data_PCV
#
_chem_comp.id PCV
_chem_comp.name "5-AMINO-3-HYDROXY-2-(2-OXO-AZETIDIN-1-YL)-PENTANOIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAD
_chem_comp.formula "C8 H14 N2 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "PROCLAVAMINIC ACID"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2000-01-21
_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 202.208
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PCV
_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 1DRT
_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
PCV N1 N1 N 0 1 N N N N N N 2.935 6.871 5.763 -0.754 0.815 -0.547 N1 PCV 1
PCV C8 C8 C 0 1 N N N N N N 4.310 6.572 5.789 -0.995 1.550 0.554 C8 PCV 2
PCV O1 O1 O 0 1 N N N N N N 5.316 7.105 5.364 -1.059 1.253 1.728 O1 PCV 3
PCV C9 C9 C 0 1 N N N N N N 4.018 5.343 6.566 -1.154 2.867 -0.159 C9 PCV 4
PCV C7 C7 C 0 1 N N N N N N 2.584 5.723 6.510 -0.884 2.003 -1.391 C7 PCV 5
PCV C1 C1 C 0 1 N N S N N N 2.177 7.977 5.147 -0.480 -0.602 -0.799 C1 PCV 6
PCV C2 C2 C 0 1 N N R N N N 0.970 7.508 4.238 0.796 -1.014 -0.063 C2 PCV 7
PCV C4 C4 C 0 1 N N N N N N 1.284 6.275 3.327 1.943 -0.088 -0.474 C4 PCV 8
PCV C5 C5 C 0 1 N N N N N N 1.868 6.693 1.951 3.245 -0.574 0.164 C5 PCV 9
PCV N2 N2 N 0 1 N N N N N N 1.174 6.056 0.828 4.346 0.314 -0.230 N2 PCV 10
PCV O3 O3 O 0 1 N N N N N N -0.125 7.180 5.040 0.586 -0.914 1.347 O3 PCV 11
PCV C3 C3 C 0 1 N N N N N N 1.734 9.006 6.194 -1.636 -1.433 -0.304 C3 PCV 12
PCV O2 O2 O 0 1 N N N N N N 1.769 10.304 5.914 -2.590 -0.897 0.207 O2 PCV 13
PCV O4 O4 O 0 1 N N N N N N 1.345 8.682 7.309 -1.605 -2.769 -0.430 O4 PCV 14
PCV HC91 1HC9 H 0 0 N N N N N N 4.362 4.343 6.211 -0.375 3.597 0.059 HC91 PCV 15
PCV HC92 2HC9 H 0 0 N N N N N N 4.522 5.145 7.540 -2.161 3.282 -0.112 HC92 PCV 16
PCV HC71 1HC7 H 0 0 N N N N N N 1.991 5.822 7.449 0.042 2.267 -1.902 HC71 PCV 17
PCV HC72 2HC7 H 0 0 N N N N N N 1.826 5.005 6.116 -1.734 1.953 -2.072 HC72 PCV 18
PCV HC1 HC1 H 0 1 N N N N N N 2.890 8.474 4.449 -0.350 -0.762 -1.869 HC1 PCV 19
PCV H22 2H2 H 0 1 N N N N N N 0.757 8.371 3.565 1.049 -2.042 -0.321 H22 PCV 20
PCV HC41 1HC4 H 0 0 N N N N N N 1.954 5.551 3.846 1.730 0.926 -0.137 HC41 PCV 21
PCV HC42 2HC4 H 0 0 N N N N N N 0.385 5.626 3.202 2.045 -0.096 -1.559 HC42 PCV 22
PCV HC51 1HC5 H 0 0 N N N N N N 1.876 7.802 1.839 3.459 -1.589 -0.173 HC51 PCV 23
PCV HC52 2HC5 H 0 0 N N N N N N 2.965 6.499 1.905 3.143 -0.566 1.250 HC52 PCV 24
PCV HN21 1HN2 H 0 0 N N N N N N 1.557 6.330 -0.076 4.158 1.213 0.189 HN21 PCV 25
PCV HN22 2HN2 H 0 0 N N N N N N 0.170 6.233 0.869 5.180 -0.043 0.211 HN22 PCV 26
PCV HO3 HO3 H 0 1 N N N N N N -0.849 6.898 4.494 0.365 0.009 1.532 HO3 PCV 27
PCV HO4 HO4 H 0 1 N N N N N N 1.070 9.319 7.957 -2.346 -3.303 -0.112 HO4 PCV 28
#
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
PCV N1 C8 SING N N 1
PCV N1 C7 SING N N 2
PCV N1 C1 SING N N 3
PCV C8 O1 DOUB N N 4
