data_98J
#
_chem_comp.id 98J
_chem_comp.name "5-HYDROXY-3-OXOPENTANOIC ACID"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H8 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2011-06-23
_chem_comp.pdbx_modified_date 2014-09-05
_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 132.115
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 98J
_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 2Y91
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
98J C12 C12 C 0 1 N N N N N N 21.988 9.462 66.734 -2.220 -0.079 0.001 C12 98J 1
98J O1 O1 O 0 1 N N N N N N 24.816 8.676 67.096 0.138 1.110 0.002 O1 98J 2
98J O14 O14 O 0 1 N N N N N N 21.448 10.306 67.489 -2.102 1.123 -0.002 O14 98J 3
98J O13 O13 O 0 1 N N N N N N 22.114 9.630 65.491 -3.442 -0.633 0.001 O13 98J 4
98J C3 C3 C 0 1 N N N N N N 22.500 8.184 67.366 -0.994 -0.956 -0.000 C3 98J 5
98J C2 C2 C 0 1 N N N N N N 23.897 7.902 66.861 0.241 -0.094 0.001 C2 98J 6
98J C9 C9 C 0 1 N N N N N N 24.145 6.670 66.028 1.606 -0.732 -0.001 C9 98J 7
98J C10 C10 C 0 1 N N N N N N 23.758 6.991 64.586 2.680 0.358 0.000 C10 98J 8
98J O11 O11 O 0 1 N N N N N N 24.119 8.351 64.280 3.974 -0.247 -0.001 O11 98J 9
98J H31C H31C H 0 0 N N N N N N 21.836 7.349 67.096 -0.998 -1.587 0.889 H31C 98J 10
98J H32C H32C H 0 0 N N N N N N 22.521 8.298 68.460 -0.998 -1.584 -0.891 H32C 98J 11
98J H91C H91C H 0 0 N N N N N N 25.209 6.394 66.077 1.718 -1.353 0.888 H91C 98J 12
98J H92C H92C H 0 0 N N N N N N 23.533 5.836 66.402 1.717 -1.350 -0.891 H92C 98J 13
98J H13 H13 H 0 1 N N N N N N 21.744 10.470 65.245 -4.198 -0.030 -0.002 H13 98J 14
98J H101 H101 H 0 0 N N N N N N 24.288 6.309 63.904 2.568 0.979 -0.889 H101 98J 15
98J H102 H102 H 0 0 N N N N N N 22.673 6.864 64.461 2.569 0.976 0.891 H102 98J 16
98J H11 H11 H 0 1 N N N N N N 24.421 8.784 65.070 4.705 0.386 -0.000 H11 98J 17
#
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
98J O1 C2 DOUB N N 1
98J C2 C3 SING N N 2
98J C2 C9 SING N N 3
98J C3 C12 SING N N 4
98J C12 O13 SING N N 5
98J C12 O14 DOUB N N 6
98J C9 C10 SING N N 7
98J C10 O11 SING N N 8
98J C3 H31C SING N N 9
98J C3 H32C SING N N 10
98J C9 H91C SING N N 11
98J C9 H92C SING N N 12
98J O13 H13 SING N N 13
98J C10 H101 SING N N 14
98J C10 H102 SING N N 15
98J O11 H11 SING N N 16
#
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
98J SMILES ACDLabs 12.01 O=C(O)CC(=O)CCO
98J InChI InChI 1.03 InChI=1S/C5H8O4/c6-2-1-4(7)3-5(8)9/h6H,1-3H2,(H,8,9)
98J InChIKey InChI 1.03 ANTBRXMMNBUYMS-UHFFFAOYSA-N
98J SMILES_CANONICAL CACTVS 3.385 OCCC(=O)CC(O)=O
98J SMILES CACTVS 3.385 OCCC(=O)CC(O)=O
98J SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 C(CO)C(=O)CC(=O)O
98J SMILES "OpenEye OEToolkits" 1.9.2 C(CO)C(=O)CC(=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
98J "SYSTEMATIC NAME" ACDLabs 12.01 "5-hydroxy-3-oxopentanoic acid"
