data_SYM
#
_chem_comp.id SYM
_chem_comp.name 2S,4R-4-METHYLGLUTAMATE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H10 N O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge -1
_chem_comp.pdbx_initial_date 2004-02-16
_chem_comp.pdbx_modified_date 2011-06-04
_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 160.148
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SYM
_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 1SD3
_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
SYM CB CB C 0 1 N N N N N N 34.417 15.309 38.931 -0.024 0.597 0.691 CB SYM 1
SYM CG1 CG1 C 0 1 N N R N N N 34.877 15.921 37.596 1.403 0.794 0.177 CG1 SYM 2
SYM CG2 CG2 C 0 1 N N N N N N 36.168 16.728 37.761 2.257 1.435 1.273 CG2 SYM 3
SYM CD CD C 0 1 N N N N N N 35.008 14.838 36.504 1.990 -0.542 -0.200 CD SYM 4
SYM OE1 OE1 O 0 1 N N N N N N 35.101 13.629 36.851 3.242 -0.614 -0.680 OE1 SYM 5
SYM OE2 OE2 O 0 1 N N N N N N 35.027 15.194 35.296 1.334 -1.548 -0.071 OE2 SYM 6
SYM C C C 0 1 N N N N N N 32.749 13.813 40.114 -2.288 -0.208 0.081 C SYM 7
SYM OT1 OT1 O -1 1 N N N N N N 33.609 12.913 40.329 -2.510 -1.377 0.704 OT1 SYM 8
SYM OT2 OT2 O 0 1 N N N N N N 31.717 13.961 40.811 -3.189 0.586 -0.051 OT2 SYM 9
SYM N N N 0 1 N N N N N N 32.028 15.941 39.012 -1.021 1.166 -1.472 N SYM 10
SYM CA CA C 0 1 N N S N N N 32.969 14.782 38.937 -0.916 0.113 -0.453 CA SYM 11
SYM HB1 1HB H 0 1 N N N N N N 34.566 16.038 39.761 -0.023 -0.144 1.490 HB1 SYM 12
SYM HB2 2HB H 0 1 N N N N N N 35.121 14.506 39.250 -0.406 1.544 1.074 HB2 SYM 13
SYM HG1 HG1 H 0 1 N N N N N N 34.090 16.637 37.261 1.388 1.444 -0.698 HG1 SYM 14
SYM HG21 1HG2 H 0 0 N N N N N N 36.974 16.115 38.228 3.269 1.594 0.900 HG21 SYM 15
SYM HG22 2HG2 H 0 0 N N N N N N 36.501 17.171 36.794 1.821 2.392 1.560 HG22 SYM 16
SYM HG23 3HG2 H 0 0 N N N N N N 36.063 17.507 38.552 2.289 0.776 2.140 HG23 SYM 17
SYM HE1 HE1 H 0 1 N N N N N N 35.182 12.962 36.179 3.618 -1.471 -0.922 HE1 SYM 18
SYM HN1 1HN H 0 1 N N N N N N 32.190 16.621 38.270 -1.696 0.846 -2.151 HN1 SYM 19
SYM HN2 2HN H 0 1 N N N N N N 31.070 15.592 39.016 -1.427 1.970 -1.017 HN2 SYM 20
SYM HA HA H 0 1 N N N N N N 32.775 14.215 37.997 -0.482 -0.782 -0.899 HA SYM 21
#
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
SYM CB CG1 SING N N 1
SYM CB CA SING N N 2
SYM CB HB1 SING N N 3
SYM CB HB2 SING N N 4
SYM CG1 CG2 SING N N 5
SYM CG1 CD SING N N 6
SYM CG1 HG1 SING N N 7
SYM CG2 HG21 SING N N 8
SYM CG2 HG22 SING N N 9
SYM CG2 HG23 SING N N 10
SYM CD OE1 SING N N 11
SYM CD OE2 DOUB N N 12
SYM OE1 HE1 SING N N 13
SYM C OT1 SING N N 14
SYM C OT2 DOUB N N 15
SYM C CA SING N N 16
SYM N CA SING N N 17
SYM N HN1 SING N N 18
SYM N HN2 SING N N 19
SYM CA HA SING N N 20
#
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
SYM SMILES ACDLabs 10.04 "[O-]C(=O)C(N)CC(C(=O)O)C"
SYM SMILES_CANONICAL CACTVS 3.341 C[C@H](C[C@H](N)C([O-])=O)C(O)=O
SYM SMILES CACTVS 3.341 C[CH](C[CH](N)C([O-])=O)C(O)=O
SYM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[C@H](C[C@@H](C(=O)[O-])N)C(=O)O
SYM SMILES "OpenEye OEToolkits" 1.5.0 CC(CC(C(=O)[O-])N)C(=O)O
SYM InChI InChI 1.03 InChI=1S/C6H11NO4/c1-3(5(8)9)2-4(7)6(10)11/h3-4H,2,7H2,1H3,(H,8,9)(H,10,11)/p-1/t3-,4+/m1/s1
SYM InChIKey InChI 1.03 KRKRAOXTGDJWNI-DMTCNVIQSA-M
#
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
SYM "SYSTEMATIC NAME" ACDLabs 10.04 (2S,4R)-2-amino-4-carboxypentanoate
SYM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (2S,4R)-2-amino-5-hydroxy-4-methyl-5-oxo-pentanoate
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
SYM 'Create component' 2004-02-16 RCSB
SYM 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id SYM
_pdbe_chem_comp_drugbank_details.drugbank_id DB03425
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 2s,4r-4-Methylglutamate
_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 SYM
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03425
_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.'
