data_J54
#
_chem_comp.id J54
_chem_comp.name '(2R)-3-{[(BENZYLAMINO)CARBONYL]AMINO}-2-HYDROXYPROPANOIC ACID'
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C11 H14 N2 O4'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2007-06-13
_chem_comp.pdbx_modified_date 2024-09-27
_chem_comp.pdbx_ambiguous_flag ?
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 238.240
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code J54
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details 'Corina V3.40'
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_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
J54 O02 O02 O 0 1 N N N N N N 8.499 4.180 -0.689 -5.765 -0.746 0.317 O02 J54 1
J54 C06 C06 C 0 1 N N N N N N 8.759 5.041 0.061 -4.976 -0.080 -0.311 C06 J54 2
J54 C05 C05 C 0 1 N N R N N N 10.201 5.511 0.038 -3.571 -0.580 -0.526 C05 J54 3
J54 O18 O18 O 0 1 N N N N N N 10.423 6.848 0.296 -3.450 -1.902 0.001 O18 J54 4
J54 C04 C04 C 0 1 N N N N N N 11.104 5.130 -1.064 -2.585 0.346 0.189 C04 J54 5
J54 N02 N02 N 0 1 N N N N N N 12.262 5.961 -1.160 -1.214 -0.069 -0.118 N02 J54 6
J54 C03 C03 C 0 1 N N N N N N 13.192 5.576 -2.072 -0.172 0.606 0.406 C03 J54 7
J54 O01 O01 O 0 1 N N N N N N 13.046 4.604 -2.683 -0.369 1.560 1.134 O01 J54 8
J54 N01 N01 N 0 1 N N N N N N 14.258 6.320 -2.307 1.089 0.224 0.123 N01 J54 9
J54 C02 C02 C 0 1 N N N N N N 15.491 5.908 -2.996 2.222 0.957 0.693 C02 J54 10
J54 C01 C01 C 0 1 Y N N N N N 15.622 6.412 -4.423 3.511 0.333 0.226 C01 J54 11
J54 CE1 CE1 C 0 1 Y N N N N N 14.595 7.127 -5.004 4.110 0.774 -0.940 CE1 J54 12
J54 CD1 CD1 C 0 1 Y N N N N N 14.714 7.622 -6.319 5.293 0.201 -1.369 CD1 J54 13
J54 CG CG C 0 1 Y N N N N N 15.880 7.351 -7.017 5.877 -0.813 -0.632 CG J54 14
J54 CD2 CD2 C 0 1 Y N N N N N 16.880 6.611 -6.455 5.279 -1.253 0.534 CD2 J54 15
J54 CE2 CE2 C 0 1 Y N N N N N 16.775 6.145 -5.166 4.099 -0.677 0.965 CE2 J54 16
J54 OXT OXT O 0 1 N Y N N N N 7.950 5.327 1.117 -5.353 1.103 -0.820 OXT J54 17
J54 H05 H05 H 0 1 N N N N N N 10.480 4.881 0.895 -3.349 -0.592 -1.593 H05 J54 18
J54 HOT HOT H 0 1 N N N N N N 7.205 4.738 1.115 -6.266 1.380 -0.659 HOT J54 19
J54 H18 H18 H 0 1 N N N N N N 10.474 6.986 1.235 -3.633 -1.967 0.948 H18 J54 20
J54 H041 1H04 H 0 0 N N N N N N 11.437 4.095 -0.893 -2.738 1.371 -0.149 H041 J54 21
J54 H042 2H04 H 0 0 N N N N N N 10.541 5.243 -2.002 -2.749 0.290 1.265 H042 J54 22
J54 H02 H02 H 0 1 N N N N N N 12.380 6.775 -0.591 -1.056 -0.830 -0.698 H02 J54 23
J54 H01 H01 H 0 1 N N N N N N 14.223 7.265 -1.982 1.247 -0.537 -0.457 H01 J54 24
J54 H021 1H02 H 0 0 N N N N N N 16.343 6.301 -2.422 2.183 1.997 0.367 H021 J54 25
J54 H022 2H02 H 0 0 N N N N N N 15.465 4.810 -3.053 2.172 0.916 1.781 H022 J54 26
J54 HE1 HE1 H 0 1 N N N N N N 13.689 7.310 -4.445 3.654 1.565 -1.516 HE1 J54 27
J54 HE2 HE2 H 0 1 N N N N N N 17.581 5.574 -4.729 3.633 -1.018 1.878 HE2 J54 28
J54 HD1 HD1 H 0 1 N N N N N N 13.918 8.197 -6.770 5.760 0.544 -2.280 HD1 J54 29
J54 HG HG H 0 1 N N N N N N 15.999 7.731 -8.021 6.801 -1.261 -0.968 HG J54 30
J54 HD2 HD2 H 0 1 N N N N N N 17.766 6.389 -7.031 5.735 -2.044 1.109 HD2 J54 31
