data_XLX
#
_chem_comp.id XLX
_chem_comp.name "4,4'-(ethylenediimino)bis[4-oxobutyrate]"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H18 N2 O6"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "1,2-bis(maleimido)ethane, hydrolyzed open form"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2012-08-06
_chem_comp.pdbx_modified_date 2021-03-13
_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 274.270
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code XLX
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 4G37
_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
XLX O13 O13 O 0 1 N N N N N N 26.249 -90.739 12.069 2.578 -1.250 0.010 O13 XLX 1
XLX C12 C12 C 0 1 N N N N N N 26.774 -91.792 12.386 2.493 -0.040 0.010 C12 XLX 2
XLX C11 C11 C 0 1 N N N N N N 27.751 -91.879 13.534 3.743 0.803 0.005 C11 XLX 3
XLX N8 N8 N 0 1 N N N N N N 26.508 -92.911 11.711 1.282 0.551 0.008 N8 XLX 4
XLX C7 C7 C 0 1 N N N N N N 27.097 -94.192 12.046 0.067 -0.268 0.006 C7 XLX 5
XLX C6 C6 C 0 1 N N N N N N 26.111 -95.017 12.864 -1.162 0.642 0.004 C6 XLX 6
XLX N1 N1 N 0 1 N N N N N N 24.832 -95.150 12.181 -2.377 -0.177 0.003 N1 XLX 7
XLX C2 C2 C 0 1 N N N N N N 23.739 -95.688 12.739 -3.588 0.414 0.001 C2 XLX 8
XLX O15 O15 O 0 1 N N N N N N 22.679 -95.792 12.134 -3.673 1.624 -0.000 O15 XLX 9
XLX C3 C3 C 0 1 N N N N N N 23.871 -96.154 14.162 -4.837 -0.429 -0.001 C3 XLX 10
XLX H1 H1 H 0 1 N N N N N N 27.430 -92.390 14.454 3.753 1.431 -0.886 H1 XLX 11
XLX H2 H2 H 0 1 N N N N N N 28.794 -92.146 13.311 3.759 1.432 0.894 H2 XLX 12
XLX H4 H4 H 0 1 N N N N N N 25.874 -92.864 10.939 1.214 1.518 0.007 H4 XLX 13
XLX H5 H5 H 0 1 N N N N N N 27.346 -94.732 11.121 0.055 -0.898 -0.883 H5 XLX 14
XLX H6 H6 H 0 1 N N N N N N 28.013 -94.030 12.633 0.052 -0.897 0.897 H6 XLX 15
XLX H7 H7 H 0 1 N N N N N N 26.534 -96.019 13.029 -1.150 1.272 0.894 H7 XLX 16
XLX H8 H8 H 0 1 N N N N N N 25.949 -94.523 13.833 -1.147 1.271 -0.886 H8 XLX 17
XLX H9 H9 H 0 1 N N N N N N 24.765 -94.820 11.239 -2.309 -1.145 0.003 H9 XLX 18
XLX H10 H10 H 0 1 N N N N N N 23.121 -96.842 14.578 -4.850 -1.058 -0.891 H10 XLX 19
XLX H11 H11 H 0 1 N N N N N N 24.865 -96.413 14.557 -4.853 -1.057 0.890 H11 XLX 20
XLX C1 C1 C 0 1 N N N N N N ? ? ? -6.067 0.482 -0.003 C1 XLX 21
XLX C4 C4 C 0 1 N N N N N N ? ? ? -7.316 -0.361 -0.004 C4 XLX 22
XLX O2 O2 O 0 1 N N N N N N ? ? ? -7.232 -1.566 -0.004 O2 XLX 23
XLX O1 O1 O 0 1 N N N N N N ? ? ? -8.523 0.228 -0.007 O1 XLX 24
XLX C9 C9 C 0 1 N N N N N N ? ? ? 4.972 -0.108 0.002 C9 XLX 25
XLX C10 C10 C 0 1 N N N N N N ? ? ? 6.240 0.747 -0.003 C10 XLX 26
XLX C13 C13 C 0 1 N N N N N N ? ? ? 7.451 -0.150 -0.007 C13 XLX 27
XLX O4 O4 O 0 1 N N N N N N ? ? ? 8.683 0.385 -0.011 O4 XLX 28
XLX O3 O3 O 0 1 N N N N N N ? ? ? 7.314 -1.350 -0.005 O3 XLX 29
XLX H3 H3 H 0 1 N N N N N N ? ? ? -6.054 1.112 0.887 H3 XLX 30
XLX H12 H12 H 0 1 N N N N N N ? ? ? -6.052 1.111 -0.893 H12 XLX 31
XLX H13 H13 H 0 1 N N N N N N ? ? ? -9.295 -0.354 -0.007 H13 XLX 32
XLX H14 H14 H 0 1 N N N N N N ? ? ? 4.961 -0.737 0.892 H14 XLX 33
XLX H15 H15 H 0 1 N N N N N N ? ? ? 4.955 -0.738 -0.888 H15 XLX 34
XLX H16 H16 H 0 1 N N N N N N ? ? ? 6.251 1.376 -0.894 H16 XLX 35
XLX H17 H17 H 0 1 N N N N N N ? ? ? 6.257 1.377 0.886 H17 XLX 36
