data_PMX
#
_chem_comp.id PMX
_chem_comp.name 3-chloro-N-[(2E)-4-methoxy-4-oxobut-2-enoyl]-L-tyrosine
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H14 Cl N O6"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "(+)-Xylariamide A"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2010-11-02
_chem_comp.pdbx_modified_date 2020-06-17
_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 327.717
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PMX
_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 3P4V
_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
PMX C C C 0 1 N N N N N N 17.203 5.891 10.741 0.410 -3.692 0.352 C PMX 1
PMX N N N 0 1 N N N N N N 17.760 5.899 13.153 -0.213 -1.348 0.444 N PMX 2
PMX O O O 0 1 N N N N N N 17.186 4.667 10.739 -0.613 -3.885 0.965 O PMX 3
PMX CL CL CL 0 0 N N N N N N 18.844 12.513 12.297 2.209 3.217 1.246 CL PMX 4
PMX CA CA C 0 1 N N S N N N 17.715 6.669 11.920 0.803 -2.289 -0.034 CA PMX 5
PMX CB CB C 0 1 N N N N N N 19.016 7.416 11.643 2.154 -1.946 0.596 CB PMX 6
PMX CG CG C 0 1 Y N N N N N 19.327 8.631 12.503 2.605 -0.592 0.112 CG PMX 7
PMX OAA OAA O 0 1 N N N N N N 15.514 6.121 13.647 -1.459 -1.670 -1.365 OAA PMX 8
PMX CAC CAC C 0 1 Y N N N N N 20.314 9.695 14.637 3.794 0.750 -1.476 CAC PMX 9
PMX CAD CAD C 0 1 N N N N N N 15.587 4.320 15.506 -3.430 0.082 -0.556 CAD PMX 10
PMX CAE CAE C 0 1 N N N N N N 16.653 4.674 14.956 -2.335 -0.158 0.184 CAE PMX 11
PMX CAF CAF C 0 1 N N N N N N 16.579 5.595 13.922 -1.311 -1.107 -0.299 CAF PMX 12
PMX CAK CAK C 0 1 Y N N N N N 19.920 11.034 14.114 3.434 1.894 -0.779 CAK PMX 13
PMX OAL OAL O 0 1 N N N N N N 20.198 12.178 14.846 3.841 3.114 -1.217 OAL PMX 14
PMX OAM OAM O 0 1 N N N N N N 16.766 2.991 17.103 -4.305 1.592 0.992 OAM PMX 15
PMX CAN CAN C 0 1 N N N N N N 15.649 3.356 16.656 -4.452 1.029 -0.074 CAN PMX 16
PMX CAS CAS C 0 1 Y N N N N N 19.247 11.161 12.813 2.661 1.789 0.370 CAS PMX 17
PMX OAU OAU O 0 1 N N N N N N 14.567 2.862 17.105 -5.551 1.271 -0.816 OAU PMX 18
PMX CAV CAV C 0 1 N N N N N N 14.549 2.157 18.305 -6.515 2.214 -0.280 CAV PMX 19
PMX CD1 CD1 C 0 1 Y N N N N N 18.955 9.927 12.008 2.249 0.546 0.812 CD1 PMX 20
PMX CD2 CD2 C 0 1 Y N N N N N 20.026 8.497 13.849 3.378 -0.490 -1.030 CD2 PMX 21
PMX OXT OXT O 0 1 N N N N N N 16.677 6.558 9.660 1.200 -4.725 0.021 OXT PMX 22
PMX HN HN H 0 1 N N N N N N 18.645 5.567 13.480 -0.095 -0.899 1.296 HN PMX 23
PMX HA HA H 0 1 N N N N N N 16.956 7.448 12.086 0.880 -2.219 -1.120 HA PMX 24
PMX HB HB H 0 1 N N N N N N 19.835 6.698 11.797 2.054 -1.929 1.681 HB PMX 25
PMX HBA HBA H 0 1 N N N N N N 18.967 7.767 10.602 2.890 -2.697 0.311 HBA PMX 26
