data_5TX
#
_chem_comp.id 5TX
_chem_comp.name "((3S,5S)-1,5-dihydroxy-3-methyl-2-oxopyrrolidin-3-yl)phosphonic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H10 N O6 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-12-01
_chem_comp.pdbx_modified_date 2016-11-18
_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 211.110
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 5TX
_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 5EU9
_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
5TX C01 C1 C 0 1 N N S N N N -52.462 10.106 -23.756 2.017 0.849 0.662 C01 5TX 1
5TX C02 C2 C 0 1 N N N N N N -52.393 10.665 -22.297 0.565 1.377 0.671 C02 5TX 2
5TX C03 C3 C 0 1 N N S N N N -53.309 11.883 -22.288 -0.118 0.437 -0.349 C03 5TX 3
5TX C04 C4 C 0 1 N N N N N N -53.430 12.257 -23.637 0.734 -0.813 -0.330 C04 5TX 4
5TX P05 P1 P 0 1 N N N N N N -55.139 11.461 -21.693 -1.821 0.055 0.177 P05 5TX 5
5TX O06 O1 O 0 1 N N N N N N -55.967 12.709 -21.868 -1.790 -0.668 1.616 O06 5TX 6
5TX O07 O2 O 0 1 N N N N N N -55.507 10.397 -22.697 -2.601 1.310 0.273 O07 5TX 7
5TX O08 O3 O 0 1 N N N N N N -54.962 10.893 -20.323 -2.509 -0.923 -0.900 O08 5TX 8
5TX C09 C5 C 0 1 N N N N N N -52.821 12.959 -21.333 -0.118 1.068 -1.742 C09 5TX 9
5TX O10 O4 O 0 1 N N N N N N -53.935 13.261 -24.210 0.396 -1.891 -0.771 O10 5TX 10
5TX N12 N1 N 0 1 N N N N N N -52.996 11.246 -24.500 1.921 -0.555 0.245 N12 5TX 11
5TX O13 O5 O 0 1 N N N N N N -51.114 9.969 -24.220 2.807 1.591 -0.270 O13 5TX 12
5TX O11 O6 O 0 1 N N N N N N -53.024 11.238 -25.868 2.947 -1.514 0.427 O11 5TX 13
5TX H1 H1 H 0 1 N N N N N N -53.071 9.193 -23.830 2.450 0.918 1.660 H1 5TX 14
5TX H2 H2 H 0 1 N N N N N N -52.748 9.911 -21.579 0.118 1.271 1.660 H2 5TX 15
5TX H3 H3 H 0 1 N N N N N N -51.363 10.956 -22.044 0.525 2.413 0.335 H3 5TX 16
5TX H4 H4 H 0 1 N N N N N N -56.574 12.588 -22.589 -2.664 -0.900 1.958 H4 5TX 17
5TX H5 H5 H 0 1 N N N N N N -55.117 9.956 -20.346 -2.050 -1.767 -1.015 H5 5TX 18
5TX H6 H6 H 0 1 N N N N N N -52.768 12.549 -20.314 0.909 1.248 -2.059 H6 5TX 19
5TX H7 H7 H 0 1 N N N N N N -51.822 13.299 -21.644 -0.603 0.393 -2.447 H7 5TX 20
5TX H8 H8 H 0 1 N N N N N N -53.520 13.809 -21.350 -0.660 2.013 -1.713 H8 5TX 21
5TX H9 H9 H 0 1 N N N N N N -50.698 9.239 -23.776 3.729 1.304 -0.320 H9 5TX 22
5TX H10 H10 H 0 1 N N N N N N -53.411 12.047 -26.182 2.724 -2.395 0.096 H10 5TX 23
#
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
5TX O11 N12 SING N N 1
5TX N12 C01 SING N N 2
5TX N12 C04 SING N N 3
5TX O13 C01 SING N N 4
5TX O10 C04 DOUB N N 5
5TX C01 C02 SING N N 6
5TX C04 C03 SING N N 7
5TX O07 P05 DOUB N N 8
5TX C02 C03 SING N N 9
5TX C03 P05 SING N N 10
5TX C03 C09 SING N N 11
5TX O06 P05 SING N N 12
5TX P05 O08 SING N N 13
5TX C01 H1 SING N N 14
5TX C02 H2 SING N N 15
5TX C02 H3 SING N N 16
5TX O06 H4 SING N N 17
5TX O08 H5 SING N N 18
5TX C09 H6 SING N N 19
5TX C09 H7 SING N N 20
5TX C09 H8 SING N N 21
5TX O13 H9 SING N N 22
5TX O11 H10 SING N N 23
#
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
5TX InChI InChI 1.03 InChI=1S/C5H10NO6P/c1-5(13(10,11)12)2-3(7)6(9)4(5)8/h3,7,9H,2H2,1H3,(H2,10,11,12)/t3-,5-/m0/s1
5TX InChIKey InChI 1.03 VVBLYPMICKYZTP-UCORVYFPSA-N
5TX SMILES_CANONICAL CACTVS 3.385 C[C@@]1(C[C@H](O)N(O)C1=O)[P](O)(O)=O
5TX SMILES CACTVS 3.385 C[C]1(C[CH](O)N(O)C1=O)[P](O)(O)=O
5TX SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 C[C@@]1(C[C@@H](N(C1=O)O)O)P(=O)(O)O
5TX SMILES "OpenEye OEToolkits" 2.0.4 CC1(CC(N(C1=O)O)O)P(=O)(O)O
#
_pdbx_chem_comp_identifier.comp_id 5TX
_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
