data_VPM
#
_chem_comp.id VPM
_chem_comp.name "(2S)-2-hydroxy-2-(propan-2-yl)butanedioic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H12 O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2014-03-04
_chem_comp.pdbx_modified_date 2014-08-15
_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 176.167
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VPM
_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 4OV9
_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
VPM CAA CAA C 0 1 N N N N N N 73.904 56.751 9.057 2.850 -0.068 -0.743 CAA VPM 1
VPM CAK CAK C 0 1 N N N N N N 75.367 56.963 9.447 1.685 -0.997 -0.394 CAK VPM 2
VPM CAB CAB C 0 1 N N N N N N 76.302 56.689 8.263 1.891 -1.567 1.011 CAB VPM 3
VPM CAL CAL C 0 1 N N S N N N 75.677 58.263 10.226 0.374 -0.211 -0.438 CAL VPM 4
VPM CAJ CAJ C 0 1 N N N N N N 77.105 58.223 10.791 0.477 0.989 0.467 CAJ VPM 5
VPM OAF OAF O 0 1 N N N N N N 77.435 57.349 11.523 0.711 0.823 1.778 OAF VPM 6
VPM OAD OAD O 0 1 N N N N N N 77.877 59.392 10.751 0.349 2.102 0.013 OAD VPM 7
VPM OAG OAG O 0 1 N N N N N N 75.554 59.360 9.350 0.124 0.223 -1.777 OAG VPM 8
VPM CAH CAH C 0 1 N N N N N N 74.747 58.486 11.427 -0.774 -1.107 0.031 CAH VPM 9
VPM CAI CAI C 0 1 N N N N N N 73.571 59.458 11.294 -2.066 -0.332 -0.013 CAI VPM 10
VPM OAE OAE O 0 1 N N N N N N 73.747 60.622 11.129 -2.068 0.819 -0.382 OAE VPM 11
VPM OAC OAC O 0 1 N N N N N N 72.281 58.941 11.227 -3.214 -0.920 0.357 OAC VPM 12
VPM H1 H1 H 0 1 N N N N N N 73.259 56.955 9.925 2.891 0.749 -0.022 H1 VPM 13
VPM H2 H2 H 0 1 N N N N N N 73.641 57.435 8.236 3.784 -0.628 -0.711 H2 VPM 14
VPM H3 H3 H 0 1 N N N N N N 73.759 55.711 8.729 2.703 0.338 -1.744 H3 VPM 15
VPM H4 H4 H 0 1 N N N N N N 75.583 56.156 10.163 1.644 -1.814 -1.115 H4 VPM 16
VPM H5 H5 H 0 1 N N N N N N 77.345 56.850 8.574 1.933 -0.750 1.732 H5 VPM 17
VPM H6 H6 H 0 1 N N N N N N 76.175 55.649 7.929 1.062 -2.229 1.260 H6 VPM 18
VPM H7 H7 H 0 1 N N N N N N 76.057 57.372 7.436 2.825 -2.127 1.043 H7 VPM 19
VPM H8 H8 H 0 1 N N N N N N 78.221 57.607 11.991 0.769 1.622 2.319 H8 VPM 20
VPM H9 H9 H 0 1 N N N N N N 76.325 59.910 9.421 0.045 -0.499 -2.416 H9 VPM 21
VPM H10 H10 H 0 1 N N N N N N 74.325 57.506 11.692 -0.849 -1.974 -0.624 H10 VPM 22
VPM H11 H11 H 0 1 N N N N N N 75.373 58.851 12.254 -0.583 -1.437 1.052 H11 VPM 23
VPM H12 H12 H 0 1 N N N N N N 71.667 59.643 11.044 -4.017 -0.383 0.312 H12 VPM 24
#
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
VPM CAB CAK SING N N 1
VPM CAA CAK SING N N 2
VPM OAG CAL SING N N 3
VPM CAK CAL SING N N 4
VPM CAL CAJ SING N N 5
VPM CAL CAH SING N N 6
VPM OAD CAJ DOUB N N 7
VPM CAJ OAF SING N N 8
VPM OAE CAI DOUB N N 9
VPM OAC CAI SING N N 10
VPM CAI CAH SING N N 11
VPM CAA H1 SING N N 12
VPM CAA H2 SING N N 13
VPM CAA H3 SING N N 14
VPM CAK H4 SING N N 15
VPM CAB H5 SING N N 16
VPM CAB H6 SING N N 17
VPM CAB H7 SING N N 18
VPM OAF H8 SING N N 19
VPM OAG H9 SING N N 20
VPM CAH H10 SING N N 21
VPM CAH H11 SING N N 22
VPM OAC H12 SING N N 23
#
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
VPM SMILES ACDLabs 12.01 O=C(O)C(O)(CC(=O)O)C(C)C
VPM InChI InChI 1.03 InChI=1S/C7H12O5/c1-4(2)7(12,6(10)11)3-5(8)9/h4,12H,3H2,1-2H3,(H,8,9)(H,10,11)/t7-/m0/s1
VPM InChIKey InChI 1.03 BITYXLXUCSKTJS-ZETCQYMHSA-N
VPM SMILES_CANONICAL CACTVS 3.385 CC(C)[C@@](O)(CC(O)=O)C(O)=O
VPM SMILES CACTVS 3.385 CC(C)[C](O)(CC(O)=O)C(O)=O
VPM SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 CC(C)[C@@](CC(=O)O)(C(=O)O)O
VPM SMILES "OpenEye OEToolkits" 1.7.6 CC(C)C(CC(=O)O)(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