PMX HAC HAC H 0 1 N N N N N N 20.810 9.610 15.593 4.394 0.829 -2.371 HAC PMX 27
PMX HAD HAD H 0 1 N N N N N N 14.638 4.701 15.160 -3.561 -0.419 -1.504 HAD PMX 28
PMX HAE HAE H 0 1 N N N N N N 17.603 4.274 15.277 -2.204 0.342 1.132 HAE PMX 29
PMX HOAL HOAL H 0 0 N N N N N N 19.883 12.940 14.375 3.227 3.536 -1.833 HOAL PMX 30
PMX HAV HAV H 0 1 N N N N N N 13.525 1.815 18.515 -7.348 2.317 -0.975 HAV PMX 31
PMX HAVA HAVA H 0 0 N N N N N N 15.217 1.287 18.229 -6.884 1.851 0.679 HAVA PMX 32
PMX HAVB HAVB H 0 0 N N N N N N 14.891 2.812 19.120 -6.036 3.184 -0.142 HAVB PMX 33
PMX HD1 HD1 H 0 1 N N N N N N 18.462 10.015 11.051 1.648 0.463 1.706 HD1 PMX 34
PMX HD2 HD2 H 0 1 N N N N N N 20.308 7.523 14.220 3.659 -1.380 -1.573 HD2 PMX 35
PMX HOXT HOXT H 0 0 N N N N N N 16.355 5.929 9.025 0.909 -5.606 0.294 HOXT PMX 36
#
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
PMX C O DOUB N N 1
PMX C CA SING N N 2
PMX C OXT SING N N 3
PMX N CA SING N N 4
PMX N CAF SING N N 5
PMX CL CAS SING N N 6
PMX CA CB SING N N 7
PMX CB CG SING N N 8
PMX CG CD1 DOUB Y N 9
PMX CG CD2 SING Y N 10
PMX OAA CAF DOUB N N 11
PMX CAC CAK SING Y N 12
PMX CAC CD2 DOUB Y N 13
PMX CAD CAE DOUB N N 14
PMX CAD CAN SING N N 15
PMX CAE CAF SING N N 16
PMX CAK OAL SING N N 17
PMX CAK CAS DOUB Y N 18
PMX OAM CAN DOUB N E 19
PMX CAN OAU SING N N 20
PMX CAS CD1 SING Y N 21
PMX OAU CAV SING N N 22
PMX N HN SING N N 23
PMX CA HA SING N N 24
PMX CB HB SING N N 25
PMX CB HBA SING N N 26
PMX CAC HAC SING N N 27
PMX CAD HAD SING N N 28
PMX CAE HAE SING N N 29
PMX OAL HOAL SING N N 30
PMX CAV HAV SING N N 31
PMX CAV HAVA SING N N 32
PMX CAV HAVB SING N N 33
PMX CD1 HD1 SING N N 34
PMX CD2 HD2 SING N N 35
PMX OXT HOXT 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
PMX SMILES ACDLabs 12.01 Clc1cc(ccc1O)CC(C(=O)O)NC(=O)\C=C\C(=O)OC
PMX SMILES_CANONICAL CACTVS 3.370 COC(=O)\C=C\C(=O)N[C@@H](Cc1ccc(O)c(Cl)c1)C(O)=O
PMX SMILES CACTVS 3.370 COC(=O)C=CC(=O)N[CH](Cc1ccc(O)c(Cl)c1)C(O)=O
PMX SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 COC(=O)/C=C/C(=O)N[C@@H](Cc1ccc(c(c1)Cl)O)C(=O)O
PMX SMILES "OpenEye OEToolkits" 1.7.0 COC(=O)C=CC(=O)NC(Cc1ccc(c(c1)Cl)O)C(=O)O
PMX InChI InChI 1.03 InChI=1S/C14H14ClNO6/c1-22-13(19)5-4-12(18)16-10(14(20)21)7-8-2-3-11(17)9(15)6-8/h2-6,10,17H,7H2,1H3,(H,16,18)(H,20,21)/b5-4+/t10-/m0/s1
PMX InChIKey InChI 1.03 KCOKHEIACSQLBQ-YEZKRMTDSA-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
PMX "SYSTEMATIC NAME" ACDLabs 12.01 3-chloro-N-[(2E)-4-methoxy-4-oxobut-2-enoyl]-L-tyrosine
