data_GXP
#
_chem_comp.id GXP
_chem_comp.name '(4S)-4-hydroxy-2,5-dioxopentanoic acid'
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C5 H6 O5'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2014-01-16
_chem_comp.pdbx_modified_date 2024-09-27
_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 146.098
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GXP
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 4OE7
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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
GXP O O O 0 1 N N N N N N -28.624 23.258 -22.953 -3.668 -0.522 0.284 O GXP 1
GXP C C C 0 1 N N N N N N -28.961 22.249 -22.330 -2.750 -0.669 -0.487 C GXP 2
GXP C1 C1 C 0 1 N N S N N N -29.920 22.302 -21.134 -1.541 0.226 -0.398 C1 GXP 3
GXP O1 O1 O 0 1 N N N N N N -30.379 23.645 -20.849 -1.717 1.161 0.669 O1 GXP 4
GXP C2 C2 C 0 1 N N N N N N -31.129 21.389 -21.379 -0.296 -0.622 -0.132 C2 GXP 5
GXP C3 C3 C 0 1 N N N N N N -32.444 21.966 -20.842 0.928 0.257 -0.165 C3 GXP 6
GXP C4 C4 C 0 1 N N N N N N -33.249 22.775 -21.851 2.276 -0.334 0.067 C4 GXP 7
GXP O3 O3 O 0 1 N N N N N N -32.847 22.860 -23.039 2.389 -1.522 0.282 O3 GXP 8
GXP O4 O4 O 0 1 N N N N N N -34.276 23.342 -21.422 3.369 0.451 0.037 O4 GXP 9
GXP H1 H1 H 0 1 N N N N N N -28.566 21.292 -22.638 -2.793 -1.445 -1.237 H1 GXP 10
GXP H2 H2 H 0 1 N N N N N N -29.382 21.917 -20.255 -1.419 0.766 -1.337 H2 GXP 11
GXP H3 H3 H 0 1 N N N N N N -29.987 24.252 -21.466 -1.832 0.750 1.536 H3 GXP 12
GXP H4 H4 H 0 1 N N N N N N -31.234 21.232 -22.463 -0.379 -1.092 0.848 H4 GXP 13
GXP H7 H7 H 0 1 N N N N N N -34.686 23.831 -22.126 4.222 0.023 0.193 H7 GXP 14
GXP O2 O2 O 0 1 N Y N N N N ? ? ? 0.816 1.440 -0.379 O2 GXP 15
GXP H8 H8 H 0 1 N N N N N N -30.944 20.424 -20.885 -0.211 -1.393 -0.898 H8 GXP 16
#
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
GXP O3 C4 DOUB N N 1
GXP O C DOUB N N 2
GXP C C1 SING N N 3
GXP C4 O4 SING N N 4
GXP C4 C3 SING N N 5
GXP C2 C1 SING N N 6
GXP C2 C3 SING N N 7
GXP C1 O1 SING N N 8
GXP C H1 SING N N 9
GXP C1 H2 SING N N 10
GXP O1 H3 SING N N 11
GXP C2 H4 SING N N 12
GXP O4 H7 SING N N 13
GXP C3 O2 DOUB N N 14
GXP C2 H8 SING N N 15
#
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
GXP SMILES ACDLabs 12.01 'O=CC(O)CC(=O)C(=O)O'
GXP InChI InChI 1.03 'InChI=1S/C5H6O5/c6-2-3(7)1-4(8)5(9)10/h2-3,7H,1H2,(H,9,10)/t3-/m0/s1'
GXP InChIKey InChI 1.03 QZKCWTOLHHFWCD-VKHMYHEASA-N
GXP SMILES_CANONICAL CACTVS 3.385 'O[C@@H](CC(=O)C(O)=O)C=O'
GXP SMILES CACTVS 3.385 'O[CH](CC(=O)C(O)=O)C=O'
GXP SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.6 'C([C@@H](C=O)O)C(=O)C(=O)O'
GXP SMILES 'OpenEye OEToolkits' 1.7.6 'C(C(C=O)O)C(=O)C(=O)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
GXP 'SYSTEMATIC NAME' ACDLabs 12.01 '(4S)-4-hydroxy-2,5-dioxopentanoic acid'
GXP 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.7.6 '(4S)-4-oxidanyl-2,5-bis(oxidanylidene)pentanoic 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
GXP 'Create component' 2014-01-16 RCSB
GXP 'Initial release' 2014-12-24 RCSB
