data_G8X
#
_chem_comp.id G8X
_chem_comp.name "(2~{S},3~{R})-3-oxidanylpyrrolidine-2-carboxylic acid"
_chem_comp.type "L-peptide linking"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C5 H9 N O3"
_chem_comp.mon_nstd_parent_comp_id PRO
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-08-06
_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 131.130
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code G8X
_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 7CNQ
_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
G8X O2 O2 O 0 1 N N N N N N 0.660 12.797 62.539 -0.146 1.819 -0.410 O2 G8X 1
G8X OXT O O 0 1 N N N Y N Y -2.226 10.995 63.710 -2.394 0.204 0.609 O1 G8X 2
G8X N N N 0 1 N N N Y Y N -0.942 13.108 65.012 0.879 -1.400 0.085 N G8X 3
G8X CB CB C 0 1 N N R N N N -0.222 13.859 62.884 0.687 0.999 0.412 C3 G8X 4
G8X CG CG C 0 1 N N N N N N 0.420 14.768 63.915 2.001 0.657 -0.329 C4 G8X 5
G8X CD CD C 0 1 N N N N N N -0.066 14.268 65.270 2.247 -0.821 0.066 C5 G8X 6
G8X CA CA C 0 1 N N S Y N N -1.372 13.196 63.602 0.009 -0.359 0.674 C2 G8X 7
G8X C C C 0 1 N N N Y N Y -1.612 11.836 63.020 -1.347 -0.391 0.016 C1 G8X 8
G8X O O1 O 0 1 N N N Y N Y -1.256 11.617 61.838 -1.490 -0.951 -1.045 OXT G8X 9
G8X H1 H1 H 0 1 N N N N N N 0.160 12.072 62.183 0.230 2.688 -0.608 H1 G8X 10
G8X HXT HXT H 0 1 N N N Y N Y -2.364 10.206 63.200 -3.244 0.157 0.148 H2 G8X 11
G8X H H H 0 1 N N N Y Y N -1.738 13.138 65.616 0.852 -2.246 0.633 H3 G8X 12
G8X HB2 HB2 H 0 1 N N N N N N -0.568 14.428 62.009 0.902 1.502 1.354 H5 G8X 13
G8X HG2 HG2 H 0 1 N N N N N N 1.516 14.703 63.853 1.872 0.752 -1.407 H6 G8X 14
G8X HG3 HG3 H 0 1 N N N N N N 0.105 15.810 63.756 2.816 1.291 0.021 H7 G8X 15
G8X HD2 HD2 H 0 1 N N N N N N 0.790 13.964 65.890 2.705 -0.884 1.053 H8 G8X 16
G8X HD3 HD3 H 0 1 N N N N N N -0.629 15.060 65.785 2.866 -1.320 -0.679 H9 G8X 17
G8X HA HA H 0 1 N N N Y N N -2.278 13.813 63.513 -0.092 -0.522 1.747 H10 G8X 18
#
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
G8X O C DOUB N N 1
G8X O2 CB SING N N 2
G8X CB CA SING N N 3
G8X CB CG SING N N 4
G8X C CA SING N N 5
G8X C OXT SING N N 6
G8X CA N SING N N 7
G8X CG CD SING N N 8
G8X N CD SING N N 9
G8X O2 H1 SING N N 10
G8X OXT HXT SING N N 11
G8X N H SING N N 12
G8X CB HB2 SING N N 13
G8X CG HG2 SING N N 14
G8X CG HG3 SING N N 15
G8X CD HD2 SING N N 16
G8X CD HD3 SING N N 17
G8X CA HA SING N N 18
#
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
G8X InChI InChI 1.03 InChI=1S/C5H9NO3/c7-3-1-2-6-4(3)5(8)9/h3-4,6-7H,1-2H2,(H,8,9)/t3-,4+/m1/s1
G8X InChIKey InChI 1.03 BJBUEDPLEOHJGE-DMTCNVIQSA-N
G8X SMILES_CANONICAL CACTVS 3.385 O[C@@H]1CCN[C@@H]1C(O)=O
G8X SMILES CACTVS 3.385 O[CH]1CCN[CH]1C(O)=O
G8X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C1CN[C@@H]([C@@H]1O)C(=O)O
G8X SMILES "OpenEye OEToolkits" 2.0.7 C1CNC(C1O)C(=O)O
#
_pdbx_chem_comp_identifier.comp_id G8X
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier "(2~{S},3~{R})-3-oxidanylpyrrolidine-2-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
G8X 'Create component' 2020-08-06 PDBJ
G8X 'Initial release' 2021-06-16 RCSB
G8X '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
G8X O2 O 5.123 1.861 1
G8X OXT O 3.803 -2.710 2
G8X N N 6.755 -1.661 3
G8X CB C 6.005 0.647 4
G8X CG C 7.505 0.647 5
G8X CD C 7.968 -0.780 6
