data_5PU
#
_chem_comp.id 5PU
_chem_comp.name "4-[(2~{R})-2-carboxy-5-(oxidanylamino)-5-oxidanylidene-pentyl]benzoic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H15 N O6"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms JHU242
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-11-05
_chem_comp.pdbx_modified_date 2021-03-01
_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 281.261
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 5PU
_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 5ELY
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
5PU CAG C1 C 0 1 Y N N N N N 23.141 46.949 41.486 -2.001 1.603 0.703 CAG 5PU 1
5PU CAI C2 C 0 1 Y N N N N N 23.843 46.312 40.421 -3.138 0.854 0.922 CAI 5PU 2
5PU CAS C3 C 0 1 Y N N N N N 24.399 45.065 40.678 -3.478 -0.170 0.036 CAS 5PU 3
5PU CAO C4 C 0 1 N N N N N N 25.244 44.283 39.615 -4.694 -0.976 0.264 CAO 5PU 4
5PU OAE O1 O 0 1 N N N N N N 25.336 44.817 38.543 -5.402 -0.749 1.225 OAE 5PU 5
5PU OAA O2 O 0 1 N N N N N N 25.849 43.230 39.973 -5.019 -1.964 -0.592 OAA 5PU 6
5PU CAJ C5 C 0 1 Y N N N N N 24.316 44.476 41.912 -2.662 -0.429 -1.067 CAJ 5PU 7
5PU CAH C6 C 0 1 Y N N N N N 23.630 45.070 42.969 -1.528 0.328 -1.275 CAH 5PU 8
5PU CAR C7 C 0 1 Y N N N N N 23.052 46.317 42.734 -1.197 1.341 -0.393 CAR 5PU 9
5PU CAM C8 C 0 1 N N N N N N 22.300 46.960 43.944 0.041 2.168 -0.629 CAM 5PU 10
5PU CAT C9 C 0 1 N N R N N N 20.767 47.124 43.695 1.201 1.593 0.187 CAT 5PU 11
5PU CAP C10 C 0 1 N N N N N N 20.198 47.877 44.933 2.402 2.494 0.055 CAP 5PU 12
5PU OAF O3 O 0 1 N N N N N N 19.818 47.202 45.892 3.216 2.684 1.105 OAF 5PU 13
5PU OAB O4 O 0 1 N N N N N N 20.332 49.106 44.908 2.631 3.045 -0.995 OAB 5PU 14
5PU CAL C11 C 0 1 N N N N N N 20.122 45.730 43.592 1.550 0.198 -0.335 CAL 5PU 15
5PU CAK C12 C 0 1 N N N N N N 18.642 45.743 43.074 2.624 -0.426 0.558 CAK 5PU 16
5PU CAQ C13 C 0 1 N N N N N N 18.095 44.307 43.238 2.968 -1.800 0.044 CAQ 5PU 17
5PU OAC O5 O 0 1 N N N N N N 18.562 43.328 42.615 2.409 -2.237 -0.940 OAC 5PU 18
5PU NAN N1 N 0 1 N N N N N N 17.091 44.183 44.081 3.897 -2.544 0.677 NAN 5PU 19
5PU OAD O6 O 0 1 N N N N N N 16.695 42.937 44.500 4.220 -3.835 0.194 OAD 5PU 20
5PU H1 H1 H 0 1 N N N N N N 22.680 47.914 41.332 -1.740 2.398 1.385 H1 5PU 21
5PU H2 H2 H 0 1 N N N N N N 23.939 46.780 39.453 -3.765 1.059 1.778 H2 5PU 22
5PU H3 H3 H 0 1 N N N N N N 26.394 42.919 39.260 -5.825 -2.464 -0.401 H3 5PU 23
5PU H4 H4 H 0 1 N N N N N N 24.797 43.522 42.070 -2.919 -1.220 -1.757 H4 5PU 24
5PU H5 H5 H 0 1 N N N N N N 23.549 44.585 43.931 -0.896 0.129 -2.128 H5 5PU 25
5PU H6 H6 H 0 1 N N N N N N 22.445 46.320 44.827 0.296 2.145 -1.689 H6 5PU 26
5PU H7 H7 H 0 1 N N N N N N 22.732 47.953 44.137 -0.145 3.197 -0.322 H7 5PU 27
5PU H8 H8 H 0 1 N N N N N N 20.588 47.704 42.777 0.910 1.527 1.235 H8 5PU 28
5PU H9 H9 H 0 1 N N N N N N 19.637 47.773 46.630 3.974 3.271 0.973 H9 5PU 29
5PU H10 H10 H 0 1 N N N N N N 20.134 45.270 44.591 0.658 -0.428 -0.323 H10 5PU 30
5PU H11 H11 H 0 1 N N N N N N 20.724 45.122 42.901 1.926 0.275 -1.355 H11 5PU 31
5PU H12 H12 H 0 1 N N N N N N 18.615 46.039 42.015 3.516 0.200 0.546 H12 5PU 32
5PU H13 H13 H 0 1 N N N N N N 18.040 46.447 43.667 2.248 -0.503 1.578 H13 5PU 33
5PU H14 H14 H 0 1 N N N N N N 16.617 44.997 44.416 4.344 -2.194 1.464 H14 5PU 34