GXP 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id GXP
_pdbx_chem_comp_pcm.modified_residue_id LYS
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Covalent chemical modification'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom C3
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom NZ
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
_pdbx_chem_comp_pcm.first_instance_model_db_code 4OE7
#
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
GXP O O 11.600 -0.142 1
GXP C C 10.301 0.608 2
GXP C1 C 9.002 -0.142 3
GXP O1 O 9.002 -1.643 4
GXP C2 C 7.702 0.608 5
GXP C3 C 6.404 -0.142 6
GXP C4 C 5.104 0.608 7
GXP O3 O 3.805 -0.142 8
GXP O4 O 5.104 2.107 9
GXP O2 O 6.404 -1.643 10
#
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
GXP O3 C4 DOUBLE NONE 1
GXP O C DOUBLE NONE 2
GXP C C1 SINGLE NONE 3
GXP C4 O4 SINGLE NONE 4
GXP C4 C3 SINGLE NONE 5
GXP C2 C1 SINGLE NONE 6
GXP C2 C3 SINGLE NONE 7
GXP C1 O1 SINGLE BEGINWEDGE 8
GXP C3 O2 DOUBLE NONE 9
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id GXP
_pdbe_chem_comp_rdkit_properties.exactmw 146.022
_pdbe_chem_comp_rdkit_properties.amw 146.098
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 16
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.400
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_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 64.875
_pdbe_chem_comp_rdkit_properties.tpsa 91.670
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.410
_pdbe_chem_comp_rdkit_properties.CrippenMR 29.331
_pdbe_chem_comp_rdkit_properties.chi0v 4.541
_pdbe_chem_comp_rdkit_properties.chi1v 2.021
_pdbe_chem_comp_rdkit_properties.chi2v 0.505
_pdbe_chem_comp_rdkit_properties.chi3v 0.505
_pdbe_chem_comp_rdkit_properties.chi4v 0.180
_pdbe_chem_comp_rdkit_properties.chi0n 10.541
_pdbe_chem_comp_rdkit_properties.chi1n 4.837
_pdbe_chem_comp_rdkit_properties.chi2n 0.505
_pdbe_chem_comp_rdkit_properties.chi3n 0.505
_pdbe_chem_comp_rdkit_properties.chi4n 0.180
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.230
_pdbe_chem_comp_rdkit_properties.kappa1 2.792
_pdbe_chem_comp_rdkit_properties.kappa2 3.731
_pdbe_chem_comp_rdkit_properties.kappa3 2.930
_pdbe_chem_comp_rdkit_properties.Phi 1.042
#
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
GXP UniChem PDBe GXP
GXP UniChem ZINC ZINC000100624191
GXP UniChem SureChEMBL SCHEMBL17285690
GXP UniChem PubChem 118534747
#
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
GXP O -1.422 1.804 0.728 ETKDGv3 1
GXP C -1.994 0.746 0.520 ETKDGv3 2
GXP C1 -1.341 -0.339 -0.295 ETKDGv3 3
GXP O1 -0.890 0.176 -1.521 ETKDGv3 4
GXP C2 -0.180 -1.008 0.464 ETKDGv3 5
GXP C3 0.989 -0.085 0.692 ETKDGv3 6
GXP C4 2.043 0.089 -0.320 ETKDGv3 7
GXP O3 2.010 -0.562 -1.399 ETKDGv3 8
GXP O4 3.088 0.979 -0.084 ETKDGv3 9
GXP H1 -2.997 0.598 0.909 ETKDGv3 10
GXP H2 -2.103 -1.130 -0.485 ETKDGv3 11
GXP H3 -1.696 0.341 -2.077 ETKDGv3 12
GXP H4 -0.550 -1.383 1.444 ETKDGv3 13
GXP H7 3.822 1.111 -0.769 ETKDGv3 14
GXP O2 1.060 0.563 1.771 ETKDGv3 15
GXP H8 0.160 -1.899 -0.107 ETKDGv3 16
#