data_GME
#
_chem_comp.id GME
_chem_comp.name '5-O-methyl-glutamic acid'
_chem_comp.type 'L-peptide linking'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C6 H11 N O4'
_chem_comp.mon_nstd_parent_comp_id GLU
_chem_comp.pdbx_synonyms '(2S)-2-amino-5-methoxy-5-oxopentanoic acid'
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2009-10-09
_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 161.156
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GME
_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 2KNN
_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
GME C C C 0 1 N N N Y N Y -2.020 -1.230 -4.461 2.795 0.302 -0.026 C GME 1
GME N N N 0 1 N N N Y Y N -0.146 -1.256 -6.037 1.696 -1.859 0.140 N GME 2
GME O O O 0 1 N N N Y N Y -1.452 -0.366 -3.785 3.438 -0.022 0.945 O GME 3
GME CA CA C 0 1 N N S Y N N -1.291 -1.999 -5.538 1.601 -0.515 -0.447 CA GME 4
GME CB CB C 0 1 N N N N N N -0.885 -3.370 -4.996 0.320 0.165 0.041 CB GME 5
GME CD CD C 0 1 N N N N N N 0.391 -4.699 -3.271 -2.157 0.074 -0.012 CD GME 6
GME CG CG C 0 1 N N N N N N -0.014 -3.318 -3.749 -0.896 -0.596 -0.492 CG GME 7
GME CX CX C 0 1 N N N N N N -1.349 -5.594 -1.982 -4.527 0.273 0.140 CX GME 8
GME OE1 OE1 O 0 1 N N N N N N 1.055 -5.421 -4.041 -2.091 1.059 0.684 OE1 GME 9
GME OE2 OE2 O 0 1 N N N N N N 0.002 -5.109 -1.952 -3.355 -0.424 -0.359 OE2 GME 10
GME H H H 0 1 N N N Y Y N 0.315 -1.789 -6.746 1.717 -1.812 1.148 H GME 11
GME HA HA H 0 1 N N N Y N N -1.966 -2.145 -6.394 1.580 -0.594 -1.534 HA GME 12
GME H1B H1B H 0 1 N N N N N N -0.318 -3.890 -5.782 0.300 0.164 1.130 H1B GME 13
GME H2B H2B H 0 1 N N N N N N -1.804 -3.919 -4.744 0.294 1.192 -0.323 H2B GME 14
GME H1G H1G H 0 1 N N N N N N 0.897 -2.748 -3.983 -0.876 -0.595 -1.582 H1G GME 15
GME H2G H2G H 0 1 N N N N N N -0.581 -2.823 -2.947 -0.869 -1.623 -0.129 H2G GME 16
GME H1X H1X H 0 1 N N N N N N -1.649 -5.909 -0.971 -4.514 0.273 1.229 H1X GME 17
GME H2X H2X H 0 1 N N N N N N -2.018 -4.793 -2.330 -4.521 1.301 -0.224 H2X GME 18
GME H3X H3X H 0 1 N N N N N N -1.415 -6.452 -2.668 -5.427 -0.231 -0.213 H3X GME 19
GME OXT OXT O 0 1 N Y N Y N Y -3.401 -1.509 -4.218 3.142 1.394 -0.726 OXT GME 20
GME H2 H2 H 0 1 N Y N Y Y N -0.455 -0.386 -6.422 0.941 -2.447 -0.179 H2 GME 21
GME HXT HXT H 0 1 N Y N Y N Y -3.719 -0.951 -3.518 3.913 1.888 -0.415 HXT GME 22
#
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
GME C O DOUB N N 1
GME C OXT SING N N 2
GME N H SING N N 3
GME N CA SING N N 4
GME N H2 SING N N 5
GME CA C SING N N 6
GME CA CB SING N N 7
GME CB H2B SING N N 8
GME CB CG SING N N 9
GME CD OE2 SING N N 10
GME CG CD SING N N 11
GME CG H1G SING N N 12
GME CX OE2 SING N N 13
GME CX H1X SING N N 14
GME OE1 CD DOUB N N 15
GME HA CA SING N N 16
GME H1B CB SING N N 17