5PU H15 H15 H 0 1 N N N N N N 17.180 42.273 44.023 4.896 -4.291 0.714 H15 5PU 35
#
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
5PU OAE CAO DOUB N N 1
5PU CAO OAA SING N N 2
5PU CAO CAS SING N N 3
5PU CAI CAS DOUB Y N 4
5PU CAI CAG SING Y N 5
5PU CAS CAJ SING Y N 6
5PU CAG CAR DOUB Y N 7
5PU CAJ CAH DOUB Y N 8
5PU OAC CAQ DOUB N N 9
5PU CAR CAH SING Y N 10
5PU CAR CAM SING N N 11
5PU CAK CAQ SING N N 12
5PU CAK CAL SING N N 13
5PU CAQ NAN SING N N 14
5PU CAL CAT SING N N 15
5PU CAT CAM SING N N 16
5PU CAT CAP SING N N 17
5PU NAN OAD SING N N 18
5PU OAB CAP DOUB N N 19
5PU CAP OAF SING N N 20
5PU CAG H1 SING N N 21
5PU CAI H2 SING N N 22
5PU OAA H3 SING N N 23
5PU CAJ H4 SING N N 24
5PU CAH H5 SING N N 25
5PU CAM H6 SING N N 26
5PU CAM H7 SING N N 27
5PU CAT H8 SING N N 28
5PU OAF H9 SING N N 29
5PU CAL H10 SING N N 30
5PU CAL H11 SING N N 31
5PU CAK H12 SING N N 32
5PU CAK H13 SING N N 33
5PU NAN H14 SING N N 34
5PU OAD H15 SING N N 35
#
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
5PU InChI InChI 1.03 InChI=1S/C13H15NO6/c15-11(14-20)6-5-10(13(18)19)7-8-1-3-9(4-2-8)12(16)17/h1-4,10,20H,5-7H2,(H,14,15)(H,16,17)(H,18,19)/t10-/m1/s1
5PU InChIKey InChI 1.03 VUDGMYIWOPKVSL-SNVBAGLBSA-N
5PU SMILES_CANONICAL CACTVS 3.385 ONC(=O)CC[C@H](Cc1ccc(cc1)C(O)=O)C(O)=O
5PU SMILES CACTVS 3.385 ONC(=O)CC[CH](Cc1ccc(cc1)C(O)=O)C(O)=O
5PU SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 c1cc(ccc1C[C@@H](CCC(=O)NO)C(=O)O)C(=O)O
5PU SMILES "OpenEye OEToolkits" 2.0.4 c1cc(ccc1CC(CCC(=O)NO)C(=O)O)C(=O)O
#
_pdbx_chem_comp_identifier.comp_id 5PU
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.4
_pdbx_chem_comp_identifier.identifier "4-[(2~{R})-2-carboxy-5-(oxidanylamino)-5-oxidanylidene-pentyl]benzoic 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
5PU 'Create component' 2015-11-05 EBI
5PU 'Initial release' 2016-04-27 RCSB
5PU 'Modify synonyms' 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 5PU
_pdbx_chem_comp_synonyms.name JHU242
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id 5PU
_pdbe_chem_comp_synonyms.name JHU242
_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
5PU CAG C 12.899 0.375 1
5PU CAI C 12.899 1.875 2
5PU CAS C 11.600 2.625 3
5PU CAO C 11.600 4.125 4
5PU OAE O 12.899 4.875 5
5PU OAA O 10.301 4.875 6
5PU CAJ C 10.301 1.875 7
5PU CAH C 10.301 0.375 8
5PU CAR C 11.600 -0.375 9
5PU CAM C 11.600 -1.875 10
5PU CAT C 10.301 -2.625 11
5PU CAP C 10.301 -4.125 12
5PU OAF O 9.002 -4.875 13
5PU OAB O 11.600 -4.875 14
5PU CAL C 9.002 -1.875 15
5PU CAK C 7.702 -2.625 16
5PU CAQ C 6.404 -1.875 17
5PU OAC O 6.404 -0.375 18
5PU NAN N 5.104 -2.625 19
5PU OAD O 3.805 -1.875 20
#
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
5PU OAE CAO DOUBLE NONE 1
5PU CAO OAA SINGLE NONE 2
5PU CAO CAS SINGLE NONE 3
5PU CAI CAS SINGLE NONE 4
5PU CAI CAG DOUBLE NONE 5
5PU CAS CAJ DOUBLE NONE 6
5PU CAG CAR SINGLE NONE 7
5PU CAJ CAH SINGLE NONE 8
5PU OAC CAQ DOUBLE NONE 9
5PU CAR CAH DOUBLE NONE 10
5PU CAR CAM SINGLE NONE 11
5PU CAK CAQ SINGLE NONE 12
5PU CAK CAL SINGLE NONE 13
5PU CAQ NAN SINGLE NONE 14
5PU CAT CAL SINGLE BEGINDASH 15
5PU CAT CAM SINGLE NONE 16
5PU CAT CAP SINGLE NONE 17
5PU NAN OAD SINGLE NONE 18
5PU OAB CAP DOUBLE NONE 19
