data_MLZ
#
_chem_comp.id MLZ
_chem_comp.name N-METHYL-LYSINE
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C7 H16 N2 O2'
_chem_comp.mon_nstd_parent_comp_id LYS
_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 160.214
_chem_comp.one_letter_code K
_chem_comp.three_letter_code MLZ
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1XER
_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
MLZ N N N 0 1 N N N Y Y N 21.135 7.501 5.557 0.306 -2.126 -2.601 N MLZ 1
MLZ CA CA C 0 1 N N S Y N N 20.063 8.383 5.107 0.164 -0.696 -2.695 CA MLZ 2
MLZ CB CB C 0 1 N N N N N N 19.940 8.313 3.578 1.172 0.050 -1.819 CB MLZ 3
MLZ CG CG C 0 1 N N N N N N 20.779 9.328 2.812 1.029 -0.210 -0.314 CG MLZ 4
MLZ CD CD C 0 1 N N N N N N 22.231 9.360 3.277 2.018 0.595 0.536 CD MLZ 5
MLZ CE CE C 0 1 N N N N N N 23.069 10.325 2.425 1.909 0.286 2.031 CE MLZ 6
MLZ NZ NZ N 0 1 N N N N N N 24.346 10.709 3.091 2.885 1.034 2.814 NZ MLZ 7
MLZ CM CM C 0 1 N N N N N N ? ? ? 2.795 0.688 4.225 CM MLZ 8
MLZ C C C 0 1 N N N Y N Y 18.696 8.162 5.743 0.373 -0.338 -4.153 C MLZ 9
MLZ O O O 0 1 N N N Y N Y 17.917 9.106 5.896 1.159 -0.891 -4.911 O MLZ 10
MLZ OXT OXT O 0 1 N Y N Y N Y 18.410 6.921 6.117 -0.389 0.723 -4.529 OXT MLZ 11
MLZ H 1HN H 0 1 N N N Y Y N 21.216 7.547 6.572 -0.419 -2.715 -2.974 H MLZ 12
MLZ H2 2HN H 0 1 N Y N Y Y N 22.019 7.703 5.091 1.013 -2.509 -1.994 H2 MLZ 13
MLZ HA HA H 0 1 N N N Y N N 20.372 9.397 5.451 -0.871 -0.473 -2.418 HA MLZ 14
MLZ HB2 1HB H 0 1 N N N N N N 20.167 7.281 3.221 2.192 -0.230 -2.117 HB2 MLZ 15
MLZ HB3 2HB H 0 1 N N N N N N 18.869 8.393 3.275 1.090 1.129 -2.004 HB3 MLZ 16
MLZ HG2 1HG H 0 1 N N N N N N 20.714 9.152 1.712 1.197 -1.280 -0.139 HG2 MLZ 17
MLZ HG3 2HG H 0 1 N N N N N N 20.320 10.343 2.859 0.000 0.000 0.000 HG3 MLZ 18
MLZ HD2 1HD H 0 1 N N N N N N 22.307 9.601 4.362 1.866 1.669 0.377 HD2 MLZ 19
MLZ HD3 2HD H 0 1 N N N N N N 22.677 8.338 3.296 3.041 0.368 0.210 HD3 MLZ 20
MLZ HE2 1HE H 0 1 N N N N N N 23.256 9.905 1.409 0.902 0.522 2.390 HE2 MLZ 21
MLZ HE3 2HE H 0 1 N N N N N N 22.477 11.226 2.139 2.071 -0.786 2.190 HE3 MLZ 22
MLZ HZ HZ H 0 1 N N N N N N 25.127 11.257 3.450 2.710 2.032 2.701 HZ MLZ 23
MLZ HCM1 1HCM H 0 0 N N N N N N 0.955 0.287 0.498 2.237 1.456 4.766 HCM1 MLZ 24
MLZ HCM2 2HCM H 0 0 N N N N N N -1.085 -0.122 -0.224 3.796 0.608 4.659 HCM2 MLZ 25
MLZ HCM3 3HCM H 0 0 N N N N N N -0.853 -0.599 -0.392 2.283 -0.271 4.347 HCM3 MLZ 26
MLZ HXT HXT H 0 1 N Y N Y N Y 17.557 6.783 6.513 -0.266 1.020 -5.456 HXT MLZ 27
#
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
MLZ N CA SING N N 1
