data_PXY
#
_chem_comp.id PXY
_chem_comp.name PARA-XYLENE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C8 H10'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2024-09-27
_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 106.165
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PXY
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 187L
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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
PXY C1 C1 C 0 1 Y N N N N N 26.645 6.141 4.668 0.000 0.001 1.382 C1 PXY 1
PXY C2 C2 C 0 1 Y N N N N N 26.781 5.671 3.444 1.197 -0.000 0.691 C2 PXY 2
PXY C3 C3 C 0 1 Y N N N N N 27.270 6.472 2.435 1.197 -0.000 -0.691 C3 PXY 3
PXY C4 C4 C 0 1 Y N N N N N 27.583 7.775 2.686 0.000 0.000 -1.382 C4 PXY 4
PXY C5 C5 C 0 1 Y N N N N N 27.442 8.266 3.939 -1.197 0.000 -0.691 C5 PXY 5
PXY C6 C6 C 0 1 Y N N N N N 26.979 7.434 4.947 -1.197 -0.002 0.691 C6 PXY 6
PXY "C1'" "C1'" C 0 1 N N N N N N 26.137 5.226 5.770 0.000 0.001 2.889 "C1'" PXY 7
PXY "C4'" "C4'" C 0 1 N N N N N N 28.102 8.664 1.552 0.000 0.000 -2.889 "C4'" PXY 8
PXY H2 H2 H 0 1 N N N N N N 26.489 4.622 3.266 2.132 -0.001 1.231 H2 PXY 9
PXY H3 H3 H 0 1 N N N N N N 27.411 6.067 1.418 2.132 -0.001 -1.231 H3 PXY 10
PXY H5 H5 H 0 1 N N N N N N 27.698 9.320 4.134 -2.132 0.001 -1.231 H5 PXY 11
PXY H6 H6 H 0 1 N N N N N N 26.875 7.804 5.980 -2.132 -0.002 1.231 H6 PXY 12
PXY "H1'1" "1H1'" H 0 0 N N N N N N 26.022 5.623 6.805 0.001 1.029 3.252 "H1'1" PXY 13
PXY "H1'2" "2H1'" H 0 0 N N N N N N 25.164 4.787 5.447 -0.890 -0.511 3.252 "H1'2" PXY 14
PXY "H1'3" "3H1'" H 0 0 N N N N N N 26.785 4.320 5.807 0.889 -0.513 3.252 "H1'3" PXY 15
PXY "H4'1" "1H4'" H 0 0 N N N N N N 28.358 9.729 1.757 -0.001 -1.026 -3.252 "H4'1" PXY 16
PXY "H4'2" "2H4'" H 0 0 N N N N N N 28.988 8.169 1.091 -0.889 0.515 -3.252 "H4'2" PXY 17
PXY "H4'3" "3H4'" H 0 0 N N N N N N 27.369 8.631 0.712 0.890 0.513 -3.252 "H4'3" PXY 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
PXY C1 C2 DOUB Y N 1
PXY C1 C6 SING Y N 2
PXY C1 "C1'" SING N N 3
PXY C2 C3 SING Y N 4
PXY C2 H2 SING N N 5
PXY C3 C4 DOUB Y N 6
PXY C3 H3 SING N N 7
PXY C4 C5 SING Y N 8
PXY C4 "C4'" SING N N 9
PXY C5 C6 DOUB Y N 10
PXY C5 H5 SING N N 11
PXY C6 H6 SING N N 12
PXY "C1'" "H1'1" SING N N 13
PXY "C1'" "H1'2" SING N N 14
PXY "C1'" "H1'3" SING N N 15
PXY "C4'" "H4'1" SING N N 16
PXY "C4'" "H4'2" SING N N 17
PXY "C4'" "H4'3" SING N N 18
#
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
PXY SMILES ACDLabs 10.04 'c1cc(ccc1C)C'
PXY SMILES_CANONICAL CACTVS 3.341 'Cc1ccc(C)cc1'
PXY SMILES CACTVS 3.341 'Cc1ccc(C)cc1'
PXY SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'Cc1ccc(cc1)C'
PXY SMILES 'OpenEye OEToolkits' 1.5.0 'Cc1ccc(cc1)C'
PXY InChI InChI 1.03 'InChI=1S/C8H10/c1-7-3-5-8(2)6-4-7/h3-6H,1-2H3'
PXY InChIKey InChI 1.03 URLKBWYHVLBVBO-UHFFFAOYSA-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
PXY 'SYSTEMATIC NAME' ACDLabs 10.04 1,4-dimethylbenzene
PXY 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 1,4-dimethylbenzene
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
PXY 'Create component' 1999-07-08 RCSB
PXY 'Modify descriptor' 2011-06-04 RCSB
PXY 'Modify PCM' 2024-09-27 PDBE
#
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_pdbx_chem_comp_pcm.comp_id_linking_atom
