data_NCB
#
_chem_comp.id NCB
_chem_comp.name N-CARBAMOYL-ALANINE
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C4 H8 N2 O3'
_chem_comp.mon_nstd_parent_comp_id ALA
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-10-10
_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 132.118
_chem_comp.one_letter_code A
_chem_comp.three_letter_code NCB
_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 1QMV
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
_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
NCB N N N 0 1 N N N Y Y N 26.255 -9.244 72.762 -0.358 -0.319 -0.653 N NCB 1
NCB CA CA C 0 1 N N R Y N N 24.936 -9.561 72.302 0.492 0.078 0.470 CA NCB 2
NCB C C C 0 1 N N N Y N Y 23.996 -9.811 73.468 -0.333 0.137 1.729 C NCB 3
NCB O O O 0 1 N N N Y N Y 23.479 -10.985 73.580 -1.512 -0.126 1.691 O NCB 4
NCB OXT OXT O 0 1 N Y N Y N Y 23.686 -8.801 74.262 0.239 0.481 2.893 OXT NCB 5
NCB CB CB C 0 1 N N N N N N 24.373 -8.835 71.126 1.616 -0.944 0.645 CB NCB 6
NCB O3 O3 O 0 1 N N N N N N 27.857 -8.616 71.537 0.883 0.835 -2.088 O3 NCB 7
NCB C3 C3 C 0 1 N N N N N N 27.342 -9.658 72.069 -0.076 0.114 -1.898 C3 NCB 8
NCB N2 N2 N 0 1 N N N N N N 27.901 -10.831 71.856 -0.859 -0.251 -2.932 N2 NCB 9
NCB H H H 0 1 N N N Y Y N 26.345 -9.571 73.723 -1.125 -0.894 -0.502 H NCB 10
NCB HA HA H 0 1 N N N Y N N 25.070 -10.529 71.765 0.921 1.060 0.271 HA NCB 11
NCB HXT HO H 0 1 N Y N Y N Y 23.097 -8.957 74.991 -0.290 0.519 3.701 HXT NCB 12
NCB HB3 3HB H 0 1 N N N N N N 23.346 -9.081 70.767 1.187 -1.926 0.844 HB3 NCB 13
NCB HB2 2HB H 0 1 N N N N N N 24.426 -7.739 71.325 2.214 -0.986 -0.265 HB2 NCB 14
NCB HB1 1HB H 0 1 N N N N N N 25.082 -8.938 70.271 2.249 -0.648 1.482 HB1 NCB 15
NCB H22 2H2 H 0 1 N N N N N N 27.490 -11.662 72.280 -0.656 0.060 -3.828 H22 NCB 16
NCB H21 1H2 H 0 1 N N N N N N 28.719 -11.142 71.333 -1.626 -0.826 -2.781 H21 NCB 17
#
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
NCB N CA SING N N 1
NCB N C3 SING N N 2
NCB N H SING N N 3
NCB CA C SING N N 4
NCB CA CB SING N N 5
NCB CA HA SING N N 6
NCB C O DOUB N N 7
NCB C OXT SING N N 8
NCB OXT HXT SING N N 9
NCB CB HB3 SING N N 10
NCB CB HB2 SING N N 11
NCB CB HB1 SING N N 12
NCB O3 C3 DOUB N N 13
NCB C3 N2 SING N N 14
NCB N2 H22 SING N N 15
NCB N2 H21 SING N N 16
#
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
NCB SMILES ACDLabs 10.04 'O=C(O)C(NC(=O)N)C'
NCB SMILES_CANONICAL CACTVS 3.341 'C[C@@H](NC(N)=O)C(O)=O'
NCB SMILES CACTVS 3.341 'C[CH](NC(N)=O)C(O)=O'
NCB SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C[C@H](C(=O)O)NC(=O)N'
NCB SMILES 'OpenEye OEToolkits' 1.5.0 'CC(C(=O)O)NC(=O)N'
NCB InChI InChI 1.03 'InChI=1S/C4H8N2O3/c1-2(3(7)8)6-4(5)9/h2H,1H3,(H,7,8)(H3,5,6,9)/t2-/m1/s1'
NCB InChIKey InChI 1.03 LUSWEUMSEVLFEQ-UWTATZPHSA-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
NCB 'SYSTEMATIC NAME' ACDLabs 10.04 N-carbamoyl-D-alanine
NCB 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2R)-2-(aminocarbonylamino)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
NCB 'Create component' 1999-10-10 EBI
NCB 'Modify descriptor' 2011-06-04 RCSB
NCB 'Modify backbone' 2023-11-03 PDBE
NCB 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id NCB
_pdbx_chem_comp_pcm.modified_residue_id ALA
_pdbx_chem_comp_pcm.type Carbamoylation
_pdbx_chem_comp_pcm.category 'Named protein modification'
_pdbx_chem_comp_pcm.position 'Amino-acid backbone'
_pdbx_chem_comp_pcm.polypeptide_position N-terminal
_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 PTM-0374
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
_pdbx_chem_comp_pcm.first_instance_model_db_code 1QMV
#
_pdbe_chem_comp_drugbank_details.comp_id NCB
_pdbe_chem_comp_drugbank_details.drugbank_id DB04048
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name N-Carbamoyl-Alanine
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id NCB
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04048
_pdbe_chem_comp_drugbank_classification.parent 'N-carbamoyl-alpha amino acids'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Carboxylic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as n-carbamoyl-alpha amino acids. These are compounds containing an alpha amino acid which bears an carbamoyl group at its terminal nitrogen atom.'