MLZ N H SING N N 2
MLZ N H2 SING N N 3
MLZ CA CB SING N N 4
MLZ CA C SING N N 5
MLZ CA HA SING N N 6
MLZ CB CG SING N N 7
MLZ CB HB2 SING N N 8
MLZ CB HB3 SING N N 9
MLZ CG CD SING N N 10
MLZ CG HG2 SING N N 11
MLZ CG HG3 SING N N 12
MLZ CD CE SING N N 13
MLZ CD HD2 SING N N 14
MLZ CD HD3 SING N N 15
MLZ CE NZ SING N N 16
MLZ CE HE2 SING N N 17
MLZ CE HE3 SING N N 18
MLZ NZ CM SING N N 19
MLZ NZ HZ SING N N 20
MLZ CM HCM1 SING N N 21
MLZ CM HCM2 SING N N 22
MLZ CM HCM3 SING N N 23
MLZ C O DOUB N N 24
MLZ C OXT SING N N 25
MLZ OXT HXT SING N N 26
#
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
MLZ SMILES ACDLabs 10.04 'O=C(O)C(N)CCCCNC'
MLZ SMILES_CANONICAL CACTVS 3.341 'CNCCCC[C@H](N)C(O)=O'
MLZ SMILES CACTVS 3.341 'CNCCCC[CH](N)C(O)=O'
MLZ SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'CNCCCC[C@@H](C(=O)O)N'
MLZ SMILES 'OpenEye OEToolkits' 1.5.0 'CNCCCCC(C(=O)O)N'
MLZ InChI InChI 1.03 'InChI=1S/C7H16N2O2/c1-9-5-3-2-4-6(8)7(10)11/h6,9H,2-5,8H2,1H3,(H,10,11)/t6-/m0/s1'
MLZ InChIKey InChI 1.03 PQNASZJZHFPQLE-LURJTMIESA-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
MLZ 'SYSTEMATIC NAME' ACDLabs 10.04 N~6~-methyl-L-lysine
MLZ 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2S)-2-amino-6-methylamino-hexanoic 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
MLZ 'Create component' 1999-07-08 RCSB
MLZ 'Modify descriptor' 2011-06-04 RCSB
MLZ 'Modify backbone' 2023-11-03 PDBE
MLZ 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id MLZ
_pdbx_chem_comp_pcm.modified_residue_id LYS
_pdbx_chem_comp_pcm.type Methylation
_pdbx_chem_comp_pcm.category 'Named protein 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 ?
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom ?
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession PTM-0194
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession PTM-0193
_pdbx_chem_comp_pcm.first_instance_model_db_code 1XER
#
_pdbe_chem_comp_drugbank_details.comp_id MLZ
_pdbe_chem_comp_drugbank_details.drugbank_id DB01714
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Epsilon-N-methyllysine
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 1188-07-4
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
MLZ N-Epsilon-methyllysine DrugBank ?
MLZ N(6)-Methyllysine DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id MLZ
_pdbe_chem_comp_drugbank_classification.drugbank_id DB01714
_pdbe_chem_comp_drugbank_classification.parent 'L-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 l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.'