VPM "SYSTEMATIC NAME" ACDLabs 12.01 "(2S)-2-hydroxy-2-(propan-2-yl)butanedioic acid"
VPM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2S)-2-oxidanyl-2-propan-2-yl-butanedioic 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
VPM 'Create component' 2014-03-04 PDBJ
VPM 'Initial release' 2014-08-20 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
VPM CAA C 8.667 0.921 1
VPM CAK C 7.702 -0.228 2
VPM CAB C 9.002 -0.978 3
VPM CAL C 6.404 -0.978 4
VPM CAJ C 5.104 -1.728 5
VPM OAF O 5.104 -3.228 6
VPM OAD O 3.805 -0.978 7
VPM OAG O 7.154 -2.277 8
VPM CAH C 5.654 0.322 9
VPM CAI C 5.393 1.799 10
VPM OAE O 3.983 2.312 11
VPM OAC O 6.542 2.763 12
#
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
VPM CAB CAK SINGLE NONE 1
VPM CAA CAK SINGLE NONE 2
VPM CAL OAG SINGLE BEGINWEDGE 3
VPM CAK CAL SINGLE NONE 4
VPM CAL CAJ SINGLE NONE 5
VPM CAL CAH SINGLE NONE 6
VPM OAD CAJ DOUBLE NONE 7
VPM CAJ OAF SINGLE NONE 8
VPM OAE CAI DOUBLE NONE 9
VPM OAC CAI SINGLE NONE 10
VPM CAI CAH SINGLE NONE 11
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id VPM
_pdbe_chem_comp_rdkit_properties.exactmw 176.068
_pdbe_chem_comp_rdkit_properties.amw 176.168
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.714
_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 86.754
_pdbe_chem_comp_rdkit_properties.tpsa 94.830
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.067
_pdbe_chem_comp_rdkit_properties.CrippenMR 39.676
_pdbe_chem_comp_rdkit_properties.chi0v 5.541
_pdbe_chem_comp_rdkit_properties.chi1v 2.521
_pdbe_chem_comp_rdkit_properties.chi2v 0.918
_pdbe_chem_comp_rdkit_properties.chi3v 0.918
_pdbe_chem_comp_rdkit_properties.chi4v 0.359
_pdbe_chem_comp_rdkit_properties.chi0n 17.541
_pdbe_chem_comp_rdkit_properties.chi1n 8.245
_pdbe_chem_comp_rdkit_properties.chi2n 0.918
_pdbe_chem_comp_rdkit_properties.chi3n 0.918
_pdbe_chem_comp_rdkit_properties.chi4n 0.359
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.100
_pdbe_chem_comp_rdkit_properties.kappa1 2.227
_pdbe_chem_comp_rdkit_properties.kappa2 3.532
_pdbe_chem_comp_rdkit_properties.kappa3 2.197
_pdbe_chem_comp_rdkit_properties.Phi 0.656
#
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
VPM UniChem PDBe VPM
VPM UniChem 'KEGG LIGAND' C02504
VPM UniChem ChEBI 35128
VPM UniChem ZINC ZINC000000389562
VPM UniChem SureChEMBL SCHEMBL1409965
VPM UniChem HMDB HMDB0000402
VPM UniChem NMRShiftDB 60023216
VPM UniChem Nikkaji J319.987H
VPM UniChem LipidMaps LMFA01170083
VPM UniChem MetaboLights MTBLC35128
VPM UniChem BRENDA 13432
VPM UniChem ACTor 49601-06-1
VPM UniChem PubChem 5280523
#
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
VPM CAA -1.930 -0.204 0.047 ETKDGv3 1
VPM CAK -0.643 -0.247 0.890 ETKDGv3 2
VPM CAB -0.219 -1.711 1.113 ETKDGv3 3
VPM CAL 0.508 0.682 0.341 ETKDGv3 4
VPM CAJ 0.086 2.134 0.523 ETKDGv3 5
VPM OAF -0.519 2.835 -0.519 ETKDGv3 6
VPM OAD 0.232 2.700 1.640 ETKDGv3 7
VPM OAG 1.696 0.476 1.075 ETKDGv3 8
VPM CAH 0.840 0.455 -1.164 ETKDGv3 9
VPM CAI 1.430 -0.889 -1.472 ETKDGv3 10
VPM OAE 2.561 -1.207 -1.017 ETKDGv3 11
VPM OAC 0.734 -1.779 -2.285 ETKDGv3 12
VPM H1 -2.745 -0.742 0.576 ETKDGv3 13
VPM H2 -2.266 0.841 -0.112 ETKDGv3 14
VPM H3 -1.780 -0.693 -0.938 ETKDGv3 15
VPM H4 -0.918 0.138 1.898 ETKDGv3 16
VPM H5 -0.989 -2.232 1.722 ETKDGv3 17
VPM H6 -0.126 -2.262 0.157 ETKDGv3 18
VPM H7 0.740 -1.776 1.667 ETKDGv3 19
VPM H8 -0.821 3.794 -0.394 ETKDGv3 20
VPM H9 1.486 0.547 2.044 ETKDGv3 21
VPM H10 -0.059 0.610 -1.796 ETKDGv3 22
VPM H11 1.581 1.219 -1.488 ETKDGv3 23
VPM H12 1.119 -2.689 -2.507 ETKDGv3 24
#