data_X2X
#
_chem_comp.id X2X
_chem_comp.name "(2S)-2-hydroxy-2-methyl-3-oxobutanoic 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 2014-01-06
_chem_comp.pdbx_modified_date 2014-01-17
_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 X2X
_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 4OAN
_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
X2X OAD OAD O 0 1 N N N N N N 84.464 66.916 56.519 1.200 -1.509 -0.009 OAD X2X 1
X2X CAH CAH C 0 1 N N N N N N 85.503 66.550 57.114 1.220 -0.304 -0.089 CAH X2X 2
X2X OAE OAE O 0 1 N N N N N N 85.515 66.278 58.356 2.353 0.328 -0.433 OAE X2X 3
X2X CAI CAI C 0 1 N N S N N N 86.753 66.399 56.318 -0.030 0.490 0.191 CAI X2X 4
X2X CAB CAB C 0 1 N N N N N N 86.937 64.943 56.034 -0.025 0.952 1.650 CAB X2X 5
X2X OAF OAF O 0 1 N N N N N N 86.670 67.118 55.123 -0.073 1.631 -0.669 OAF X2X 6
X2X CAG CAG C 0 1 N N N N N N 87.857 66.990 57.119 -1.240 -0.373 -0.058 CAG X2X 7
X2X OAC OAC O 0 1 N N N N N N 88.688 66.278 57.658 -1.174 -1.567 0.108 OAC X2X 8
X2X CAA CAA C 0 1 N N N N N N 87.905 68.468 57.321 -2.532 0.254 -0.516 CAA X2X 9
X2X H1 H1 H 0 1 N N N N N N 84.644 66.399 58.716 3.128 -0.224 -0.607 H1 X2X 10
X2X H2 H2 H 0 1 N N N N N N 87.001 64.389 56.982 0.850 1.576 1.830 H2 X2X 11
X2X H3 H3 H 0 1 N N N N N N 86.082 64.573 55.450 -0.929 1.526 1.852 H3 X2X 12
X2X H4 H4 H 0 1 N N N N N N 87.864 64.796 55.460 0.008 0.082 2.306 H4 X2X 13
X2X H5 H5 H 0 1 N N N N N N 85.782 67.433 55.004 -0.078 1.413 -1.611 H5 X2X 14
X2X H6 H6 H 0 1 N N N N N N 88.750 68.721 57.979 -2.372 0.765 -1.466 H6 X2X 15
X2X H7 H7 H 0 1 N N N N N N 88.035 68.967 56.349 -3.287 -0.521 -0.642 H7 X2X 16
X2X H8 H8 H 0 1 N N N N N N 86.966 68.805 57.784 -2.870 0.974 0.230 H8 X2X 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
X2X OAF CAI SING N N 1
X2X CAB CAI SING N N 2
X2X CAI CAH SING N N 3
X2X CAI CAG SING N N 4
X2X OAD CAH DOUB N N 5
X2X CAH OAE SING N N 6
X2X CAG CAA SING N N 7
X2X CAG OAC DOUB N N 8
X2X OAE H1 SING N N 9
X2X CAB H2 SING N N 10
X2X CAB H3 SING N N 11
X2X CAB H4 SING N N 12
X2X OAF H5 SING N N 13
X2X CAA H6 SING N N 14
X2X CAA H7 SING N N 15
X2X CAA H8 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
X2X SMILES ACDLabs 12.01 O=C(O)C(O)(C(=O)C)C
X2X InChI InChI 1.03 InChI=1S/C5H8O4/c1-3(6)5(2,9)4(7)8/h9H,1-2H3,(H,7,8)/t5-/m0/s1
X2X InChIKey InChI 1.03 NMDWGEGFJUBKLB-YFKPBYRVSA-N
X2X SMILES_CANONICAL CACTVS 3.385 CC(=O)[C@](C)(O)C(O)=O
X2X SMILES CACTVS 3.385 CC(=O)[C](C)(O)C(O)=O
X2X SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 CC(=O)[C@@](C)(C(=O)O)O
X2X SMILES "OpenEye OEToolkits" 1.7.6 CC(=O)C(C)(C(=O)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
X2X "SYSTEMATIC NAME" ACDLabs 12.01 "(2S)-2-hydroxy-2-methyl-3-oxobutanoic acid"
X2X "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2S)-2-methyl-2-oxidanyl-3-oxidanylidene-butanoic 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