#
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
J54 O02 C06 DOUB N N 1
J54 C06 C05 SING N N 2
J54 C06 OXT SING N N 3
J54 C05 O18 SING N N 4
J54 C05 C04 SING N N 5
J54 C05 H05 SING N N 6
J54 O18 H18 SING N N 7
J54 C04 N02 SING N N 8
J54 C04 H041 SING N N 9
J54 C04 H042 SING N N 10
J54 N02 C03 SING N N 11
J54 N02 H02 SING N N 12
J54 C03 O01 DOUB N N 13
J54 C03 N01 SING N N 14
J54 N01 C02 SING N N 15
J54 N01 H01 SING N N 16
J54 C02 C01 SING N N 17
J54 C02 H021 SING N N 18
J54 C02 H022 SING N N 19
J54 C01 CE1 SING Y N 20
J54 C01 CE2 DOUB Y N 21
J54 CE1 CD1 DOUB Y N 22
J54 CE1 HE1 SING N N 23
J54 CD1 CG SING Y N 24
J54 CD1 HD1 SING N N 25
J54 CG CD2 DOUB Y N 26
J54 CG HG SING N N 27
J54 CD2 CE2 SING Y N 28
J54 CD2 HD2 SING N N 29
J54 CE2 HE2 SING N N 30
J54 OXT HOT SING N N 31
#
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
J54 SMILES ACDLabs 10.04 'O=C(O)C(O)CNC(=O)NCc1ccccc1'
J54 SMILES_CANONICAL CACTVS 3.341 'O[C@H](CNC(=O)NCc1ccccc1)C(O)=O'
J54 SMILES CACTVS 3.341 'O[CH](CNC(=O)NCc1ccccc1)C(O)=O'
J54 SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'c1ccc(cc1)CNC(=O)NC[C@H](C(=O)O)O'
J54 SMILES 'OpenEye OEToolkits' 1.5.0 'c1ccc(cc1)CNC(=O)NCC(C(=O)O)O'
J54 InChI InChI 1.03 'InChI=1S/C11H14N2O4/c14-9(10(15)16)7-13-11(17)12-6-8-4-2-1-3-5-8/h1-5,9,14H,6-7H2,(H,15,16)(H2,12,13,17)/t9-/m1/s1'
J54 InChIKey InChI 1.03 KGFDIRSBGRVEFZ-SECBINFHSA-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
J54 'SYSTEMATIC NAME' ACDLabs 10.04 '(2R)-3-[(benzylcarbamoyl)amino]-2-hydroxypropanoic acid'
J54 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2R)-2-hydroxy-3-(phenylmethylcarbamoylamino)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
J54 'Create component' 2007-06-13 RCSB
J54 'Modify descriptor' 2011-06-04 RCSB
J54 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id J54
_pdbx_chem_comp_pcm.modified_residue_id SER
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Covalent chemical modification'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom C06
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom OG
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
_pdbe_chem_comp_drugbank_details.comp_id J54
_pdbe_chem_comp_drugbank_details.drugbank_id DB08007
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name '(2R)-3-{[(BENZYLAMINO)CARBONYL]AMINO}-2-HYDROXYPROPANOIC ACID'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_synonyms.comp_id J54
_pdbe_chem_comp_synonyms.name '(2R)-3-{[(BENZYLAMINO)CARBONYL]AMINO}-2-HYDROXYPROPANOIC ACID'
_pdbe_chem_comp_synonyms.provenance DrugBank
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id J54
_pdbe_chem_comp_drugbank_classification.drugbank_id DB08007
_pdbe_chem_comp_drugbank_classification.parent 'Benzene and substituted derivatives'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Benzene and substituted derivatives'
_pdbe_chem_comp_drugbank_classification.superclass Benzenoids
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as benzene and substituted derivatives. These are aromatic compounds containing one monocyclic ring system consisting of benzene.'
