data_CGU
#
_chem_comp.id CGU
_chem_comp.name 'GAMMA-CARBOXY-GLUTAMIC ACID'
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C6 H9 N O6'
_chem_comp.mon_nstd_parent_comp_id GLU
_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 191.139
_chem_comp.one_letter_code E
_chem_comp.three_letter_code CGU
_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 ?
_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
CGU N N N 0 1 N N N Y Y N 84.153 39.598 35.110 -0.340 1.828 1.451 N CGU 1
CGU CA CA C 0 1 N N S Y N N 84.103 40.544 36.215 -0.320 0.360 1.436 CA CGU 2
CGU C C C 0 1 N N N Y N Y 85.312 41.493 36.033 0.145 -0.150 2.775 C CGU 3
CGU O O O 0 1 N N N Y N Y 85.129 42.700 35.847 0.913 0.506 3.437 O CGU 4
CGU OXT OXT O 0 1 N Y N Y N Y 86.524 40.944 35.948 -0.292 -1.334 3.231 OXT CGU 5
CGU CB CB C 0 1 N N N N N N 84.084 39.812 37.571 0.634 -0.125 0.344 CB CGU 6
CGU CG CG C 0 1 N N N N N N 82.904 39.995 38.557 0.161 0.392 -1.015 CG CGU 7
CGU CD1 CD1 C 0 1 N N N N N N 82.437 38.657 39.146 1.102 -0.085 -2.090 CD1 CGU 8
CGU CD2 CD2 C 0 1 N N N N N N 81.785 40.785 37.909 -1.226 -0.125 -1.294 CD2 CGU 9
CGU OE11 OE11 O 0 0 N N N N N N 81.395 38.662 39.841 2.053 -0.771 -1.799 OE11 CGU 10
CGU OE12 OE12 O 0 0 N N N N N N 83.104 37.615 38.942 0.883 0.249 -3.371 OE12 CGU 11
CGU OE21 OE21 O 0 0 N N N N N N 80.951 40.183 37.202 -1.779 -0.836 -0.489 OE21 CGU 12
CGU OE22 OE22 O 0 0 N N N N N N 81.749 42.011 38.135 -1.847 0.202 -2.438 OE22 CGU 13
CGU H H H 0 1 N N N Y Y N 83.356 38.972 35.229 0.603 2.129 1.641 H CGU 14
CGU H2 HN2 H 0 1 N Y N Y Y N 85.044 39.107 35.037 -0.556 2.125 0.511 HN2 CGU 15
CGU HA HA H 0 1 N N N Y N N 83.162 41.143 36.211 -1.324 -0.014 1.233 HA CGU 16
CGU HXT HXT H 0 1 N Y N Y N Y 87.266 41.526 35.836 0.006 -1.661 4.091 HXT CGU 17
CGU HB2 HB2 H 0 1 N N N N N N 84.208 38.720 37.378 1.637 0.249 0.546 HB2 CGU 18
CGU HB3 HB3 H 0 1 N N N N N N 85.028 40.057 38.110 0.649 -1.215 0.332 HB3 CGU 19
CGU HG HG H 0 1 N N N N N N 83.262 40.593 39.426 0.146 1.482 -1.003 HG CGU 20
CGU HE12 HE12 H 0 0 N N N N N N 82.814 36.786 39.306 1.486 -0.057 -4.061 HE12 CGU 21
CGU HE22 HE22 H 0 0 N N N N N N 81.047 42.506 37.728 -2.737 -0.129 -2.618 HE22 CGU 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
CGU N CA SING N N 1
CGU N H SING N N 2
CGU N H2 SING N N 3
CGU CA C SING N N 4
CGU CA CB SING N N 5
CGU CA HA SING N N 6
CGU C O DOUB N N 7
CGU C OXT SING N N 8
CGU OXT HXT SING N N 9
CGU CB CG SING N N 10
CGU CB HB2 SING N N 11
CGU CB HB3 SING N N 12
CGU CG CD1 SING N N 13
CGU CG CD2 SING N N 14
CGU CG HG SING N N 15
CGU CD1 OE11 DOUB N N 16
CGU CD1 OE12 SING N N 17
CGU CD2 OE21 DOUB N N 18
CGU CD2 OE22 SING N N 19
CGU OE12 HE12 SING N N 20
CGU OE22 HE22 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
CGU SMILES ACDLabs 10.04 'O=C(O)C(C(=O)O)CC(N)C(=O)O'