PMX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "(2S)-3-(3-chloro-4-hydroxy-phenyl)-2-[[(E)-4-methoxy-4-oxo-but-2-enoyl]amino]propanoic 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
PMX 'Create component' 2010-11-02 PDBJ
PMX 'Modify aromatic_flag' 2011-06-04 RCSB
PMX 'Modify descriptor' 2011-06-04 RCSB
PMX 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id PMX
_pdbx_chem_comp_synonyms.name "(+)-Xylariamide A"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id PMX
_pdbe_chem_comp_synonyms.name '(+)-Xylariamide A'
_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
PMX C C 8.196 -1.268 1
PMX N N 6.897 0.983 2
PMX O O 9.495 -0.517 3
PMX CL Cl 3.000 -5.768 4
PMX CA C 6.897 -0.517 5
PMX CB C 5.598 -1.268 6
PMX CG C 5.598 -2.768 7
PMX OAA O 9.495 0.983 8
PMX CAC C 6.897 -5.018 9
PMX CAD C 9.495 3.982 10
PMX CAE C 8.196 3.232 11
PMX CAF C 8.196 1.732 12
PMX CAK C 5.598 -5.768 13
PMX OAL O 5.598 -7.268 14
PMX OAM O 8.196 6.232 15
PMX CAN C 9.495 5.482 16
PMX CAS C 4.299 -5.018 17
PMX OAU O 10.794 6.232 18
PMX CAV C 10.794 7.732 19
PMX CD1 C 4.299 -3.518 20
PMX CD2 C 6.897 -3.518 21
PMX OXT O 8.196 -2.768 22
#
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
PMX C O DOUBLE NONE 1
PMX C CA SINGLE NONE 2
PMX C OXT SINGLE NONE 3
PMX N CA SINGLE NONE 4
PMX N CAF SINGLE NONE 5
PMX CL CAS SINGLE NONE 6
PMX CA CB SINGLE BEGINDASH 7
PMX CB CG SINGLE NONE 8
PMX CG CD1 DOUBLE NONE 9
PMX CG CD2 SINGLE NONE 10
PMX OAA CAF DOUBLE NONE 11
PMX CAC CAK SINGLE NONE 12
PMX CAC CD2 DOUBLE NONE 13
PMX CAD CAE DOUBLE NONE 14
PMX CAD CAN SINGLE ENDDOWNRIGHT 15
PMX CAE CAF SINGLE ENDUPRIGHT 16
PMX CAK OAL SINGLE NONE 17
PMX CAK CAS DOUBLE NONE 18
PMX OAM CAN DOUBLE NONE 19
PMX CAN OAU SINGLE NONE 20
PMX CAS CD1 SINGLE NONE 21
PMX OAU CAV SINGLE NONE 22
#
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
PMX MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
PMX amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
PMX peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
PMX phenyl F3 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
PMX CG S1 1
PMX CAC S1 1
PMX CAK S1 1
PMX CAS S1 1
PMX CD1 S1 1
PMX CD2 S1 1
PMX N F1 1
PMX CAF F1 1
PMX OAA F1 1
PMX CAE F1 1
PMX O F2 1
PMX C F2 1
PMX CA F2 1
PMX N F2 1
PMX CG F3 1
PMX CD1 F3 1
PMX CAS F3 1
PMX CAK F3 1
PMX CAC F3 1
PMX CD2 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PMX
_pdbe_chem_comp_rdkit_properties.exactmw 327.051
_pdbe_chem_comp_rdkit_properties.amw 327.720
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 22
_pdbe_chem_comp_rdkit_properties.NumAtoms 36
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.214
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 150.602
