data_QDC
#
_chem_comp.id QDC
_chem_comp.name "(R)-3-butyl-2-oxopentanedioic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H14 O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "(3~{R})-3-butyl-2-oxidanylidene-pentanedioic acid"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-10-25
_chem_comp.pdbx_modified_date 2022-10-28
_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 202.204
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code QDC
_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 8BAY
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
QDC C7 C1 C 0 1 N N N N N N 17.459 312.799 43.959 1.763 -0.232 0.555 C7 QDC 1
QDC C8 C2 C 0 1 N N N N N N 17.099 311.502 43.280 2.364 -1.477 -0.044 C8 QDC 2
QDC O1 O1 O 0 1 N N N N N N 20.581 315.483 45.867 -0.380 3.747 0.105 O1 QDC 3
QDC C1 C3 C 0 1 N N N N N N 18.723 313.980 45.709 -0.166 1.322 0.445 C1 QDC 4
QDC C5 C4 C 0 1 N N N N N N 20.860 309.928 45.087 -2.890 -2.021 0.221 C5 QDC 5
QDC C6 C5 C 0 1 N N N N N N 21.433 309.747 43.707 -4.240 -1.862 -0.482 C6 QDC 6
QDC C4 C6 C 0 1 N N N N N N 20.717 311.388 45.467 -1.914 -0.966 -0.306 C4 QDC 7
QDC O4 O2 O 0 1 N N N N N N 18.153 314.276 46.746 -0.815 1.372 1.463 O4 QDC 8
QDC C3 C7 C 0 1 N N N N N N 19.849 312.156 44.480 -0.564 -1.125 0.397 C3 QDC 9
QDC O3 O3 O 0 1 N N N N N N 17.606 311.137 42.240 1.794 -2.051 -0.942 O3 QDC 10
QDC C2 C8 C 0 1 N N R N N N 18.518 312.656 45.055 0.374 0.002 -0.041 C2 QDC 11
QDC C C9 C 0 1 N N N N N N 19.680 314.992 45.055 0.102 2.567 -0.329 C QDC 12
QDC O O4 O 0 1 N N N N N N 19.594 315.301 43.874 0.753 2.518 -1.351 O QDC 13
QDC O2 O5 O 0 1 N N N N N N 16.193 310.812 43.925 3.532 -1.949 0.419 O2 QDC 14
QDC H1 H1 H 0 1 N N N N N N 17.842 313.494 43.197 1.681 -0.352 1.635 H1 QDC 15
QDC H2 H2 H 0 1 N N N N N N 16.548 313.217 44.411 2.402 0.623 0.332 H2 QDC 16
QDC H3 H3 H 0 1 N N N N N N 21.133 316.096 45.395 -0.181 4.527 -0.431 H3 QDC 17
QDC H4 H4 H 0 1 N N N N N N 19.867 309.455 45.122 -3.022 -1.890 1.295 H4 QDC 18
QDC H5 H5 H 0 1 N N N N N N 21.526 309.438 45.813 -2.492 -3.016 0.022 H5 QDC 19
QDC H6 H6 H 0 1 N N N N N N 21.516 308.674 43.482 -4.935 -2.613 -0.107 H6 QDC 20
QDC H7 H7 H 0 1 N N N N N N 20.772 310.226 42.970 -4.638 -0.867 -0.283 H7 QDC 21
QDC H8 H8 H 0 1 N N N N N N 22.430 310.209 43.661 -4.109 -1.992 -1.556 H8 QDC 22
QDC H9 H9 H 0 1 N N N N N N 21.716 311.847 45.492 -1.783 -1.097 -1.380 H9 QDC 23
QDC H10 H10 H 0 1 N N N N N N 20.259 311.451 46.465 -2.313 0.029 -0.107 H10 QDC 24
QDC H11 H11 H 0 1 N N N N N N 19.628 311.494 43.630 -0.709 -1.079 1.476 H11 QDC 25