#
_pdbe_chem_comp_drugbank_targets.comp_id J54
_pdbe_chem_comp_drugbank_targets.drugbank_id DB08007
_pdbe_chem_comp_drugbank_targets.name 'Chymotrypsin-like elastase family member 1'
_pdbe_chem_comp_drugbank_targets.organism Humans
_pdbe_chem_comp_drugbank_targets.uniprot_id Q9UNI1
_pdbe_chem_comp_drugbank_targets.pharmacologically_active unknown
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
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
J54 O02 O 9.495 5.535 1
J54 C06 C 8.196 4.785 2
J54 C05 C 8.196 3.285 3
J54 O18 O 9.495 2.535 4
J54 C04 C 6.897 2.535 5
J54 N02 N 6.897 1.035 6
J54 C03 C 5.598 0.285 7
J54 O01 O 4.299 1.035 8
J54 N01 N 5.598 -1.215 9
J54 C02 C 4.299 -1.965 10
J54 C01 C 4.299 -3.465 11
J54 CE1 C 3.000 -4.215 12
J54 CD1 C 3.000 -5.715 13
J54 CG C 4.299 -6.465 14
J54 CD2 C 5.598 -5.715 15
J54 CE2 C 5.598 -4.215 16
J54 OXT O 6.897 5.535 17
#
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
J54 O02 C06 DOUBLE NONE 1
J54 C06 C05 SINGLE NONE 2
J54 C06 OXT SINGLE NONE 3
J54 C05 O18 SINGLE BEGINDASH 4
J54 C05 C04 SINGLE NONE 5
J54 C04 N02 SINGLE NONE 6
J54 N02 C03 SINGLE NONE 7
J54 C03 O01 DOUBLE NONE 8
J54 C03 N01 SINGLE NONE 9
J54 N01 C02 SINGLE NONE 10
J54 C02 C01 SINGLE NONE 11
J54 C01 CE1 DOUBLE NONE 12
J54 C01 CE2 SINGLE NONE 13
J54 CE1 CD1 SINGLE NONE 14
J54 CD1 CG DOUBLE NONE 15
J54 CG CD2 SINGLE NONE 16
J54 CD2 CE2 DOUBLE NONE 17
#
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
J54 MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
J54 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
J54 C01 S1 1
J54 CE1 S1 1
J54 CD1 S1 1
J54 CG S1 1
J54 CD2 S1 1
J54 CE2 S1 1
J54 C01 F1 1
J54 CE1 F1 1
J54 CD1 F1 1
J54 CG F1 1
J54 CD2 F1 1
J54 CE2 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id J54
_pdbe_chem_comp_rdkit_properties.exactmw 238.095
_pdbe_chem_comp_rdkit_properties.amw 238.243
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.273
_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 118.226
_pdbe_chem_comp_rdkit_properties.tpsa 98.660
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.123
_pdbe_chem_comp_rdkit_properties.CrippenMR 60.057
_pdbe_chem_comp_rdkit_properties.chi0v 8.027
_pdbe_chem_comp_rdkit_properties.chi1v 3.961
_pdbe_chem_comp_rdkit_properties.chi2v 1.202
_pdbe_chem_comp_rdkit_properties.chi3v 1.202
_pdbe_chem_comp_rdkit_properties.chi4v 0.579
_pdbe_chem_comp_rdkit_properties.chi0n 22.027
_pdbe_chem_comp_rdkit_properties.chi1n 10.672
_pdbe_chem_comp_rdkit_properties.chi2n 1.202
_pdbe_chem_comp_rdkit_properties.chi3n 1.202
_pdbe_chem_comp_rdkit_properties.chi4n 0.579
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.080
_pdbe_chem_comp_rdkit_properties.kappa1 3.457
_pdbe_chem_comp_rdkit_properties.kappa2 6.491
_pdbe_chem_comp_rdkit_properties.kappa3 4.984
_pdbe_chem_comp_rdkit_properties.Phi 1.320
#
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
J54 UniChem DrugBank DB08007
J54 UniChem PubChem 24820112
J54 UniChem 'Probes And Drugs' PD005259
#
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
J54 O02 4.136 1.241 -1.836 ETKDGv3 1
J54 C06 3.942 1.481 -0.613 ETKDGv3 2
J54 C05 4.066 0.388 0.415 ETKDGv3 3
J54 O18 4.833 -0.693 -0.060 ETKDGv3 4
J54 C04 2.692 -0.076 0.938 ETKDGv3 5
J54 N02 1.811 -0.555 -0.131 ETKDGv3 6
J54 C03 0.496 -1.047 0.153 ETKDGv3 7
J54 O01 0.080 -1.091 1.343 ETKDGv3 8
J54 N01 -0.345 -1.492 -0.920 ETKDGv3 9
J54 C02 -1.712 -1.960 -0.706 ETKDGv3 10
J54 C01 -2.617 -0.803 -0.382 ETKDGv3 11
J54 CE1 -2.947 0.090 -1.332 ETKDGv3 12
J54 CD1 -3.817 1.239 -1.003 ETKDGv3 13
J54 CG -4.274 1.400 0.244 ETKDGv3 14
J54 CD2 -3.910 0.428 1.295 ETKDGv3 15
J54 CE2 -3.124 -0.616 1.001 ETKDGv3 16
J54 OXT 3.580 2.763 -0.210 ETKDGv3 17
J54 H05 4.615 0.818 1.281 ETKDGv3 18
J54 HOT 3.479 3.511 -0.885 ETKDGv3 19
J54 H18 4.335 -1.125 -0.801 ETKDGv3 20
J54 H041 2.198 0.771 1.462 ETKDGv3 21
J54 H042 2.847 -0.891 1.677 ETKDGv3 22
J54 H02 2.120 -0.526 -1.129 ETKDGv3 23
J54 H01 0.032 -1.487 -1.895 ETKDGv3 24
J54 H021 -1.727 -2.720 0.106 ETKDGv3 25
J54 H022 -2.079 -2.462 -1.628 ETKDGv3 26
J54 HE1 -2.579 -0.020 -2.345 ETKDGv3 27
J54 HE2 -2.860 -1.322 1.778 ETKDGv3 28
J54 HD1 -4.082 1.951 -1.774 ETKDGv3 29
J54 HG -4.910 2.242 0.486 ETKDGv3 30
J54 HD2 -4.279 0.563 2.304 ETKDGv3 31
#