XLX H18 H18 H 0 1 N N N N N N ? ? ? 9.428 -0.231 -0.013 H18 XLX 37
#
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
XLX O13 C12 DOUB N N 1
XLX C12 C11 SING N N 2
XLX C11 H1 SING N N 3
XLX C11 H2 SING N N 4
XLX C11 C9 SING N N 5
XLX N8 C7 SING N N 6
XLX N8 C12 SING N N 7
XLX N8 H4 SING N N 8
XLX C7 C6 SING N N 9
XLX C7 H5 SING N N 10
XLX C7 H6 SING N N 11
XLX C6 H7 SING N N 12
XLX C6 H8 SING N N 13
XLX N1 C2 SING N N 14
XLX N1 C6 SING N N 15
XLX N1 H9 SING N N 16
XLX C2 C3 SING N N 17
XLX O15 C2 DOUB N N 18
XLX C3 H10 SING N N 19
XLX C3 H11 SING N N 20
XLX C3 C1 SING N N 21
XLX C1 C4 SING N N 22
XLX C1 H3 SING N N 23
XLX C1 H12 SING N N 24
XLX C4 O2 DOUB N N 25
XLX C4 O1 SING N N 26
XLX O1 H13 SING N N 27
XLX C9 C10 SING N N 28
XLX C9 H14 SING N N 29
XLX C9 H15 SING N N 30
XLX C10 C13 SING N N 31
XLX C10 H16 SING N N 32
XLX C10 H17 SING N N 33
XLX C13 O4 SING N N 34
XLX C13 O3 DOUB N N 35
XLX O4 H18 SING N N 36
#
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
XLX SMILES ACDLabs 12.01 O=C(NCCNC(=O)CCC(=O)O)CCCC(=O)O
XLX InChI InChI 1.03 InChI=1S/C11H18N2O6/c14-8(2-1-3-10(16)17)12-6-7-13-9(15)4-5-11(18)19/h1-7H2,(H,12,14)(H,13,15)(H,16,17)(H,18,19)
XLX InChIKey InChI 1.03 JUHMDCQKNGDTCV-UHFFFAOYSA-N
XLX SMILES_CANONICAL CACTVS 3.370 OC(=O)CCCC(=O)NCCNC(=O)CCC(O)=O
XLX SMILES CACTVS 3.370 OC(=O)CCCC(=O)NCCNC(=O)CCC(O)=O
XLX SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C(CC(=O)NCCNC(=O)CCC(=O)O)CC(=O)O
XLX SMILES "OpenEye OEToolkits" 1.7.6 C(CC(=O)NCCNC(=O)CCC(=O)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
XLX "SYSTEMATIC NAME" ACDLabs 12.01 "5-({2-[(3-carboxypropanoyl)amino]ethyl}amino)-5-oxopentanoic acid"
XLX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "5-oxidanylidene-5-[2-[(4-oxidanyl-4-oxidanylidene-butanoyl)amino]ethylamino]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
XLX 'Create component' 2012-08-06 RCSB
XLX 'Modify name' 2012-08-08 RCSB
XLX 'Modify synonyms' 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id XLX
_pdbx_chem_comp_synonyms.name "1,2-bis(maleimido)ethane, hydrolyzed open form"
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id XLX
_pdbe_chem_comp_synonyms.name '1,2-bis(maleimido)ethane, hydrolyzed open form'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
XLX O13 O 10.301 1.875 1
XLX C12 C 10.301 0.375 2
XLX C11 C 9.002 -0.375 3
XLX N8 N 11.600 -0.375 4
XLX C7 C 12.899 0.375 5
XLX C6 C 14.198 -0.375 6
XLX N1 N 15.497 0.375 7
XLX C2 C 16.796 -0.375 8
XLX O15 O 16.796 -1.875 9
XLX C3 C 18.095 0.375 10
XLX C1 C 19.394 -0.375 11
XLX C4 C 20.693 0.375 12
XLX O2 O 21.992 -0.375 13
XLX O1 O 20.693 1.875 14
XLX C9 C 7.702 0.375 15
XLX C10 C 6.404 -0.375 16
XLX C13 C 5.104 0.375 17
XLX O4 O 3.805 -0.375 18
XLX O3 O 5.104 1.875 19
#
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
XLX O13 C12 DOUBLE NONE 1
XLX C12 C11 SINGLE NONE 2
XLX C11 C9 SINGLE NONE 3
XLX N8 C7 SINGLE NONE 4
XLX N8 C12 SINGLE NONE 5
XLX C7 C6 SINGLE NONE 6
XLX N1 C2 SINGLE NONE 7
XLX N1 C6 SINGLE NONE 8
XLX C2 C3 SINGLE NONE 9
XLX O15 C2 DOUBLE NONE 10
XLX C3 C1 SINGLE NONE 11
XLX C1 C4 SINGLE NONE 12
XLX C4 O2 DOUBLE NONE 13
XLX C4 O1 SINGLE NONE 14
XLX C9 C10 SINGLE NONE 15
XLX C10 C13 SINGLE NONE 16
XLX C13 O4 SINGLE NONE 17
XLX C13 O3 DOUBLE NONE 18