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
1 PXY CYS None Crosslinker 'Amino-acid side chain' 'Any position' "C1'" SG ? ?
2 PXY CYS None Crosslinker 'Amino-acid side chain' 'Any position' "C4'" SG ? ?
#
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
PXY C1 C 4.299 1.500 1
PXY C2 C 3.000 0.750 2
PXY C3 C 3.000 -0.750 3
PXY C4 C 4.299 -1.500 4
PXY C5 C 5.598 -0.750 5
PXY C6 C 5.598 0.750 6
PXY "C1'" C 4.299 3.000 7
PXY "C4'" C 4.299 -3.000 8
#
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
PXY C1 C2 DOUBLE NONE 1
PXY C1 C6 SINGLE NONE 2
PXY C1 "C1'" SINGLE NONE 3
PXY C2 C3 SINGLE NONE 4
PXY C3 C4 DOUBLE NONE 5
PXY C4 C5 SINGLE NONE 6
PXY C4 "C4'" SINGLE NONE 7
PXY C5 C6 DOUBLE NONE 8
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
PXY MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
PXY phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-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
PXY C1 S1 1
PXY C2 S1 1
PXY C3 S1 1
PXY C4 S1 1
PXY C5 S1 1
PXY C6 S1 1
PXY C1 F1 1
PXY C2 F1 1
PXY C3 F1 1
PXY C4 F1 1
PXY C5 F1 1
PXY C6 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PXY
_pdbe_chem_comp_rdkit_properties.exactmw 106.078
_pdbe_chem_comp_rdkit_properties.amw 106.168
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 0
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 0
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 8
_pdbe_chem_comp_rdkit_properties.NumAtoms 18
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 0
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.250
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_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 64.211
_pdbe_chem_comp_rdkit_properties.tpsa 0
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.194
_pdbe_chem_comp_rdkit_properties.CrippenMR 35.384
_pdbe_chem_comp_rdkit_properties.chi0v 4
_pdbe_chem_comp_rdkit_properties.chi1v 2
_pdbe_chem_comp_rdkit_properties.chi2v 0.625
_pdbe_chem_comp_rdkit_properties.chi3v 0.625
_pdbe_chem_comp_rdkit_properties.chi4v 0.312
_pdbe_chem_comp_rdkit_properties.chi0n 14
_pdbe_chem_comp_rdkit_properties.chi1n 7
_pdbe_chem_comp_rdkit_properties.chi2n 0.625
_pdbe_chem_comp_rdkit_properties.chi3n 0.625
_pdbe_chem_comp_rdkit_properties.chi4n 0.312
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.780
_pdbe_chem_comp_rdkit_properties.kappa1 0.942
_pdbe_chem_comp_rdkit_properties.kappa2 1.994
_pdbe_chem_comp_rdkit_properties.kappa3 1.094
_pdbe_chem_comp_rdkit_properties.Phi 0.235
#
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
PXY UniChem 'KEGG LIGAND' C06756
PXY UniChem ChEBI 27417
PXY UniChem ZINC ZINC000000968254
PXY UniChem eMolecules 480849
PXY UniChem fdasrs 6WAC1O477V
PXY UniChem HMDB HMDB0059924
PXY UniChem NMRShiftDB 10008610
PXY UniChem ACTor 68650-36-2
PXY UniChem Nikkaji J3.609I
PXY UniChem BRENDA 152198
PXY UniChem BRENDA 225228
PXY UniChem BRENDA 228804
PXY UniChem BRENDA 49336
PXY UniChem Rhea 27417
PXY UniChem ChemicalBook CB2136488
PXY UniChem 'EPA CompTox Dashboard' DTXSID2021868
PXY UniChem SureChEMBL SCHEMBL16653598
PXY UniChem SureChEMBL SCHEMBL771
PXY UniChem 'PubChem TPHARMA' 15321156
PXY UniChem PubChem 7809
PXY UniChem Mcule MCULE-3769448716
PXY UniChem ACTor 106-42-3
PXY UniChem ACTor 68411-39-2
PXY UniChem BindingDb 50008567
#
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
PXY C1 -1.408 -0.061 0.158 ETKDGv3 1
PXY C2 -0.762 -1.113 -0.374 ETKDGv3 2
PXY C3 0.709 -1.090 -0.519 ETKDGv3 3
PXY C4 1.413 -0.017 -0.120 ETKDGv3 4
PXY C5 0.697 1.158 0.432 ETKDGv3 5
PXY C6 -0.635 1.137 0.564 ETKDGv3 6
PXY "C1'" -2.903 -0.065 0.270 ETKDGv3 7
PXY "C4'" 2.900 0.026 -0.301 ETKDGv3 8
PXY H2 -1.310 -1.988 -0.705 ETKDGv3 9
PXY H3 1.208 -1.948 -0.952 ETKDGv3 10
PXY H5 1.250 2.040 0.730 ETKDGv3 11
PXY H6 -1.146 2.003 0.966 ETKDGv3 12
PXY "H1'1" -3.348 0.201 -0.712 ETKDGv3 13
PXY "H1'2" -3.240 0.672 1.029 ETKDGv3 14
PXY "H1'3" -3.269 -1.068 0.577 ETKDGv3 15
PXY "H4'1" 3.356 0.775 0.380 ETKDGv3 16
PXY "H4'2" 3.350 -0.965 -0.074 ETKDGv3 17
PXY "H4'3" 3.138 0.302 -1.350 ETKDGv3 18
#