data_2HG
#
_chem_comp.id 2HG
_chem_comp.name "(2R)-2-hydroxypentanedioic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H8 O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2010-12-16
_chem_comp.pdbx_modified_date 2011-06-04
_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 148.114
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 2HG
_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 3PUR
_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
2HG C1 C1 C 0 1 N N N N N N -5.129 -12.924 -4.819 -2.350 -0.284 0.061 C1 2HG 1
2HG O1 O1 O 0 1 N N N N N N -4.961 -14.013 -5.456 -3.152 0.181 -0.714 O1 2HG 2
2HG C2 C2 C 0 1 N N R N N N -5.925 -11.837 -5.473 -1.130 0.510 0.451 C2 2HG 3
2HG O2 O2 O 0 1 N N N N N N -4.423 -12.654 -3.792 -2.549 -1.506 0.579 O2 2HG 4
2HG C3 C3 C 0 1 N N N N N N -6.731 -12.361 -6.624 0.125 -0.202 -0.054 C3 2HG 5
2HG O3 O3 O 0 1 N N N N N N -6.708 -11.236 -4.516 -1.205 1.814 -0.129 O3 2HG 6
2HG C4 C4 C 0 1 N N N N N N -7.863 -13.327 -6.426 1.368 0.537 0.448 C4 2HG 7
2HG O4 O4 O 0 1 N N N N N N -8.474 -12.934 -8.744 2.503 -1.154 -0.737 O4 2HG 8
2HG C5 C5 C 0 1 N N N N N N -8.888 -13.405 -7.520 2.605 -0.165 -0.051 C5 2HG 9
2HG O5 O5 O 0 1 N N N N N N -9.606 -14.577 -7.626 3.820 0.309 0.268 O5 2HG 10
2HG H2 H2 H 0 1 N N N N N N -5.247 -11.085 -5.903 -1.086 0.598 1.537 H2 2HG 11
2HG HO2 HO2 H 0 1 N N N N N N -3.815 -13.366 -3.629 -3.348 -1.976 0.302 HO2 2HG 12
2HG H3 H3 H 0 1 N N N N N N -7.180 -11.475 -7.097 0.137 -1.226 0.317 H3 2HG 13
2HG H3A H3A H 0 1 N N N N N N -6.012 -12.880 -7.275 0.124 -0.211 -1.144 H3A 2HG 14
2HG HO3 HO3 H 0 1 N N N N N N -7.220 -10.543 -4.915 -1.248 1.813 -1.095 HO3 2HG 15
2HG H4 H4 H 0 1 N N N N N N -7.419 -14.329 -6.327 1.357 1.561 0.076 H4 2HG 16
2HG H4A H4A H 0 1 N N N N N N -8.391 -13.023 -5.510 1.370 0.546 1.538 H4A 2HG 17
2HG HO5 HO5 H 0 1 N N N N N N -9.671 -14.827 -8.540 4.583 -0.175 -0.075 HO5 2HG 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
2HG C1 O1 DOUB N N 1
2HG C1 C2 SING N N 2
2HG C1 O2 SING N N 3
2HG C2 C3 SING N N 4
2HG C2 O3 SING N N 5
2HG C3 C4 SING N N 6
2HG C4 C5 SING N N 7
2HG O4 C5 DOUB N N 8
2HG C5 O5 SING N N 9
2HG C2 H2 SING N N 10
2HG O2 HO2 SING N N 11
2HG C3 H3 SING N N 12
2HG C3 H3A SING N N 13
2HG O3 HO3 SING N N 14
2HG C4 H4 SING N N 15
2HG C4 H4A SING N N 16
2HG O5 HO5 SING N N 17
#
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
2HG SMILES ACDLabs 12.01 O=C(O)CCC(O)C(=O)O
2HG SMILES_CANONICAL CACTVS 3.370 O[C@H](CCC(O)=O)C(O)=O
2HG SMILES CACTVS 3.370 O[CH](CCC(O)=O)C(O)=O
2HG SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 C(CC(=O)O)[C@H](C(=O)O)O
2HG SMILES "OpenEye OEToolkits" 1.7.0 C(CC(=O)O)C(C(=O)O)O
2HG InChI InChI 1.03 InChI=1S/C5H8O5/c6-3(5(9)10)1-2-4(7)8/h3,6H,1-2H2,(H,7,8)(H,9,10)/t3-/m1/s1
2HG InChIKey InChI 1.03 HWXBTNAVRSUOJR-GSVOUGTGSA-N
#
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
2HG "SYSTEMATIC NAME" ACDLabs 12.01 "(2R)-2-hydroxypentanedioic acid"
2HG "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "(2R)-2-hydroxypentanedioic 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