PCV C8 C9 SING N N 5
PCV C9 C7 SING N N 6
PCV C9 HC91 SING N N 7
PCV C9 HC92 SING N N 8
PCV C7 HC71 SING N N 9
PCV C7 HC72 SING N N 10
PCV C1 C2 SING N N 11
PCV C1 C3 SING N N 12
PCV C1 HC1 SING N N 13
PCV C2 C4 SING N N 14
PCV C2 O3 SING N N 15
PCV C2 H22 SING N N 16
PCV C4 C5 SING N N 17
PCV C4 HC41 SING N N 18
PCV C4 HC42 SING N N 19
PCV C5 N2 SING N N 20
PCV C5 HC51 SING N N 21
PCV C5 HC52 SING N N 22
PCV N2 HN21 SING N N 23
PCV N2 HN22 SING N N 24
PCV O3 HO3 SING N N 25
PCV C3 O2 DOUB N N 26
PCV C3 O4 SING N N 27
PCV O4 HO4 SING N N 28
#
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
PCV SMILES ACDLabs 10.04 O=C1N(C(C(=O)O)C(O)CCN)CC1
PCV SMILES_CANONICAL CACTVS 3.341 NCC[C@@H](O)[C@H](N1CCC1=O)C(O)=O
PCV SMILES CACTVS 3.341 NCC[CH](O)[CH](N1CCC1=O)C(O)=O
PCV SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1CN(C1=O)[C@@H]([C@@H](CCN)O)C(=O)O
PCV SMILES "OpenEye OEToolkits" 1.5.0 C1CN(C1=O)C(C(CCN)O)C(=O)O
PCV InChI InChI 1.03 InChI=1S/C8H14N2O4/c9-3-1-5(11)7(8(13)14)10-4-2-6(10)12/h5,7,11H,1-4,9H2,(H,13,14)/t5-,7+/m1/s1
PCV InChIKey InChI 1.03 NMCINKPVAOXDJH-VDTYLAMSSA-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
PCV "SYSTEMATIC NAME" ACDLabs 10.04 "5-amino-2,4,5-trideoxy-2-(2-oxoazetidin-1-yl)-D-threo-pentonic acid"
PCV "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S,3R)-5-amino-3-hydroxy-2-(2-oxoazetidin-1-yl)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
PCV 'Create component' 2000-01-21 RCSB
PCV 'Modify descriptor' 2011-06-04 RCSB
PCV 'Modify synonyms' 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id PCV
_pdbx_chem_comp_synonyms.name "PROCLAVAMINIC ACID"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id PCV
_pdbe_chem_comp_synonyms.name 'PROCLAVAMINIC ACID'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
PCV N1 N 4.500 2.088 1
PCV C8 C 4.500 3.588 2
PCV O1 O 5.561 4.649 3
PCV C9 C 3.000 3.588 4
PCV C7 C 3.000 2.088 5
PCV C1 C 5.561 1.028 6
PCV C2 C 5.173 -0.421 7
PCV C4 C 6.233 -1.482 8
PCV C5 C 5.845 -2.931 9
PCV N2 N 6.905 -3.991 10
PCV O3 O 3.724 -0.809 11
PCV C3 C 7.010 1.416 12
PCV O2 O 8.070 0.355 13
PCV O4 O 7.398 2.865 14
#
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
PCV N1 C8 SINGLE NONE 1
PCV N1 C7 SINGLE NONE 2
PCV C1 N1 SINGLE BEGINDASH 3
PCV C8 O1 DOUBLE NONE 4
PCV C8 C9 SINGLE NONE 5
PCV C9 C7 SINGLE NONE 6
PCV C1 C2 SINGLE NONE 7
PCV C1 C3 SINGLE NONE 8
PCV C2 C4 SINGLE NONE 9
PCV C2 O3 SINGLE BEGINWEDGE 10
PCV C4 C5 SINGLE NONE 11
PCV C5 N2 SINGLE NONE 12
PCV C3 O2 DOUBLE NONE 13
PCV C3 O4 SINGLE NONE 14
#
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
PCV MurckoScaffold S1 scaffold O=C1CCN1 InChI=1S/C3H5NO/c5-3-1-2-4-3/h1-2H2,(H,4,5) MNFORVFSTILPAW-UHFFFAOYSA-N
PCV amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
PCV peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-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
PCV N1 S1 1