GME H2G CG SING N N 18
GME H2X CX SING N N 19
GME H3X CX SING N N 20
GME OXT HXT SING N N 21
#
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
GME SMILES ACDLabs 11.02 'O=C(OC)CCC(C(=O)O)N'
GME SMILES_CANONICAL CACTVS 3.352 'COC(=O)CC[C@H](N)C(O)=O'
GME SMILES CACTVS 3.352 'COC(=O)CC[CH](N)C(O)=O'
GME SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.0 'COC(=O)CC[C@@H](C(=O)O)N'
GME SMILES 'OpenEye OEToolkits' 1.7.0 'COC(=O)CCC(C(=O)O)N'
GME InChI InChI 1.03 'InChI=1S/C6H11NO4/c1-11-5(8)3-2-4(7)6(9)10/h4H,2-3,7H2,1H3,(H,9,10)/t4-/m0/s1'
GME InChIKey InChI 1.03 ZGEYCCHDTIDZAE-BYPYZUCNSA-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
GME 'SYSTEMATIC NAME' ACDLabs 11.02 '(2S)-2-amino-5-methoxy-5-oxopentanoic acid (non-preferred name)'
GME 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.6.1 '(2S)-2-azanyl-5-methoxy-5-oxo-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
GME 'Create component' 2009-10-09 RCSB
GME 'Modify descriptor' 2011-06-04 RCSB
GME 'Modify synonyms' 2021-03-01 PDBE
GME 'Modify backbone' 2023-11-03 PDBE
GME 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id GME
_pdbx_chem_comp_synonyms.name '(2S)-2-amino-5-methoxy-5-oxopentanoic acid'
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
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
_pdbx_chem_comp_pcm.first_instance_model_db_code
1 GME GLU Methylation 'Named protein modification' 'Amino-acid side chain' 'Any position' ? ? PTM-0128 ? 2KNN
2 GME GLN Deamidation 'Named protein modification' 'Amino-acid side chain' 'Any position' ? ? PTM-0127 ? ?
3 GME GLN Methylation 'Named protein modification' 'Amino-acid side chain' 'Any position' ? ? PTM-0127 ? ?
#
_pdbe_chem_comp_synonyms.comp_id GME
_pdbe_chem_comp_synonyms.name '(2S)-2-amino-5-methoxy-5-oxopentanoic acid'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
GME C C 6.897 2.625 1
GME N N 4.299 2.625 2
GME O O 8.196 1.875 3
GME CA C 5.598 1.875 4
GME CB C 5.598 0.375 5
GME CD C 4.299 -1.875 6
GME CG C 4.299 -0.375 7
GME CX C 3.000 -4.125 8
GME OE1 O 5.598 -2.625 9
GME OE2 O 3.000 -2.625 10
GME OXT O 6.897 4.125 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
GME C O DOUBLE NONE 1
GME C OXT SINGLE NONE 2
GME CA N SINGLE BEGINDASH 3
GME CA C SINGLE NONE 4
GME CA CB SINGLE NONE 5
GME CB CG SINGLE NONE 6
GME CD OE2 SINGLE NONE 7
GME CG CD SINGLE NONE 8
GME CX OE2 SINGLE NONE 9
GME OE1 CD DOUBLE NONE 10
#
_pdbe_chem_comp_substructure.comp_id GME
_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
GME O F1 1
GME C F1 1
GME CA F1 1
GME N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id GME
_pdbe_chem_comp_rdkit_properties.exactmw 161.069
_pdbe_chem_comp_rdkit_properties.amw 161.157
_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 22