CGU SMILES_CANONICAL CACTVS 3.341 'N[C@@H](CC(C(O)=O)C(O)=O)C(O)=O'
CGU SMILES CACTVS 3.341 'N[CH](CC(C(O)=O)C(O)=O)C(O)=O'
CGU SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C(C(C(=O)O)C(=O)O)[C@@H](C(=O)O)N'
CGU SMILES 'OpenEye OEToolkits' 1.5.0 'C(C(C(=O)O)C(=O)O)C(C(=O)O)N'
CGU InChI InChI 1.03 'InChI=1S/C6H9NO6/c7-3(6(12)13)1-2(4(8)9)5(10)11/h2-3H,1,7H2,(H,8,9)(H,10,11)(H,12,13)/t3-/m0/s1'
CGU InChIKey InChI 1.03 UHBYWPGGCSDKFX-VKHMYHEASA-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
CGU 'SYSTEMATIC NAME' ACDLabs 10.04 '(3S)-3-aminopropane-1,1,3-tricarboxylic acid'
CGU 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(3S)-3-aminopropane-1,1,3-tricarboxylic 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
CGU 'Create component' 1999-07-08 EBI
CGU 'Modify descriptor' 2011-06-04 RCSB
CGU 'Modify leaving atom flag' 2014-01-09 RCSB
CGU 'Modify backbone' 2023-11-03 PDBE
CGU 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id CGU
_pdbx_chem_comp_pcm.modified_residue_id GLU
_pdbx_chem_comp_pcm.type Carboxylation
_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-0039
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
_pdbx_chem_comp_pcm.first_instance_model_db_code 2PF1
#
_pdbe_chem_comp_drugbank_details.comp_id CGU
_pdbe_chem_comp_drugbank_details.drugbank_id DB03847
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'gamma-carboxy-L-glutamic acid'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 53861-57-7
_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
CGU '(3S)-3-amino-1,1,3-propanetricarboxylic acid' DrugBank ?
CGU 'gamma-carboxy-glutamic acid' DrugBank ?
CGU 'gamma-Carboxyglutamic acid' DrugBank ?
CGU 'γ-carboxy-L-glutamic acid' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id CGU
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03847
_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_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
CGU DB03847 Prothrombin Humans P00734 unknown 1
CGU DB03847 Osteocalcin Humans P02818 unknown 2
CGU DB03847 'Coagulation factor X' Humans P00742 unknown 3
#
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
CGU N N 9.953 -0.633 1
CGU CA C 9.203 0.666 2
CGU C C 9.953 1.965 3
CGU O O 11.453 1.965 4
CGU OXT O 9.203 3.264 5
CGU CB C 7.702 0.666 6
CGU CG C 6.404 -0.084 7
CGU CD1 C 5.104 0.666 8
CGU CD2 C 6.404 -1.584 9
CGU OE11 O 3.805 -0.084 10
CGU OE12 O 5.104 2.166 11
CGU OE21 O 5.104 -2.334 12
CGU OE22 O 7.702 -2.334 13
#
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
CGU CA N SINGLE BEGINWEDGE 1
CGU CA C SINGLE NONE 2
CGU CA CB SINGLE NONE 3
CGU C O DOUBLE NONE 4
CGU C OXT SINGLE NONE 5
CGU CB CG SINGLE NONE 6
CGU CG CD1 SINGLE NONE 7
CGU CG CD2 SINGLE NONE 8
CGU CD1 OE11 DOUBLE NONE 9
CGU CD1 OE12 SINGLE NONE 10
CGU CD2 OE21 DOUBLE NONE 11
CGU CD2 OE22 SINGLE NONE 12