X2X 'Create component' 2014-01-06 RCSB
X2X 'Initial release' 2014-01-22 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
X2X OAD O 7.702 2.250 1
X2X CAH C 7.702 0.750 2
X2X OAE O 9.002 0.000 3
X2X CAI C 6.404 0.000 4
X2X CAB C 5.654 1.299 5
X2X OAF O 7.154 -1.299 6
X2X CAG C 5.104 -0.750 7
X2X OAC O 5.104 -2.250 8
X2X CAA C 3.805 0.000 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
X2X OAF CAI SINGLE NONE 1
X2X CAI CAB SINGLE BEGINDASH 2
X2X CAI CAH SINGLE NONE 3
X2X CAI CAG SINGLE NONE 4
X2X OAD CAH DOUBLE NONE 5
X2X CAH OAE SINGLE NONE 6
X2X CAG CAA SINGLE NONE 7
X2X CAG OAC DOUBLE NONE 8
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id X2X
_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 1
_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 -0.589
_pdbe_chem_comp_rdkit_properties.CrippenMR 28.941
_pdbe_chem_comp_rdkit_properties.chi0v 4.133
_pdbe_chem_comp_rdkit_properties.chi1v 1.816
_pdbe_chem_comp_rdkit_properties.chi2v 0.607
_pdbe_chem_comp_rdkit_properties.chi3v 0.607
_pdbe_chem_comp_rdkit_properties.chi4v 0.093
_pdbe_chem_comp_rdkit_properties.chi0n 12.133
_pdbe_chem_comp_rdkit_properties.chi1n 5.633
_pdbe_chem_comp_rdkit_properties.chi2n 0.607
_pdbe_chem_comp_rdkit_properties.chi3n 0.607
_pdbe_chem_comp_rdkit_properties.chi4n 0.093
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.900
_pdbe_chem_comp_rdkit_properties.kappa1 1.791
_pdbe_chem_comp_rdkit_properties.kappa2 2.144
_pdbe_chem_comp_rdkit_properties.kappa3 1.499
_pdbe_chem_comp_rdkit_properties.Phi 0.427
#
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
X2X UniChem PDBe X2X
X2X UniChem 'KEGG LIGAND' C06010
X2X UniChem ChEBI 18409
X2X UniChem ZINC ZINC000000895425
X2X UniChem SureChEMBL SCHEMBL108620
X2X UniChem HMDB HMDB0006855
X2X UniChem NMRShiftDB 60023278
X2X UniChem 'EPA CompTox Dashboard' DTXSID70331535
X2X UniChem MetaboLights MTBLC18409
X2X UniChem BRENDA 101726
X2X UniChem BRENDA 10817
X2X UniChem BRENDA 162428
X2X UniChem BRENDA 259990
X2X UniChem BRENDA 141427
X2X UniChem 'PubChem TPHARMA' 16422653
X2X UniChem PubChem 440878
X2X UniChem Nikkaji J2.362.063D
X2X UniChem LipidMaps LMFA01050460
#
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
X2X OAD -1.253 0.249 -2.168 ETKDGv3 1
X2X CAH -0.847 0.626 -1.035 ETKDGv3 2
X2X OAE -0.851 1.983 -0.720 ETKDGv3 3
X2X CAI -0.404 -0.385 -0.008 ETKDGv3 4
X2X CAB -1.515 -0.518 1.053 ETKDGv3 5
X2X OAF -0.217 -1.631 -0.637 ETKDGv3 6
X2X CAG 0.913 0.080 0.602 ETKDGv3 7
X2X OAC 0.958 0.480 1.757 ETKDGv3 8
X2X CAA 2.175 0.093 -0.212 ETKDGv3 9
X2X H1 -1.160 2.672 -1.395 ETKDGv3 10
X2X H2 -2.452 -0.888 0.583 ETKDGv3 11
X2X H3 -1.724 0.462 1.534 ETKDGv3 12
X2X H4 -1.214 -1.241 1.842 ETKDGv3 13
X2X H5 0.098 -2.275 0.050 ETKDGv3 14
X2X H6 1.986 -0.259 -1.249 ETKDGv3 15
X2X H7 2.928 -0.573 0.259 ETKDGv3 16
X2X H8 2.578 1.126 -0.257 ETKDGv3 17
#