5PU CAP OAF SINGLE NONE 20
#
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
5PU MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
5PU amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
5PU phenyl F2 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
5PU CAG S1 1
5PU CAI S1 1
5PU CAS S1 1
5PU CAJ S1 1
5PU CAH S1 1
5PU CAR S1 1
5PU NAN F1 1
5PU CAQ F1 1
5PU OAC F1 1
5PU CAK F1 1
5PU CAG F2 1
5PU CAI F2 1
5PU CAS F2 1
5PU CAJ F2 1
5PU CAH F2 1
5PU CAR F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 5PU
_pdbe_chem_comp_rdkit_properties.exactmw 281.090
_pdbe_chem_comp_rdkit_properties.amw 281.264
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 35
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.308
_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 135.750
_pdbe_chem_comp_rdkit_properties.tpsa 123.930
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.804
_pdbe_chem_comp_rdkit_properties.CrippenMR 66.862
_pdbe_chem_comp_rdkit_properties.chi0v 9.397
_pdbe_chem_comp_rdkit_properties.chi1v 4.677
_pdbe_chem_comp_rdkit_properties.chi2v 1.661
_pdbe_chem_comp_rdkit_properties.chi3v 1.661
_pdbe_chem_comp_rdkit_properties.chi4v 0.874
_pdbe_chem_comp_rdkit_properties.chi0n 24.397
_pdbe_chem_comp_rdkit_properties.chi1n 11.849
_pdbe_chem_comp_rdkit_properties.chi2n 1.661
_pdbe_chem_comp_rdkit_properties.chi3n 1.661
_pdbe_chem_comp_rdkit_properties.chi4n 0.874
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.410
_pdbe_chem_comp_rdkit_properties.kappa1 4.558
_pdbe_chem_comp_rdkit_properties.kappa2 7.246
_pdbe_chem_comp_rdkit_properties.kappa3 4.694
_pdbe_chem_comp_rdkit_properties.Phi 1.651
#
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
5PU UniChem ChEMBL CHEMBL3818203
5PU UniChem PDBe 5PU
5PU UniChem ZINC ZINC000003818088
5PU UniChem PubChem 118987238
5PU UniChem BindingDb 50180950
5PU UniChem BRENDA 239473
#
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
5PU CAG -2.374 0.250 1.240 ETKDGv3 1
5PU CAI -3.657 0.089 0.896 ETKDGv3 2
5PU CAS -4.070 0.163 -0.529 ETKDGv3 3
5PU CAO -5.491 -0.014 -0.902 ETKDGv3 4
5PU OAE -6.358 -0.227 -0.012 ETKDGv3 5
5PU OAA -5.884 0.053 -2.236 ETKDGv3 6
5PU CAJ -3.134 0.390 -1.469 ETKDGv3 7
5PU CAH -1.717 0.563 -1.088 ETKDGv3 8
5PU CAR -1.347 0.506 0.202 ETKDGv3 9
5PU CAM 0.104 0.646 0.593 ETKDGv3 10
5PU CAT 0.885 -0.670 0.379 ETKDGv3 11
5PU CAP 0.304 -1.770 1.231 ETKDGv3 12
5PU OAF -0.342 -2.844 0.626 ETKDGv3 13
5PU OAB 0.382 -1.712 2.488 ETKDGv3 14
5PU CAL 2.389 -0.510 0.695 ETKDGv3 15
5PU CAK 3.138 0.309 -0.367 ETKDGv3 16
5PU CAQ 4.609 0.315 -0.081 ETKDGv3 17
5PU OAC 5.362 -0.516 -0.657 ETKDGv3 18
5PU NAN 5.154 1.231 0.872 ETKDGv3 19
5PU OAD 6.479 1.223 1.157 ETKDGv3 20
5PU H1 -2.088 0.189 2.283 ETKDGv3 21
5PU H2 -4.392 -0.098 1.670 ETKDGv3 22
5PU H3 -6.856 -0.067 -2.499 ETKDGv3 23
5PU H4 -3.397 0.448 -2.518 ETKDGv3 24
5PU H5 -0.981 0.731 -1.865 ETKDGv3 25
5PU H6 0.180 0.964 1.657 ETKDGv3 26
5PU H7 0.549 1.461 -0.014 ETKDGv3 27
5PU H8 0.784 -0.975 -0.687 ETKDGv3 28
5PU H9 -0.748 -3.586 1.183 ETKDGv3 29
5PU H10 2.519 -0.035 1.693 ETKDGv3 30
5PU H11 2.855 -1.521 0.740 ETKDGv3 31
5PU H12 2.777 1.358 -0.377 ETKDGv3 32
5PU H13 2.961 -0.126 -1.375 ETKDGv3 33
5PU H14 4.528 1.898 1.377 ETKDGv3 34
5PU H15 6.877 1.880 0.530 ETKDGv3 35
#