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 79.792
_pdbe_chem_comp_rdkit_properties.tpsa 89.620
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.648
_pdbe_chem_comp_rdkit_properties.CrippenMR 36.861
_pdbe_chem_comp_rdkit_properties.chi0v 5.080
_pdbe_chem_comp_rdkit_properties.chi1v 2.244
_pdbe_chem_comp_rdkit_properties.chi2v 0.569
_pdbe_chem_comp_rdkit_properties.chi3v 0.569
_pdbe_chem_comp_rdkit_properties.chi4v 0.187
_pdbe_chem_comp_rdkit_properties.chi0n 16.080
_pdbe_chem_comp_rdkit_properties.chi1n 7.547
_pdbe_chem_comp_rdkit_properties.chi2n 0.569
_pdbe_chem_comp_rdkit_properties.chi3n 0.569
_pdbe_chem_comp_rdkit_properties.chi4n 0.187
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.100
_pdbe_chem_comp_rdkit_properties.kappa1 1.980
_pdbe_chem_comp_rdkit_properties.kappa2 4.675
_pdbe_chem_comp_rdkit_properties.kappa3 4.323
_pdbe_chem_comp_rdkit_properties.Phi 0.842
#
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
GME UniChem ChEMBL CHEMBL1233072
GME UniChem PDBe GME
GME UniChem ChEBI 21306
GME UniChem ZINC ZINC000002003955
GME UniChem eMolecules 713434
GME UniChem HMDB HMDB0061715
GME UniChem 'PubChem TPHARMA' 16044579
GME UniChem Nikkaji J206.704H
GME UniChem BRENDA 109784
GME UniChem BRENDA 136317
GME UniChem BRENDA 170858
GME UniChem BRENDA 17804
GME UniChem BRENDA 20760
GME UniChem BRENDA 44310
GME UniChem BRENDA 49163
GME UniChem BRENDA 51128
GME UniChem BRENDA 51130
GME UniChem BRENDA 51131
GME UniChem BRENDA 51720
GME UniChem BRENDA 91936
GME UniChem BRENDA 93504
GME UniChem BRENDA 93830
GME UniChem BRENDA 93838
GME UniChem BRENDA 97971
GME UniChem ChemicalBook CB2377021
GME UniChem 'EPA CompTox Dashboard' DTXSID2046171
GME UniChem SureChEMBL SCHEMBL142983
GME UniChem PubChem 68662
GME UniChem PubChem 6998933
GME UniChem Mcule MCULE-1607830290
GME UniChem ACTor 111468-12-3
GME UniChem ACTor 1499-55-4
#
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
GME C -1.264 1.264 -1.035 ETKDGv3 1
GME N -2.550 0.679 0.928 ETKDGv3 2
GME O -0.388 2.151 -1.220 ETKDGv3 3
GME CA -1.274 0.471 0.242 ETKDGv3 4
GME CB -1.033 -1.034 -0.026 ETKDGv3 5
GME CD 1.460 -1.001 0.298 ETKDGv3 6
GME CG 0.343 -1.337 -0.642 ETKDGv3 7
GME CX 3.196 0.607 1.018 ETKDGv3 8
GME OE1 1.744 -1.789 1.241 ETKDGv3 9
GME OE2 2.153 0.203 0.140 ETKDGv3 10
GME H -3.316 0.207 0.393 ETKDGv3 11
GME HA -0.466 0.852 0.906 ETKDGv3 12
GME H1B -1.131 -1.598 0.927 ETKDGv3 13
GME H2B -1.818 -1.418 -0.714 ETKDGv3 14
GME H1G 0.473 -0.780 -1.594 ETKDGv3 15
GME H2G 0.396 -2.420 -0.886 ETKDGv3 16
GME H1X 3.588 1.591 0.689 ETKDGv3 17
GME H2X 4.021 -0.136 0.994 ETKDGv3 18
GME H3X 2.806 0.702 2.053 ETKDGv3 19
GME OXT -2.218 1.018 -2.018 ETKDGv3 20
GME H2 -2.503 0.223 1.868 ETKDGv3 21
GME HXT -2.219 1.543 -2.884 ETKDGv3 22
#