data_DAM
#
_chem_comp.id DAM
_chem_comp.name N-METHYL-ALPHA-BETA-DEHYDROALANINE
_chem_comp.type 'PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C4 H7 N O2'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_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 101.104
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code DAM
_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 1LCM
_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
DAM N N N 0 1 N N N Y Y N 5.596 5.471 6.409 -1.321 -0.659 -0.000 N DAM 1
DAM CM CM C 0 1 N N N N N N 4.497 6.449 6.643 -2.711 -0.197 -0.000 CM DAM 2
DAM CA CA C 0 1 N N N Y N N 6.920 5.943 5.919 -0.275 0.270 -0.000 CA DAM 3
DAM CB CB C 0 1 N N N N N N 7.276 7.236 6.069 -0.543 1.578 0.000 CB DAM 4
DAM C C C 0 1 N N N Y N Y 7.858 4.979 5.257 1.125 -0.195 -0.000 C DAM 5
DAM O O O 0 1 N N N Y N Y 8.721 4.434 5.916 1.369 -1.386 -0.000 O DAM 6
DAM OXT OXT O 0 1 N Y N Y N Y 7.766 4.772 3.973 2.132 0.699 0.000 OXT DAM 7
DAM H HN H 0 1 N Y N Y Y N 5.767 5.030 7.290 -1.126 -1.609 0.004 H DAM 8
DAM HM1 HM1 H 0 1 N N N N N N 3.603 5.918 7.001 -2.894 0.405 0.890 HM1 DAM 9
DAM HM2 HM2 H 0 1 N N N N N N 4.814 7.183 7.399 -2.894 0.405 -0.890 HM2 DAM 10
DAM HM3 HM3 H 0 1 N N N N N N 4.263 6.969 5.702 -3.380 -1.057 -0.000 HM3 DAM 11
DAM HB1 HB1 H 0 1 N N N N N N 8.237 7.576 5.712 0.264 2.296 0.000 HB1 DAM 12
DAM HB2 HB2 H 0 1 N N N N N N 6.600 7.930 6.546 -1.568 1.919 0.000 HB2 DAM 13
DAM HXT HXT H 0 1 N Y N Y N Y 8.447 4.169 3.699 3.033 0.347 0.000 HXT DAM 14
#
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
DAM N CM SING N N 1
DAM N CA SING N N 2
DAM N H SING N N 3
DAM CM HM1 SING N N 4
DAM CM HM2 SING N N 5
DAM CM HM3 SING N N 6
DAM CA CB DOUB N N 7
DAM CA C SING N N 8
DAM CB HB1 SING N N 9
DAM CB HB2 SING N N 10
DAM C O DOUB N N 11
DAM C OXT SING N N 12
DAM OXT HXT SING N N 13
#
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
DAM SMILES ACDLabs 12.01 'O=C(O)C(=C)/NC'
DAM SMILES_CANONICAL CACTVS 3.370 'CNC(=C)C(O)=O'
DAM SMILES CACTVS 3.370 'CNC(=C)C(O)=O'
DAM SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.0 'CNC(=C)C(=O)O'
DAM SMILES 'OpenEye OEToolkits' 1.7.0 'CNC(=C)C(=O)O'
DAM InChI InChI 1.03 'InChI=1S/C4H7NO2/c1-3(5-2)4(6)7/h5H,1H2,2H3,(H,6,7)'
DAM InChIKey InChI 1.03 FLEYLGCAQDCGHN-UHFFFAOYSA-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
DAM 'SYSTEMATIC NAME' ACDLabs 12.01 '2-(methylamino)prop-2-enoic acid'
DAM 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.7.0 '2-(methylamino)prop-2-enoic 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
DAM 'Create component' 1999-07-08 RCSB
DAM 'Modify descriptor' 2011-06-04 RCSB
DAM 'Modify backbone' 2023-11-03 PDBE
DAM 'Modify PCM' 2024-09-27 PDBE
#
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_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
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
1 DAM ALA 'Dehydroamino acid' 'Named protein modification' 'Amino-acid side chain and backbone' 'Any position' ? ? ? ?
2 DAM ALA Methylation 'Named protein modification' 'Amino-acid backbone' 'Any position' ? ? ? ?
#
_pdbe_chem_comp_drugbank_details.comp_id DAM
_pdbe_chem_comp_drugbank_details.drugbank_id DB03920
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name N-Methyl-Alpha-Beta-Dehydroalanine
_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 DAM
_pdbe_chem_comp_synonyms.name N-Methyl-Alpha-Beta-Dehydroalanine
_pdbe_chem_comp_synonyms.provenance DrugBank
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id DAM
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03920
_pdbe_chem_comp_drugbank_classification.parent '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 alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).'