G8X CA C 5.541 -0.780 7
G8X C C 4.115 -1.243 8
G8X O O 3.000 -0.239 9
#
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
G8X O C DOUBLE NONE 1
G8X CB O2 SINGLE BEGINDASH 2
G8X CB CA SINGLE NONE 3
G8X CB CG SINGLE NONE 4
G8X CA C SINGLE BEGINDASH 5
G8X C OXT SINGLE NONE 6
G8X CA N SINGLE NONE 7
G8X CG CD SINGLE NONE 8
G8X N CD SINGLE NONE 9
#
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
G8X MurckoScaffold S1 scaffold C1CCNC1 InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2 RWRDLPDLKQPQOW-UHFFFAOYSA-N
G8X peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-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
G8X N S1 1
G8X CB S1 1
G8X CG S1 1
G8X CD S1 1
G8X CA S1 1
G8X O F1 1
G8X C F1 1
G8X CA F1 1
G8X N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id G8X
_pdbe_chem_comp_rdkit_properties.exactmw 131.058
_pdbe_chem_comp_rdkit_properties.amw 131.131
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 9
_pdbe_chem_comp_rdkit_properties.NumAtoms 18
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_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 65.369
_pdbe_chem_comp_rdkit_properties.tpsa 69.560
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.206
_pdbe_chem_comp_rdkit_properties.CrippenMR 30.050
_pdbe_chem_comp_rdkit_properties.chi0v 4.172
_pdbe_chem_comp_rdkit_properties.chi1v 2.060
_pdbe_chem_comp_rdkit_properties.chi2v 0.746
_pdbe_chem_comp_rdkit_properties.chi3v 0.746
_pdbe_chem_comp_rdkit_properties.chi4v 0.383
_pdbe_chem_comp_rdkit_properties.chi0n 13.172
_pdbe_chem_comp_rdkit_properties.chi1n 6.323
_pdbe_chem_comp_rdkit_properties.chi2n 0.746
_pdbe_chem_comp_rdkit_properties.chi3n 0.746
_pdbe_chem_comp_rdkit_properties.chi4n 0.383
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.610
_pdbe_chem_comp_rdkit_properties.kappa1 1.515
_pdbe_chem_comp_rdkit_properties.kappa2 2.326
_pdbe_chem_comp_rdkit_properties.kappa3 1.197
_pdbe_chem_comp_rdkit_properties.Phi 0.392
#
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
G8X UniChem PDBe G8X
G8X UniChem ChEBI 55479
G8X UniChem ChEBI 60041
G8X UniChem ZINC ZINC000004521590
G8X UniChem fdasrs 11L19HLQ3S
G8X UniChem 'PubChem TPHARMA' 16019793
G8X UniChem PubChem 7098652
G8X UniChem ACTor 567-35-1
G8X UniChem Nikkaji J191.773K
G8X UniChem 'EPA CompTox Dashboard' DTXSID70427760
G8X UniChem MetaboLights MTBLC55479
G8X UniChem MetaboLights MTBLC60041
G8X UniChem BRENDA 20195
G8X UniChem BRENDA 45146
G8X UniChem Rhea 60041
G8X UniChem ChemicalBook CB1971622
G8X UniChem eMolecules 506639
G8X UniChem SureChEMBL SCHEMBL7412
G8X UniChem PubChem 7098651
#
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
G8X O2 -0.049 1.926 0.735 ETKDGv3 1
G8X OXT 2.804 0.940 -0.729 ETKDGv3 2
G8X N 0.012 -1.322 -0.828 ETKDGv3 3
G8X CB -0.603 0.863 0.001 ETKDGv3 4
G8X CG -1.232 -0.173 0.904 ETKDGv3 5
G8X CD -1.096 -1.469 0.124 ETKDGv3 6
G8X CA 0.452 0.077 -0.782 ETKDGv3 7
G8X C 1.818 0.146 -0.152 ETKDGv3 8
G8X O 2.064 -0.487 0.910 ETKDGv3 9
G8X H1 -0.813 2.462 1.073 ETKDGv3 10
G8X HXT 3.725 1.009 -0.312 ETKDGv3 11
G8X H -0.345 -1.532 -1.790 ETKDGv3 12
G8X HB2 -1.369 1.247 -0.714 ETKDGv3 13
G8X HG2 -2.296 0.066 1.120 ETKDGv3 14
G8X HG3 -0.666 -0.249 1.859 ETKDGv3 15
G8X HD2 -2.047 -1.681 -0.417 ETKDGv3 16
G8X HD3 -0.886 -2.316 0.813 ETKDGv3 17
G8X HA 0.525 0.492 -1.814 ETKDGv3 18
#