QDC H12 H12 H 0 1 N N N N N N 20.420 313.028 44.127 -0.127 -2.087 0.129 H12 QDC 26
QDC H13 H13 H 0 1 N N N N N N 18.160 311.932 45.802 0.442 0.016 -1.129 H13 QDC 27
QDC H14 H14 H 0 1 N N N N N N 16.011 310.008 43.453 3.878 -2.751 0.004 H14 QDC 28
#
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
QDC O3 C8 DOUB N N 1
QDC C8 O2 SING N N 2
QDC C8 C7 SING N N 3
QDC C6 C5 SING N N 4
QDC O C DOUB N N 5
QDC C7 C2 SING N N 6
QDC C3 C2 SING N N 7
QDC C3 C4 SING N N 8
QDC C2 C1 SING N N 9
QDC C C1 SING N N 10
QDC C O1 SING N N 11
QDC C5 C4 SING N N 12
QDC C1 O4 DOUB N N 13
QDC C7 H1 SING N N 14
QDC C7 H2 SING N N 15
QDC O1 H3 SING N N 16
QDC C5 H4 SING N N 17
QDC C5 H5 SING N N 18
QDC C6 H6 SING N N 19
QDC C6 H7 SING N N 20
QDC C6 H8 SING N N 21
QDC C4 H9 SING N N 22
QDC C4 H10 SING N N 23
QDC C3 H11 SING N N 24
QDC C3 H12 SING N N 25
QDC C2 H13 SING N N 26
QDC O2 H14 SING N N 27
#
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
QDC InChI InChI 1.06 InChI=1S/C9H14O5/c1-2-3-4-6(5-7(10)11)8(12)9(13)14/h6H,2-5H2,1H3,(H,10,11)(H,13,14)/t6-/m1/s1
QDC InChIKey InChI 1.06 RVKQLIHFWCFUHE-ZCFIWIBFSA-N
QDC SMILES_CANONICAL CACTVS 3.385 CCCC[C@H](CC(O)=O)C(=O)C(O)=O
QDC SMILES CACTVS 3.385 CCCC[CH](CC(O)=O)C(=O)C(O)=O
QDC SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 CCCC[C@H](CC(=O)O)C(=O)C(=O)O
QDC SMILES "OpenEye OEToolkits" 3.1.0.0 CCCCC(CC(=O)O)C(=O)C(=O)O
#
_pdbx_chem_comp_identifier.comp_id QDC
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 3.1.0.0
_pdbx_chem_comp_identifier.identifier "(3~{R})-3-butyl-2-oxidanylidene-pentanedioic 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
QDC 'Create component' 2022-10-25 PDBE
QDC 'Initial release' 2022-11-02 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id QDC
_pdbx_chem_comp_synonyms.name "(3~{R})-3-butyl-2-oxidanylidene-pentanedioic acid"
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id QDC
_pdbe_chem_comp_synonyms.name '(3~{R})-3-butyl-2-oxidanylidene-pentanedioic acid'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
QDC C7 C 6.404 1.875 1
QDC C8 C 5.104 1.125 2
QDC O1 O 10.301 -0.375 3
QDC C1 C 9.002 1.875 4
QDC C5 C 6.404 -2.625 5
QDC C6 C 5.104 -3.375 6
QDC C4 C 6.404 -1.125 7
QDC O4 O 9.002 3.375 8
QDC C3 C 7.702 -0.375 9
QDC O3 O 3.805 1.875 10
QDC C2 C 7.702 1.125 11
QDC C C 10.301 1.125 12
QDC O O 11.600 1.875 13
QDC O2 O 5.104 -0.375 14
#
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
QDC O3 C8 DOUBLE NONE 1
QDC C8 O2 SINGLE NONE 2
QDC C8 C7 SINGLE NONE 3
QDC C6 C5 SINGLE NONE 4