"[(3~{S},5~{S})-3-methyl-1,5-bis(oxidanyl)-2-oxidanylidene-pyrrolidin-3-yl]phosphonic 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
5TX 'Create component' 2015-12-01 RCSB
5TX 'Initial release' 2016-11-23 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
5TX C01 C 4.807 -1.761 1
5TX C02 C 4.343 -0.334 2
5TX C03 C 5.557 0.547 3
5TX C04 C 6.770 -0.334 4
5TX P05 P 6.438 1.761 5
5TX O06 O 5.225 2.643 6
5TX O07 O 7.320 2.974 7
5TX O08 O 7.652 0.879 8
5TX C09 C 4.675 1.761 9
5TX O10 O 8.197 0.129 10
5TX N12 N 6.307 -1.761 11
5TX O13 O 3.925 -2.974 12
5TX O11 O 7.188 -2.974 13
#
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
5TX O11 N12 SINGLE NONE 1
5TX N12 C01 SINGLE NONE 2
5TX N12 C04 SINGLE NONE 3
5TX C01 O13 SINGLE BEGINWEDGE 4
5TX O10 C04 DOUBLE NONE 5
5TX C01 C02 SINGLE NONE 6
5TX C04 C03 SINGLE NONE 7
5TX O07 P05 DOUBLE NONE 8
5TX C02 C03 SINGLE NONE 9
5TX C03 P05 SINGLE NONE 10
5TX C03 C09 SINGLE BEGINWEDGE 11
5TX O06 P05 SINGLE NONE 12
5TX P05 O08 SINGLE NONE 13
#
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
5TX MurckoScaffold S1 scaffold O=C1CCCN1 InChI=1S/C4H7NO/c6-4-2-1-3-5-4/h1-3H2,(H,5,6) HNJBEVLQSNELDL-UHFFFAOYSA-N
5TX 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
5TX C01 S1 1
5TX C02 S1 1
5TX C03 S1 1
5TX C04 S1 1
5TX O10 S1 1
5TX N12 S1 1
5TX N12 F1 1
5TX C04 F1 1
5TX O10 F1 1
5TX C03 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 5TX
_pdbe_chem_comp_rdkit_properties.exactmw 211.025
_pdbe_chem_comp_rdkit_properties.amw 211.110
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 23
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.800
_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 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 88.105
_pdbe_chem_comp_rdkit_properties.tpsa 118.300
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.137
_pdbe_chem_comp_rdkit_properties.CrippenMR 39.705
_pdbe_chem_comp_rdkit_properties.chi0v 6.738
_pdbe_chem_comp_rdkit_properties.chi1v 4.352
_pdbe_chem_comp_rdkit_properties.chi2v 2.502
_pdbe_chem_comp_rdkit_properties.chi3v 2.502
_pdbe_chem_comp_rdkit_properties.chi4v 1.241
_pdbe_chem_comp_rdkit_properties.chi0n 15.844
_pdbe_chem_comp_rdkit_properties.chi1n 7.442
_pdbe_chem_comp_rdkit_properties.chi2n 1.377
_pdbe_chem_comp_rdkit_properties.chi3n 1.377
_pdbe_chem_comp_rdkit_properties.chi4n 0.684
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.460
_pdbe_chem_comp_rdkit_properties.kappa1 3.287
_pdbe_chem_comp_rdkit_properties.kappa2 2.763
_pdbe_chem_comp_rdkit_properties.kappa3 1.385
_pdbe_chem_comp_rdkit_properties.Phi 0.699
#
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
5TX UniChem ChEMBL CHEMBL5187779
5TX UniChem PDBe 5TX
5TX UniChem ZINC ZINC000584905322
5TX UniChem PubChem 122362338
#
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
5TX C01 -2.051 0.135 -0.185 ETKDGv3 1
5TX C02 -0.793 1.022 -0.045 ETKDGv3 2
5TX C03 0.413 0.072 0.211 ETKDGv3 3
5TX C04 -0.163 -1.269 -0.071 ETKDGv3 4
5TX P05 1.802 0.428 -0.933 ETKDGv3 5
5TX O06 3.074 -0.652 -0.651 ETKDGv3 6
5TX O07 1.334 0.278 -2.363 ETKDGv3 7
5TX O08 2.340 2.014 -0.684 ETKDGv3 8
5TX C09 0.886 0.151 1.670 ETKDGv3 9
5TX O10 0.491 -2.346 -0.060 ETKDGv3 10
5TX N12 -1.549 -1.219 -0.317 ETKDGv3 11
5TX O13 -2.844 0.239 0.967 ETKDGv3 12
5TX O11 -2.332 -2.310 -0.496 ETKDGv3 13
5TX H1 -2.633 0.421 -1.091 ETKDGv3 14
5TX H2 -0.661 1.592 -0.990 ETKDGv3 15
5TX H3 -0.917 1.772 0.769 ETKDGv3 16
5TX H4 3.536 -0.299 0.150 ETKDGv3 17
5TX H5 3.124 2.111 -1.281 ETKDGv3 18
5TX H6 1.685 -0.596 1.864 ETKDGv3 19
5TX H7 0.042 -0.053 2.365 ETKDGv3 20
5TX H8 1.286 1.163 1.891 ETKDGv3 21
5TX H9 -3.702 -0.214 0.759 ETKDGv3 22
5TX H10 -2.369 -2.437 -1.478 ETKDGv3 23
#