#
_pdbe_chem_comp_drugbank_targets.comp_id SYM
_pdbe_chem_comp_drugbank_targets.drugbank_id DB03425
_pdbe_chem_comp_drugbank_targets.name 'Glutamate receptor ionotropic, kainate 2'
_pdbe_chem_comp_drugbank_targets.organism Humans
_pdbe_chem_comp_drugbank_targets.uniprot_id Q13002
_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
SYM CB C 7.702 0.608 1
SYM CG1 C 6.404 -0.142 2
SYM CG2 C 6.404 -1.643 3
SYM CD C 5.104 0.608 4
SYM OE1 O 3.805 -0.142 5
SYM OE2 O 5.104 2.107 6
SYM C C 10.301 0.608 7
SYM OT1 O 11.600 -0.142 8
SYM OT2 O 10.301 2.107 9
SYM N N 9.002 -1.643 10
SYM CA C 9.002 -0.142 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
SYM CB CG1 SINGLE NONE 1
SYM CB CA SINGLE NONE 2
SYM CG1 CG2 SINGLE BEGINWEDGE 3
SYM CG1 CD SINGLE NONE 4
SYM CD OE1 SINGLE NONE 5
SYM CD OE2 DOUBLE NONE 6
SYM C OT1 SINGLE NONE 7
SYM C OT2 DOUBLE NONE 8
SYM C CA SINGLE NONE 9
SYM CA N SINGLE BEGINWEDGE 10
#
_pdbe_chem_comp_substructure.comp_id SYM
_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
SYM OT2 F1 1
SYM C F1 1
SYM CA F1 1
SYM N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id SYM
_pdbe_chem_comp_rdkit_properties.exactmw 160.062
_pdbe_chem_comp_rdkit_properties.amw 160.149
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 21
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.667
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 78.068
_pdbe_chem_comp_rdkit_properties.tpsa 103.450
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.826
_pdbe_chem_comp_rdkit_properties.CrippenMR 34.399
_pdbe_chem_comp_rdkit_properties.chi0v 5.080
_pdbe_chem_comp_rdkit_properties.chi1v 2.290
_pdbe_chem_comp_rdkit_properties.chi2v 0.641
_pdbe_chem_comp_rdkit_properties.chi3v 0.641
_pdbe_chem_comp_rdkit_properties.chi4v 0.220
_pdbe_chem_comp_rdkit_properties.chi0n 15.080
_pdbe_chem_comp_rdkit_properties.chi1n 7.093
_pdbe_chem_comp_rdkit_properties.chi2n 0.641
_pdbe_chem_comp_rdkit_properties.chi3n 0.641
_pdbe_chem_comp_rdkit_properties.chi4n 0.220
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.100
_pdbe_chem_comp_rdkit_properties.kappa1 2.195
_pdbe_chem_comp_rdkit_properties.kappa2 3.922
_pdbe_chem_comp_rdkit_properties.kappa3 3.566
_pdbe_chem_comp_rdkit_properties.Phi 0.783
#
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
SYM UniChem DrugBank DB03425
SYM UniChem PDBe SYM
SYM UniChem PubChem 131704245
SYM UniChem PubChem 49867704
SYM UniChem PubChem 6971091
SYM UniChem 'Probes And Drugs' PD059642
SYM UniChem 'EPA CompTox Dashboard' DTXSID20426268
SYM UniChem ACTor 31137-74-3
#
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
SYM CB 0.132 0.301 -0.717 ETKDGv3 1
SYM CG1 -1.010 0.418 0.317 ETKDGv3 2
SYM CG2 -2.151 1.280 -0.233 ETKDGv3 3
SYM CD -1.536 -0.936 0.714 ETKDGv3 4
SYM OE1 -1.454 -1.346 2.042 ETKDGv3 5
SYM OE2 -2.046 -1.701 -0.148 ETKDGv3 6
SYM C 2.407 -0.589 -1.251 ETKDGv3 7
SYM OT1 2.968 0.522 -1.871 ETKDGv3 8
SYM OT2 2.763 -1.743 -1.608 ETKDGv3 9
SYM N 1.947 0.329 0.964 ETKDGv3 10
SYM CA 1.380 -0.416 -0.163 ETKDGv3 11
SYM HB1 -0.239 -0.246 -1.613 ETKDGv3 12
SYM HB2 0.424 1.322 -1.052 ETKDGv3 13
SYM HG1 -0.621 0.928 1.226 ETKDGv3 14
SYM HG21 -2.964 1.364 0.519 ETKDGv3 15
SYM HG22 -1.782 2.303 -0.458 ETKDGv3 16
SYM HG23 -2.567 0.837 -1.164 ETKDGv3 17
SYM HE1 -1.799 -2.254 2.327 ETKDGv3 18
SYM HN1 2.302 1.255 0.630 ETKDGv3 19
SYM HN2 2.765 -0.203 1.341 ETKDGv3 20
SYM HA 1.081 -1.425 0.198 ETKDGv3 21
#