PCV C8 S1 1
PCV O1 S1 1
PCV C9 S1 1
PCV C7 S1 1
PCV N1 F1 1
PCV C8 F1 1
PCV O1 F1 1
PCV C9 F1 1
PCV O2 F2 1
PCV C3 F2 1
PCV C1 F2 1
PCV N1 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PCV
_pdbe_chem_comp_rdkit_properties.exactmw 202.095
_pdbe_chem_comp_rdkit_properties.amw 202.210
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.750
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 101.258
_pdbe_chem_comp_rdkit_properties.tpsa 103.860
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.618
_pdbe_chem_comp_rdkit_properties.CrippenMR 47.432
_pdbe_chem_comp_rdkit_properties.chi0v 6.527
_pdbe_chem_comp_rdkit_properties.chi1v 3.211
_pdbe_chem_comp_rdkit_properties.chi2v 1.279
_pdbe_chem_comp_rdkit_properties.chi3v 1.279
_pdbe_chem_comp_rdkit_properties.chi4v 0.710
_pdbe_chem_comp_rdkit_properties.chi0n 20.527
_pdbe_chem_comp_rdkit_properties.chi1n 9.922
_pdbe_chem_comp_rdkit_properties.chi2n 1.279
_pdbe_chem_comp_rdkit_properties.chi3n 1.279
_pdbe_chem_comp_rdkit_properties.chi4n 0.710
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.140
_pdbe_chem_comp_rdkit_properties.kappa1 2.507
_pdbe_chem_comp_rdkit_properties.kappa2 4.385
_pdbe_chem_comp_rdkit_properties.kappa3 2.020
_pdbe_chem_comp_rdkit_properties.Phi 0.785
#
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
PCV UniChem 'KEGG LIGAND' C06658
PCV UniChem ChEBI 15425
PCV UniChem ChEBI 57302
PCV UniChem SureChEMBL SCHEMBL4094685
PCV UniChem 'PubChem TPHARMA' 15121004
PCV UniChem NMRShiftDB 70074400
PCV UniChem Nikkaji J370.816K
PCV UniChem 'EPA CompTox Dashboard' DTXSID60149964
PCV UniChem BRENDA 114289
PCV UniChem BRENDA 16868
PCV UniChem BRENDA 22151
PCV UniChem Rhea 57302
PCV UniChem ACTor 112240-59-2
PCV UniChem PubChem 194953
PCV UniChem PubChem 25203549
#
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
PCV N1 -1.261 0.171 0.994 ETKDGv3 1
PCV C8 -1.522 1.582 1.354 ETKDGv3 2
PCV O1 -1.892 2.608 0.727 ETKDGv3 3
PCV C9 -1.163 1.280 2.772 ETKDGv3 4
PCV C7 -0.922 -0.080 2.381 ETKDGv3 5
PCV C1 -1.349 -0.601 -0.245 ETKDGv3 6
PCV C2 -0.381 -0.034 -1.313 ETKDGv3 7
PCV C4 1.097 -0.087 -0.873 ETKDGv3 8
PCV C5 2.000 0.682 -1.844 ETKDGv3 9
PCV N2 3.390 0.601 -1.407 ETKDGv3 10
PCV O3 -0.533 -0.741 -2.518 ETKDGv3 11
PCV C3 -1.128 -2.070 0.009 ETKDGv3 12
PCV O2 -1.890 -2.919 -0.528 ETKDGv3 13
PCV O4 -0.068 -2.502 0.801 ETKDGv3 14
PCV HC91 -0.245 1.819 3.090 ETKDGv3 15
PCV HC92 -2.034 1.397 3.453 ETKDGv3 16
PCV HC71 0.145 -0.377 2.487 ETKDGv3 17
PCV HC72 -1.633 -0.800 2.844 ETKDGv3 18
PCV HC1 -2.384 -0.476 -0.632 ETKDGv3 19
PCV H22 -0.649 1.036 -1.478 ETKDGv3 20
PCV HC41 1.206 0.361 0.138 ETKDGv3 21
PCV HC42 1.440 -1.143 -0.827 ETKDGv3 22
PCV HC51 1.914 0.239 -2.861 ETKDGv3 23
PCV HC52 1.684 1.748 -1.896 ETKDGv3 24
PCV HN21 3.492 1.168 -0.534 ETKDGv3 25
PCV HN22 3.980 1.068 -2.134 ETKDGv3 26
PCV HO3 -1.386 -0.438 -2.925 ETKDGv3 27
PCV HO4 0.092 -3.489 0.963 ETKDGv3 28
#