#
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
DAM N N 4.299 0.375 1
DAM CM C 3.000 -0.375 2
DAM CA C 5.598 -0.375 3
DAM CB C 5.598 -1.875 4
DAM C C 6.897 0.375 5
DAM O O 8.196 -0.375 6
DAM OXT O 6.897 1.875 7
#
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
DAM N CM SINGLE NONE 1
DAM N CA SINGLE NONE 2
DAM CA CB DOUBLE NONE 3
DAM CA C SINGLE NONE 4
DAM C O DOUBLE NONE 5
DAM C OXT SINGLE NONE 6
#
_pdbe_chem_comp_substructure.comp_id DAM
_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
DAM O F1 1
DAM C F1 1
DAM CA F1 1
DAM N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id DAM
_pdbe_chem_comp_rdkit_properties.exactmw 101.048
_pdbe_chem_comp_rdkit_properties.amw 101.105
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 7
_pdbe_chem_comp_rdkit_properties.NumAtoms 14
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.250
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 51.630
_pdbe_chem_comp_rdkit_properties.tpsa 49.330
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.196
_pdbe_chem_comp_rdkit_properties.CrippenMR 25.835
_pdbe_chem_comp_rdkit_properties.chi0v 3.264
_pdbe_chem_comp_rdkit_properties.chi1v 1.355
_pdbe_chem_comp_rdkit_properties.chi2v 0.305
_pdbe_chem_comp_rdkit_properties.chi3v 0.305
_pdbe_chem_comp_rdkit_properties.chi4v 0.046
_pdbe_chem_comp_rdkit_properties.chi0n 10.264
_pdbe_chem_comp_rdkit_properties.chi1n 4.711
_pdbe_chem_comp_rdkit_properties.chi2n 0.305
_pdbe_chem_comp_rdkit_properties.chi3n 0.305
_pdbe_chem_comp_rdkit_properties.chi4n 0.046
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.990
_pdbe_chem_comp_rdkit_properties.kappa1 1.046
_pdbe_chem_comp_rdkit_properties.kappa2 2.230
_pdbe_chem_comp_rdkit_properties.kappa3 1.808
_pdbe_chem_comp_rdkit_properties.Phi 0.333
#
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
DAM UniChem DrugBank DB03920
DAM UniChem fdasrs YNW06WML0Q
DAM UniChem SureChEMBL SCHEMBL1280041
DAM UniChem 'EPA CompTox Dashboard' DTXSID20233939
DAM UniChem 'Probes And Drugs' PD006642
DAM UniChem Nikkaji J445.655F
DAM UniChem PubChem 134856
DAM UniChem ACTor 84888-65-3
#
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
DAM N 0.937 0.432 0.284 ETKDGv3 1
DAM CM 1.738 -0.688 -0.200 ETKDGv3 2
DAM CA -0.464 0.613 -0.011 ETKDGv3 3
DAM CB -1.023 1.801 0.252 ETKDGv3 4
DAM C -1.296 -0.477 -0.589 ETKDGv3 5
DAM O -2.427 -0.219 -1.084 ETKDGv3 6
DAM OXT -0.854 -1.796 -0.576 ETKDGv3 7
DAM H 1.450 1.194 0.783 ETKDGv3 8
DAM HM1 2.815 -0.482 -0.023 ETKDGv3 9
DAM HM2 1.471 -1.612 0.352 ETKDGv3 10
DAM HM3 1.582 -0.827 -1.290 ETKDGv3 11
DAM HB1 -0.437 2.608 0.671 ETKDGv3 12
DAM HB2 -2.072 1.991 0.060 ETKDGv3 13
DAM HXT -1.422 -2.539 -0.964 ETKDGv3 14
#