#
_pdbe_chem_comp_substructure.comp_id CGU
_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
CGU O F1 1
CGU C F1 1
CGU CA F1 1
CGU N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id CGU
_pdbe_chem_comp_rdkit_properties.exactmw 191.043
_pdbe_chem_comp_rdkit_properties.amw 191.139
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_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 85.792
_pdbe_chem_comp_rdkit_properties.tpsa 137.920
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.426
_pdbe_chem_comp_rdkit_properties.CrippenMR 38.990
_pdbe_chem_comp_rdkit_properties.chi0v 5.897
_pdbe_chem_comp_rdkit_properties.chi1v 2.698
_pdbe_chem_comp_rdkit_properties.chi2v 0.845
_pdbe_chem_comp_rdkit_properties.chi3v 0.845
_pdbe_chem_comp_rdkit_properties.chi4v 0.355
_pdbe_chem_comp_rdkit_properties.chi0n 14.897
_pdbe_chem_comp_rdkit_properties.chi1n 6.818
_pdbe_chem_comp_rdkit_properties.chi2n 0.845
_pdbe_chem_comp_rdkit_properties.chi3n 0.845
_pdbe_chem_comp_rdkit_properties.chi4n 0.355
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.630
_pdbe_chem_comp_rdkit_properties.kappa1 3.259
_pdbe_chem_comp_rdkit_properties.kappa2 4.409
_pdbe_chem_comp_rdkit_properties.kappa3 3.518
_pdbe_chem_comp_rdkit_properties.Phi 1.105
#
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
CGU UniChem ChEMBL CHEMBL38397
CGU UniChem DrugBank DB03847
CGU UniChem PDBe CGU
CGU UniChem ChEBI 41450
CGU UniChem ChEBI 61936
CGU UniChem ZINC ZINC000002004603
CGU UniChem eMolecules 489170
CGU UniChem fdasrs 16FQV4RZKL
CGU UniChem SureChEMBL SCHEMBL39093
CGU UniChem 'PubChem TPHARMA' 49758860
CGU UniChem ACTor 53861-57-7
CGU UniChem Nikkaji J39.446G
CGU UniChem BindingDb 50076390
CGU UniChem MetaboLights MTBLC41450
CGU UniChem MetaboLights MTBLC61936
CGU UniChem BRENDA 153541
CGU UniChem BRENDA 153542
CGU UniChem 'Probes And Drugs' PD007188
CGU UniChem PubChem 104625
CGU UniChem PubChem 51351782
#
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
CGU N 1.458 -1.451 -0.893 ETKDGv3 1
CGU CA 1.542 -0.030 -0.540 ETKDGv3 2
CGU C 2.137 0.187 0.830 ETKDGv3 3
CGU O 1.976 -0.660 1.750 ETKDGv3 4
CGU OXT 2.836 1.362 1.092 ETKDGv3 5
CGU CB 0.179 0.681 -0.702 ETKDGv3 6
CGU CG -0.950 0.187 0.240 ETKDGv3 7
CGU CD1 -1.520 -1.137 -0.188 ETKDGv3 8
CGU CD2 -2.062 1.197 0.291 ETKDGv3 9
CGU OE11 -1.901 -1.317 -1.377 ETKDGv3 10
CGU OE12 -1.658 -2.160 0.744 ETKDGv3 11
CGU OE21 -2.464 1.637 1.402 ETKDGv3 12
CGU OE22 -2.665 1.636 -0.885 ETKDGv3 13
CGU H 2.431 -1.825 -0.988 ETKDGv3 14
CGU H2 1.005 -1.991 -0.122 ETKDGv3 15
CGU HA 2.231 0.452 -1.269 ETKDGv3 16
CGU HXT 3.230 1.539 2.008 ETKDGv3 17
CGU HB2 -0.148 0.597 -1.762 ETKDGv3 18
CGU HB3 0.349 1.765 -0.516 ETKDGv3 19
CGU HG -0.541 0.079 1.267 ETKDGv3 20
CGU HE12 -2.048 -3.057 0.478 ETKDGv3 21
CGU HE22 -3.419 2.311 -0.862 ETKDGv3 22
#