035 13
9S4 C5 C 6.404 1.215 14
9S4 C4 C 5.104 0.465 15
9S4 O4 O 3.805 1.215 16
9S4 N5 N 6.404 2.715 17
9S4 C10 C 7.702 3.465 18
9S4 O10 O 7.702 4.965 19
9S4 C11 C 9.002 2.715 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
9S4 C11 C10 SINGLE NONE 1
9S4 C8 O8 SINGLE BEGINWEDGE 2
9S4 N5 C10 SINGLE NONE 3
9S4 C5 N5 SINGLE BEGINWEDGE 4
9S4 O9 C9 SINGLE NONE 5
9S4 C10 O10 DOUBLE NONE 6
9S4 C8 C7 SINGLE NONE 7
9S4 C8 C9 SINGLE NONE 8
9S4 C6 C7 SINGLE BEGINDASH 9
9S4 C6 C5 SINGLE NONE 10
9S4 C6 O6 SINGLE NONE 11
9S4 C4 C5 SINGLE NONE 12
9S4 C4 O4 SINGLE BEGINDASH 13
9S4 C4 C3 SINGLE NONE 14
9S4 O6 C2 DOUBLE NONE 15
9S4 C3 C2 SINGLE NONE 16
9S4 C3 F1 SINGLE BEGINDASH 17
9S4 C2 C1 SINGLE NONE 18
9S4 C1 O1B DOUBLE NONE 19
9S4 C1 O1A SINGLE NONE 20
#
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
9S4 MurckoScaffold S1 scaffold 'C1=[O+]CCCC1' InChI=1S/C5H9O/c1-2-4-6-5-3-1/h4H,1-3,5H2/q+1 PLQXRKRRLKDDPF-UHFFFAOYSA-N
9S4 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-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
9S4 C2 S1 1
9S4 C3 S1 1
9S4 O6 S1 1
9S4 C6 S1 1
9S4 C5 S1 1
9S4 C4 S1 1
9S4 N5 F1 1
9S4 C10 F1 1
9S4 O10 F1 1
9S4 C11 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 9S4
_pdbe_chem_comp_rdkit_properties.exactmw 294.098
_pdbe_chem_comp_rdkit_properties.amw 294.255
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 37
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 9
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.727
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_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 5
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 137.368
_pdbe_chem_comp_rdkit_properties.tpsa 138.390
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.495
_pdbe_chem_comp_rdkit_properties.CrippenMR 62.648
_pdbe_chem_comp_rdkit_properties.chi0v 9.183
_pdbe_chem_comp_rdkit_properties.chi1v 4.519
_pdbe_chem_comp_rdkit_properties.chi2v 1.751
_pdbe_chem_comp_rdkit_properties.chi3v 1.751
_pdbe_chem_comp_rdkit_properties.chi4v 1.053
_pdbe_chem_comp_rdkit_properties.chi0n 26.183
_pdbe_chem_comp_rdkit_properties.chi1n 12.599
_pdbe_chem_comp_rdkit_properties.chi2n 1.751
_pdbe_chem_comp_rdkit_properties.chi3n 1.751
_pdbe_chem_comp_rdkit_properties.chi4n 1.053
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.580
_pdbe_chem_comp_rdkit_properties.kappa1 4.455
_pdbe_chem_comp_rdkit_properties.kappa2 6.729
_pdbe_chem_comp_rdkit_properties.kappa3 3.715
_pdbe_chem_comp_rdkit_properties.Phi 1.499
#
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
9S4 UniChem PDBe 9S4
9S4 UniChem PubChem 137348855
#
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
9S4 O1B -1.168 4.880 -0.611 ETKDGv3 1
9S4 C1 -0.288 3.977 -0.618 ETKDGv3 2
9S4 O1A 1.056 4.324 -0.712 ETKDGv3 3
9S4 C2 -0.672 2.559 -0.526 ETKDGv3 4
9S4 C3 -2.134 2.190 -0.393 ETKDGv3 5
9S4 F1 -2.563 2.561 0.871 ETKDGv3 6
9S4 O6 0.258 1.690 -0.497 ETKDGv3 7
9S4 C6 0.081 0.264 -0.467 ETKDGv3 8
9S4 C7 1.227 -0.374 0.341 ETKDGv3 9
9S4 C8 2.611 -0.073 -0.265 ETKDGv3 10
9S4 C9 3.734 -0.626 0.623 ETKDGv3 11
9S4 O9 3.663 -2.025 0.687 ETKDGv3 12
9S4 O8 2.697 -0.637 -1.549 ETKDGv3 13
9S4 C5 -1.295 -0.133 0.109 ETKDGv3 14
9S4 C4 -2.374 0.689 -0.613 ETKDGv3 15
9S4 O4 -3.669 0.321 -0.204 ETKDGv3 16
9S4 N5 -1.540 -1.565 -0.100 ETKDGv3 17
9S4 C10 -1.639 -2.509 0.975 ETKDGv3 18
9S4 O10 -1.524 -2.133 2.173 ETKDGv3 19
9S4 C11 -1.843 -3.958 0.675 ETKDGv3 20
9S4 H1 1.339 5.295 -0.776 ETKDGv3 21
9S4 H3 -2.728 2.756 -1.142 ETKDGv3 22
9S4 H4 0.135 -0.106 -1.515 ETKDGv3 23
9S4 H5 1.190 0.015 1.383 ETKDGv3 24
9S4 H6 1.085 -1.476 0.382 ETKDGv3 25
9S4 H7 2.738 1.033 -0.328 ETKDGv3 26
9S4 H8 3.650 -0.195 1.646 ETKDGv3 27
9S4 H9 4.717 -0.322 0.199 ETKDGv3 28
9S4 H10 4.408 -2.311 1.277 ETKDGv3 29
9S4 H11 3.451 -0.184 -2.011 ETKDGv3 30
9S4 H12 -1.321 0.117 1.194 ETKDGv3 31
9S4 H13 -2.300 0.487 -1.706 ETKDGv3 32
9S4 H14 -3.701 0.364 0.788 ETKDGv3 33
9S4 H15 -1.599 -1.922 -1.081 ETKDGv3 34
9S4 H16 -2.090 -4.518 1.602 ETKDGv3 35
9S4 H17 -0.915 -4.378 0.234 ETKDGv3 36
9S4 H18 -2.678 -4.076 -0.047 ETKDGv3 37
#