98J "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "5-oxidanyl-3-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
98J 'Create component' 2011-06-23 EBI
98J 'Other modification' 2011-06-23 EBI
98J 'Modify descriptor' 2014-09-05 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
98J C12 C 10.301 0.375 1
98J O1 O 7.702 -1.125 2
98J O14 O 10.301 -1.125 3
98J O13 O 11.600 1.125 4
98J C3 C 9.002 1.125 5
98J C2 C 7.702 0.375 6
98J C9 C 6.404 1.125 7
98J C10 C 5.104 0.375 8
98J O11 O 3.805 1.125 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
98J O1 C2 DOUBLE NONE 1
98J C2 C3 SINGLE NONE 2
98J C2 C9 SINGLE NONE 3
98J C3 C12 SINGLE NONE 4
98J C12 O13 SINGLE NONE 5
98J C12 O14 DOUBLE NONE 6
98J C9 C10 SINGLE NONE 7
98J C10 O11 SINGLE NONE 8
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id 98J
_pdbe_chem_comp_rdkit_properties.exactmw 132.042
_pdbe_chem_comp_rdkit_properties.amw 132.115
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_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 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 9
_pdbe_chem_comp_rdkit_properties.NumAtoms 17
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.600
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 63.524
_pdbe_chem_comp_rdkit_properties.tpsa 74.600
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.587
_pdbe_chem_comp_rdkit_properties.CrippenMR 28.963
_pdbe_chem_comp_rdkit_properties.chi0v 4.133
_pdbe_chem_comp_rdkit_properties.chi1v 1.816
_pdbe_chem_comp_rdkit_properties.chi2v 0.380
_pdbe_chem_comp_rdkit_properties.chi3v 0.380
_pdbe_chem_comp_rdkit_properties.chi4v 0.170
_pdbe_chem_comp_rdkit_properties.chi0n 12.133
_pdbe_chem_comp_rdkit_properties.chi1n 5.633
_pdbe_chem_comp_rdkit_properties.chi2n 0.380
_pdbe_chem_comp_rdkit_properties.chi3n 0.380
_pdbe_chem_comp_rdkit_properties.chi4n 0.170
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.900
_pdbe_chem_comp_rdkit_properties.kappa1 1.791
_pdbe_chem_comp_rdkit_properties.kappa2 4.027
_pdbe_chem_comp_rdkit_properties.kappa3 4.963
_pdbe_chem_comp_rdkit_properties.Phi 0.801
#
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
98J UniChem ZINC ZINC000098208614
98J UniChem SureChEMBL SCHEMBL418465
98J UniChem PubChem 21924264
#
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
98J C12 -2.123 -0.076 0.658 ETKDGv3 1
98J O1 0.726 -1.987 -0.547 ETKDGv3 2
98J O14 -2.207 0.141 1.897 ETKDGv3 3
98J O13 -2.666 0.831 -0.245 ETKDGv3 4
98J C3 -1.403 -1.291 0.155 ETKDGv3 5
98J C2 0.065 -1.053 -0.115 ETKDGv3 6
98J C9 0.723 0.291 0.131 ETKDGv3 7
98J C10 2.222 0.299 -0.193 ETKDGv3 8
98J O11 2.771 1.557 0.088 ETKDGv3 9
98J H31C -1.504 -2.109 0.900 ETKDGv3 10
98J H32C -1.890 -1.628 -0.784 ETKDGv3 11
98J H91C 0.589 0.566 1.199 ETKDGv3 12
98J H92C 0.217 1.056 -0.496 ETKDGv3 13
98J H13 -3.142 1.665 0.078 ETKDGv3 14
98J H101 2.741 -0.458 0.434 ETKDGv3 15
98J H102 2.388 0.036 -1.263 ETKDGv3 16
98J H11 2.493 2.160 -0.651 ETKDGv3 17
#