QDC O C DOUBLE NONE 5
QDC C2 C7 SINGLE BEGINDASH 6
QDC C3 C2 SINGLE NONE 7
QDC C3 C4 SINGLE NONE 8
QDC C2 C1 SINGLE NONE 9
QDC C C1 SINGLE NONE 10
QDC C O1 SINGLE NONE 11
QDC C5 C4 SINGLE NONE 12
QDC C1 O4 DOUBLE NONE 13
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id QDC
_pdbe_chem_comp_rdkit_properties.exactmw 202.084
_pdbe_chem_comp_rdkit_properties.amw 202.206
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.667
_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 101.575
_pdbe_chem_comp_rdkit_properties.tpsa 91.670
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.921
_pdbe_chem_comp_rdkit_properties.CrippenMR 47.911
_pdbe_chem_comp_rdkit_properties.chi0v 6.541
_pdbe_chem_comp_rdkit_properties.chi1v 3.021
_pdbe_chem_comp_rdkit_properties.chi2v 0.890
_pdbe_chem_comp_rdkit_properties.chi3v 0.890
_pdbe_chem_comp_rdkit_properties.chi4v 0.443
_pdbe_chem_comp_rdkit_properties.chi0n 20.541
_pdbe_chem_comp_rdkit_properties.chi1n 9.837
_pdbe_chem_comp_rdkit_properties.chi2n 0.890
_pdbe_chem_comp_rdkit_properties.chi3n 0.890
_pdbe_chem_comp_rdkit_properties.chi4n 0.443
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.390
_pdbe_chem_comp_rdkit_properties.kappa1 2.592
_pdbe_chem_comp_rdkit_properties.kappa2 6.123
_pdbe_chem_comp_rdkit_properties.kappa3 4.591
_pdbe_chem_comp_rdkit_properties.Phi 1.133
#
_pdbe_chem_comp_external_mappings.comp_id QDC
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 165416420
#
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
QDC C7 -1.258 0.018 -1.608 ETKDGv3 1
QDC C8 -2.306 0.900 -0.994 ETKDGv3 2
QDC O1 -2.253 -4.065 0.251 ETKDGv3 3
QDC C1 -1.279 -1.789 0.139 ETKDGv3 4
QDC C5 2.107 1.922 0.856 ETKDGv3 5
QDC C6 3.098 1.116 1.695 ETKDGv3 6
QDC C4 1.363 1.062 -0.178 ETKDGv3 7
QDC O4 -1.900 -1.481 1.192 ETKDGv3 8
QDC C3 0.298 0.156 0.467 ETKDGv3 9
QDC O3 -3.440 0.429 -0.710 ETKDGv3 10
QDC C2 -0.421 -0.755 -0.562 ETKDGv3 11
QDC C -1.456 -3.141 -0.419 ETKDGv3 12
QDC O -0.895 -3.468 -1.499 ETKDGv3 13
QDC O2 -2.017 2.232 -0.718 ETKDGv3 14
QDC H1 -0.593 0.635 -2.247 ETKDGv3 15
QDC H2 -1.751 -0.706 -2.292 ETKDGv3 16
QDC H3 -2.388 -4.999 -0.118 ETKDGv3 17
QDC H4 2.675 2.708 0.313 ETKDGv3 18
QDC H5 1.381 2.434 1.524 ETKDGv3 19
QDC H6 3.797 0.554 1.040 ETKDGv3 20
QDC H7 2.567 0.408 2.364 ETKDGv3 21
QDC H8 3.691 1.808 2.330 ETKDGv3 22
QDC H9 2.091 0.449 -0.753 ETKDGv3 23
QDC H10 0.868 1.756 -0.889 ETKDGv3 24
QDC H11 -0.440 0.781 1.014 ETKDGv3 25
QDC H12 0.795 -0.501 1.212 ETKDGv3 26
QDC H13 0.376 -1.298 -1.117 ETKDGv3 27
QDC H14 -2.710 2.837 -0.293 ETKDGv3 28
#