2HG 'Create component' 2010-12-16 PDBJ
2HG 'Modify descriptor' 2011-06-04 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
2HG C1 C 10.301 0.608 1
2HG O1 O 11.600 -0.142 2
2HG C2 C 9.002 -0.142 3
2HG O2 O 10.301 2.107 4
2HG C3 C 7.702 0.608 5
2HG O3 O 9.002 -1.643 6
2HG C4 C 6.404 -0.142 7
2HG O4 O 3.805 -0.142 8
2HG C5 C 5.104 0.608 9
2HG O5 O 5.104 2.107 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
2HG C1 O1 DOUBLE NONE 1
2HG C1 C2 SINGLE NONE 2
2HG C1 O2 SINGLE NONE 3
2HG C2 C3 SINGLE NONE 4
2HG C2 O3 SINGLE BEGINDASH 5
2HG C3 C4 SINGLE NONE 6
2HG C4 C5 SINGLE NONE 7
2HG O4 C5 DOUBLE NONE 8
2HG C5 O5 SINGLE NONE 9
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id 2HG
_pdbe_chem_comp_rdkit_properties.exactmw 148.037
_pdbe_chem_comp_rdkit_properties.amw 148.114
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 18
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 68.405
_pdbe_chem_comp_rdkit_properties.tpsa 94.830
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.703
_pdbe_chem_comp_rdkit_properties.CrippenMR 30.512
_pdbe_chem_comp_rdkit_properties.chi0v 4.541
_pdbe_chem_comp_rdkit_properties.chi1v 2.021
_pdbe_chem_comp_rdkit_properties.chi2v 0.463
_pdbe_chem_comp_rdkit_properties.chi3v 0.463
_pdbe_chem_comp_rdkit_properties.chi4v 0.159
_pdbe_chem_comp_rdkit_properties.chi0n 12.541
_pdbe_chem_comp_rdkit_properties.chi1n 5.745
_pdbe_chem_comp_rdkit_properties.chi2n 0.463
_pdbe_chem_comp_rdkit_properties.chi3n 0.463
_pdbe_chem_comp_rdkit_properties.chi4n 0.159
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.100
_pdbe_chem_comp_rdkit_properties.kappa1 2.197
_pdbe_chem_comp_rdkit_properties.kappa2 3.838
_pdbe_chem_comp_rdkit_properties.kappa3 3.849
_pdbe_chem_comp_rdkit_properties.Phi 0.843
#
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
2HG UniChem 'KEGG LIGAND' C01087
2HG UniChem ChEBI 32796
2HG UniChem ZINC ZINC000000402968
2HG UniChem SureChEMBL SCHEMBL8032
2HG UniChem HMDB HMDB0000606
2HG UniChem PubChem 439391
2HG UniChem NMRShiftDB 60020022
2HG UniChem BindingDb 50361471
2HG UniChem 'EPA CompTox Dashboard' DTXSID80897218
2HG UniChem MetaboLights MTBLC32796
2HG UniChem BRENDA 42552
2HG UniChem BRENDA 5078
2HG UniChem BRENDA 5143
2HG UniChem BRENDA 56481
2HG UniChem MedChemExpress HY-113038
2HG UniChem 'Probes And Drugs' PD088531
2HG UniChem Nikkaji J1.280.876C
2HG UniChem ACTor 636-67-9
#
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
2HG C1 -2.427 -0.429 0.079 ETKDGv3 1
2HG O1 -3.120 -1.367 -0.399 ETKDGv3 2
2HG C2 -1.075 -0.717 0.671 ETKDGv3 3
2HG O2 -2.913 0.876 0.048 ETKDGv3 4
2HG C3 0.036 -0.048 -0.161 ETKDGv3 5
2HG O3 -1.035 -0.300 2.013 ETKDGv3 6
2HG C4 1.430 -0.412 0.362 ETKDGv3 7
2HG O4 2.955 -0.377 -1.479 ETKDGv3 8
2HG C5 2.488 0.230 -0.479 ETKDGv3 9
2HG O5 2.923 1.518 -0.181 ETKDGv3 10
2HG H2 -0.911 -1.817 0.651 ETKDGv3 11
2HG HO2 -3.820 1.083 -0.351 ETKDGv3 12
2HG H3 -0.092 1.058 -0.140 ETKDGv3 13
2HG H3A -0.052 -0.384 -1.219 ETKDGv3 14
2HG HO3 -1.122 0.690 2.027 ETKDGv3 15
2HG H4 1.565 -1.515 0.345 ETKDGv3 16
2HG H4A 1.545 -0.064 1.411 ETKDGv3 17
2HG HO5 3.627 1.973 -0.750 ETKDGv3 18
#