#
_pdbe_chem_comp_substructure.comp_id XLX
_pdbe_chem_comp_substructure.substructure_name amide
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles CC(N)=O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4)
_pdbe_chem_comp_substructure.substructure_inchikeys DLFVBJFMPXGRIB-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
XLX N8 F1 1
XLX C12 F1 1
XLX O13 F1 1
XLX C11 F1 1
XLX N1 F1 2
XLX C2 F1 2
XLX O15 F1 2
XLX C3 F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id XLX
_pdbe_chem_comp_rdkit_properties.exactmw 274.116
_pdbe_chem_comp_rdkit_properties.amw 274.273
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 10
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 37
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.636
_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 135.302
_pdbe_chem_comp_rdkit_properties.tpsa 132.800
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.662
_pdbe_chem_comp_rdkit_properties.CrippenMR 64.376
_pdbe_chem_comp_rdkit_properties.chi0v 8.844
_pdbe_chem_comp_rdkit_properties.chi1v 4.119
_pdbe_chem_comp_rdkit_properties.chi2v 0.970
_pdbe_chem_comp_rdkit_properties.chi3v 0.970
_pdbe_chem_comp_rdkit_properties.chi4v 0.448
_pdbe_chem_comp_rdkit_properties.chi0n 26.844
_pdbe_chem_comp_rdkit_properties.chi1n 12.830
_pdbe_chem_comp_rdkit_properties.chi2n 0.970
_pdbe_chem_comp_rdkit_properties.chi3n 0.970
_pdbe_chem_comp_rdkit_properties.chi4n 0.448
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.120
_pdbe_chem_comp_rdkit_properties.kappa1 3.708
_pdbe_chem_comp_rdkit_properties.kappa2 9.864
_pdbe_chem_comp_rdkit_properties.kappa3 12.132
_pdbe_chem_comp_rdkit_properties.Phi 1.925
#
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
XLX UniChem PDBe XLX
XLX UniChem ZINC ZINC000098209610
XLX UniChem PubChem 137350165
#
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
XLX O13 -1.075 0.956 -1.520 ETKDGv3 1
XLX C12 -1.685 0.694 -0.448 ETKDGv3 2
XLX C11 -3.183 0.640 -0.446 ETKDGv3 3
XLX N8 -0.954 0.407 0.752 ETKDGv3 4
XLX C7 0.506 0.375 0.793 ETKDGv3 5
XLX C6 1.031 -0.906 0.141 ETKDGv3 6
XLX N1 2.488 -0.965 0.233 ETKDGv3 7
XLX C2 3.345 -0.160 -0.588 ETKDGv3 8
XLX O15 2.857 0.589 -1.477 ETKDGv3 9
XLX C3 4.830 -0.169 -0.365 ETKDGv3 10
XLX H1 -3.573 1.275 -1.271 ETKDGv3 11
XLX H2 -3.562 1.053 0.513 ETKDGv3 12
XLX H4 -1.480 0.254 1.642 ETKDGv3 13
XLX H5 0.916 1.274 0.284 ETKDGv3 14
XLX H6 0.841 0.401 1.853 ETKDGv3 15
XLX H7 0.597 -1.783 0.670 ETKDGv3 16
XLX H8 0.720 -0.964 -0.925 ETKDGv3 17
XLX H9 2.916 -1.637 0.909 ETKDGv3 18
XLX H10 5.150 -1.155 0.036 ETKDGv3 19
XLX H11 5.343 -0.027 -1.341 ETKDGv3 20
XLX C1 5.260 0.952 0.587 ETKDGv3 21
XLX C4 4.736 0.729 1.973 ETKDGv3 22
XLX O2 3.719 1.357 2.373 ETKDGv3 23
XLX O1 5.352 -0.199 2.806 ETKDGv3 24
XLX C9 -3.665 -0.806 -0.620 ETKDGv3 25
XLX C10 -5.194 -0.919 -0.560 ETKDGv3 26
XLX C13 -5.846 -0.280 -1.747 ETKDGv3 27
XLX O4 -6.389 0.997 -1.638 ETKDGv3 28
XLX O3 -5.877 -0.885 -2.852 ETKDGv3 29
XLX H3 6.370 0.982 0.629 ETKDGv3 30
XLX H12 4.912 1.935 0.200 ETKDGv3 31
XLX H13 5.001 -0.373 3.740 ETKDGv3 32
XLX H14 -3.239 -1.430 0.195 ETKDGv3 33
XLX H15 -3.297 -1.214 -1.588 ETKDGv3 34
XLX H16 -5.475 -1.994 -0.533 ETKDGv3 35
XLX H17 -5.574 -0.452 0.375 ETKDGv3 36
XLX H18 -6.821 1.447 -2.435 ETKDGv3 37
#