#
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
MLZ N N 5.598 3.000 1
MLZ CA C 6.897 2.250 2
MLZ CB C 6.897 0.750 3
MLZ CG C 5.598 0.000 4
MLZ CD C 5.598 -1.500 5
MLZ CE C 4.299 -2.250 6
MLZ NZ N 4.299 -3.750 7
MLZ CM C 3.000 -4.500 8
MLZ C C 8.196 3.000 9
MLZ O O 9.495 2.250 10
MLZ OXT O 8.196 4.500 11
#
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
MLZ CA N SINGLE BEGINDASH 1
MLZ CA CB SINGLE NONE 2
MLZ CA C SINGLE NONE 3
MLZ CB CG SINGLE NONE 4
MLZ CG CD SINGLE NONE 5
MLZ CD CE SINGLE NONE 6
MLZ CE NZ SINGLE NONE 7
MLZ NZ CM SINGLE NONE 8
MLZ C O DOUBLE NONE 9
MLZ C OXT SINGLE NONE 10
#
_pdbe_chem_comp_substructure.comp_id MLZ
_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
MLZ O F1 1
MLZ C F1 1
MLZ CA F1 1
MLZ N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id MLZ
_pdbe_chem_comp_rdkit_properties.exactmw 160.121
_pdbe_chem_comp_rdkit_properties.amw 160.217
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 27
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.857
_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 89.515
_pdbe_chem_comp_rdkit_properties.tpsa 75.350
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.212
_pdbe_chem_comp_rdkit_properties.CrippenMR 43.389
_pdbe_chem_comp_rdkit_properties.chi0v 5.211
_pdbe_chem_comp_rdkit_properties.chi1v 2.329
_pdbe_chem_comp_rdkit_properties.chi2v 0.549
_pdbe_chem_comp_rdkit_properties.chi3v 0.549
_pdbe_chem_comp_rdkit_properties.chi4v 0.197
_pdbe_chem_comp_rdkit_properties.chi0n 21.211
_pdbe_chem_comp_rdkit_properties.chi1n 10.079
_pdbe_chem_comp_rdkit_properties.chi2n 0.549
_pdbe_chem_comp_rdkit_properties.chi3n 0.549
_pdbe_chem_comp_rdkit_properties.chi4n 0.197
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.610
_pdbe_chem_comp_rdkit_properties.kappa1 1.421
_pdbe_chem_comp_rdkit_properties.kappa2 6.123
_pdbe_chem_comp_rdkit_properties.kappa3 5.816
_pdbe_chem_comp_rdkit_properties.Phi 0.791
#
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
MLZ UniChem DrugBank DB01714
MLZ UniChem PDBe MLZ
MLZ UniChem 'KEGG LIGAND' C02728
MLZ UniChem ChEBI 17604
MLZ UniChem ZINC ZINC000001529511
MLZ UniChem fdasrs FCR6T2IYVU
MLZ UniChem SureChEMBL SCHEMBL64149
MLZ UniChem HMDB HMDB0002038
MLZ UniChem NMRShiftDB 60023709
MLZ UniChem ACTor 1188-07-4
MLZ UniChem Nikkaji J80.069D
MLZ UniChem 'EPA CompTox Dashboard' DTXSID70152242
MLZ UniChem MetaboLights MTBLC17604
MLZ UniChem BRENDA 12621
MLZ UniChem BRENDA 30273
MLZ UniChem BRENDA 93334
MLZ UniChem 'Probes And Drugs' PD060273
MLZ UniChem PubChem 164795
MLZ UniChem 'PubChem TPHARMA' 15995545
#
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
MLZ N -2.722 0.038 -1.528 ETKDGv3 1
MLZ CA -2.777 -0.516 -0.171 ETKDGv3 2
MLZ CB -1.465 -1.244 0.188 ETKDGv3 3
MLZ CG -0.226 -0.332 0.231 ETKDGv3 4
MLZ CD 1.023 -1.127 0.637 ETKDGv3 5
MLZ CE 2.260 -0.235 0.807 ETKDGv3 6
MLZ NZ 2.724 0.270 -0.493 ETKDGv3 7
MLZ CM 4.049 0.878 -0.357 ETKDGv3 8
MLZ C -3.137 0.535 0.851 ETKDGv3 9
MLZ O -3.787 0.206 1.880 ETKDGv3 10
MLZ OXT -2.721 1.854 0.691 ETKDGv3 11
MLZ H -2.093 0.872 -1.555 ETKDGv3 12
MLZ H2 -3.680 0.371 -1.787 ETKDGv3 13
MLZ HA -3.581 -1.285 -0.157 ETKDGv3 14
MLZ HB2 -1.593 -1.733 1.179 ETKDGv3 15
MLZ HB3 -1.294 -2.051 -0.558 ETKDGv3 16
MLZ HG2 -0.389 0.486 0.965 ETKDGv3 17
MLZ HG3 -0.063 0.112 -0.773 ETKDGv3 18
MLZ HD2 0.829 -1.636 1.606 ETKDGv3 19
MLZ HD3 1.235 -1.911 -0.124 ETKDGv3 20
MLZ HE2 3.055 -0.856 1.278 ETKDGv3 21
MLZ HE3 2.031 0.609 1.496 ETKDGv3 22
MLZ HZ 2.073 1.029 -0.800 ETKDGv3 23
MLZ HCM1 4.797 0.112 -0.061 ETKDGv3 24
MLZ HCM2 4.361 1.301 -1.335 ETKDGv3 25
MLZ HCM3 4.034 1.699 0.394 ETKDGv3 26
MLZ HXT -2.945 2.557 1.385 ETKDGv3 27
#