_pdbe_chem_comp_rdkit_properties.tpsa 112.930
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.370
_pdbe_chem_comp_rdkit_properties.CrippenMR 76.667
_pdbe_chem_comp_rdkit_properties.chi0v 11.031
_pdbe_chem_comp_rdkit_properties.chi1v 5.443
_pdbe_chem_comp_rdkit_properties.chi2v 2.016
_pdbe_chem_comp_rdkit_properties.chi3v 2.016
_pdbe_chem_comp_rdkit_properties.chi4v 1.079
_pdbe_chem_comp_rdkit_properties.chi0n 24.275
_pdbe_chem_comp_rdkit_properties.chi1n 11.829
_pdbe_chem_comp_rdkit_properties.chi2n 1.749
_pdbe_chem_comp_rdkit_properties.chi3n 1.749
_pdbe_chem_comp_rdkit_properties.chi4n 0.937
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.540
_pdbe_chem_comp_rdkit_properties.kappa1 5.923
_pdbe_chem_comp_rdkit_properties.kappa2 8.038
_pdbe_chem_comp_rdkit_properties.kappa3 5.451
_pdbe_chem_comp_rdkit_properties.Phi 2.164
#
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
PMX UniChem ChEMBL CHEMBL463134
PMX UniChem PDBe PMX
PMX UniChem ZINC ZINC000013347539
PMX UniChem 'PubChem TPHARMA' 16845285
PMX UniChem PubChem 11738933
PMX UniChem BRENDA 19142
PMX UniChem BindingDb 50339591
PMX UniChem Nikkaji J2.188.758G
#
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
PMX C -0.882 0.206 -1.520 ETKDGv3 1
PMX N 0.806 -0.157 0.182 ETKDGv3 2
PMX O -1.506 -0.502 -2.355 ETKDGv3 3
PMX CL -5.638 -2.739 1.536 ETKDGv3 4
PMX CA -0.616 -0.319 -0.137 ETKDGv3 5
PMX CB -1.486 0.417 0.902 ETKDGv3 6
PMX CG -2.956 0.156 0.690 ETKDGv3 7
PMX OAA 1.487 -1.943 -1.161 ETKDGv3 8
PMX CAC -5.074 0.882 -0.295 ETKDGv3 9
PMX CAD 3.726 0.529 0.105 ETKDGv3 10
PMX CAE 3.259 -0.660 -0.296 ETKDGv3 11
PMX CAF 1.821 -0.951 -0.459 ETKDGv3 12
PMX CAK -5.703 -0.355 0.214 ETKDGv3 13
PMX OAL -7.060 -0.562 -0.040 ETKDGv3 14
PMX OAM 5.550 1.938 0.603 ETKDGv3 15
PMX CAN 5.167 0.791 0.243 ETKDGv3 16
PMX CAS -4.959 -1.245 0.904 ETKDGv3 17
PMX OAU 6.101 -0.216 -0.020 ETKDGv3 18
PMX CAV 7.504 -0.012 0.099 ETKDGv3 19
PMX CD1 -3.524 -0.975 1.144 ETKDGv3 20
PMX CD2 -3.777 1.125 -0.073 ETKDGv3 21
PMX OXT -0.461 1.485 -1.872 ETKDGv3 22
PMX HN 1.083 0.515 0.932 ETKDGv3 23
PMX HA -0.869 -1.403 -0.093 ETKDGv3 24
PMX HB -1.284 1.511 0.858 ETKDGv3 25
PMX HBA -1.200 0.080 1.923 ETKDGv3 26
PMX HAC -5.667 1.594 -0.854 ETKDGv3 27
PMX HAD 3.048 1.345 0.314 ETKDGv3 28
PMX HAE 3.956 -1.445 -0.563 ETKDGv3 29
PMX HOAL -7.563 -1.382 0.274 ETKDGv3 30
PMX HAV 8.033 -0.952 -0.160 ETKDGv3 31
PMX HAVA 7.760 0.269 1.143 ETKDGv3 32
PMX HAVB 7.832 0.789 -0.596 ETKDGv3 33
PMX HD1 -2.933 -1.703 1.687 ETKDGv3 34
PMX HD2 -3.330 2.033 -0.458 ETKDGv3 35
PMX HOXT -0.644 1.856 -2.797 ETKDGv3 36
#