#
_pdbe_chem_comp_drugbank_targets.comp_id NCB
_pdbe_chem_comp_drugbank_targets.drugbank_id DB04048
_pdbe_chem_comp_drugbank_targets.name Peroxiredoxin-2
_pdbe_chem_comp_drugbank_targets.organism Humans
_pdbe_chem_comp_drugbank_targets.uniprot_id P32119
_pdbe_chem_comp_drugbank_targets.pharmacologically_active unknown
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
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
NCB N N 6.404 0.375 1
NCB CA C 7.702 -0.375 2
NCB C C 9.002 0.375 3
NCB O O 10.301 -0.375 4
NCB OXT O 9.002 1.875 5
NCB CB C 7.702 -1.875 6
NCB O3 O 5.104 -1.875 7
NCB C3 C 5.104 -0.375 8
NCB N2 N 3.805 0.375 9
#
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
NCB N CA SINGLE NONE 1
NCB N C3 SINGLE NONE 2
NCB CA C SINGLE NONE 3
NCB CA CB SINGLE BEGINWEDGE 4
NCB C O DOUBLE NONE 5
NCB C OXT SINGLE NONE 6
NCB O3 C3 DOUBLE NONE 7
NCB C3 N2 SINGLE NONE 8
#
_pdbe_chem_comp_substructure.comp_id NCB
_pdbe_chem_comp_substructure.substructure_name peptide
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles NCC=O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2
_pdbe_chem_comp_substructure.substructure_inchikeys 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
NCB O F1 1
NCB C F1 1
NCB CA F1 1
NCB N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id NCB
_pdbe_chem_comp_rdkit_properties.exactmw 132.053
_pdbe_chem_comp_rdkit_properties.amw 132.119
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 9
_pdbe_chem_comp_rdkit_properties.NumAtoms 17
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_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 63.342
_pdbe_chem_comp_rdkit_properties.tpsa 92.420
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.872
_pdbe_chem_comp_rdkit_properties.CrippenMR 29.817
_pdbe_chem_comp_rdkit_properties.chi0v 4.119
_pdbe_chem_comp_rdkit_properties.chi1v 1.783
_pdbe_chem_comp_rdkit_properties.chi2v 0.401
_pdbe_chem_comp_rdkit_properties.chi3v 0.401
_pdbe_chem_comp_rdkit_properties.chi4v 0.141
_pdbe_chem_comp_rdkit_properties.chi0n 12.119
_pdbe_chem_comp_rdkit_properties.chi1n 5.533
_pdbe_chem_comp_rdkit_properties.chi2n 0.401
_pdbe_chem_comp_rdkit_properties.chi3n 0.401
_pdbe_chem_comp_rdkit_properties.chi4n 0.141
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.260
_pdbe_chem_comp_rdkit_properties.kappa1 1.618
_pdbe_chem_comp_rdkit_properties.kappa2 2.907
_pdbe_chem_comp_rdkit_properties.kappa3 3.333
_pdbe_chem_comp_rdkit_properties.Phi 0.523
#
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
NCB UniChem DrugBank DB04048
NCB UniChem PDBe NCB
NCB UniChem ZINC ZINC000082071078
NCB UniChem SureChEMBL SCHEMBL2792653
NCB UniChem PubChem 1535935
NCB UniChem BRENDA 30228
NCB UniChem BRENDA 30823
NCB UniChem 'Probes And Drugs' PD006526
#
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
NCB N 0.660 -0.160 -0.299 ETKDGv3 1
NCB CA -0.585 -0.635 0.312 ETKDGv3 2
NCB C -1.456 0.533 0.676 ETKDGv3 3
NCB O -2.002 0.583 1.810 ETKDGv3 4
NCB OXT -1.684 1.547 -0.250 ETKDGv3 5
NCB CB -1.335 -1.563 -0.646 ETKDGv3 6
NCB O3 1.554 0.643 1.709 ETKDGv3 7
NCB C3 1.690 0.479 0.467 ETKDGv3 8
NCB N2 2.880 0.934 -0.177 ETKDGv3 9
NCB H 0.813 -0.286 -1.326 ETKDGv3 10
NCB HA -0.340 -1.219 1.227 ETKDGv3 11
NCB HXT -2.277 2.336 -0.021 ETKDGv3 12
NCB HB3 -0.695 -2.433 -0.906 ETKDGv3 13
NCB HB2 -1.606 -1.027 -1.582 ETKDGv3 14
NCB HB1 -2.262 -1.942 -0.166 ETKDGv3 15
NCB H22 3.010 0.807 -1.205 ETKDGv3 16
NCB H21 3.634 1.400 0.376 ETKDGv3 17
#