data_G8M
#
_chem_comp.id G8M
_chem_comp.name "(1S,2R)-2-[(S)-amino(carboxy)methyl]cyclobutanecarboxylic acid"
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C7 H11 N O4"
_chem_comp.mon_nstd_parent_comp_id GLU
_chem_comp.pdbx_synonyms "(2S,1'R,2'S)-2-(2'-carboxycyclobutyl)glycine"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2012-07-30
_chem_comp.pdbx_modified_date 2021-03-13
_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 173.167
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code G8M
_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 4G8M
_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
G8M CD CD C 0 1 N N N N N N 5.785 25.813 20.912 -2.082 0.559 -0.071 CD G8M 1
G8M OE1 OE1 O 0 1 N N N N N N 4.853 25.180 20.367 -1.984 0.487 -1.273 OE1 G8M 2
G8M OE2 OE2 O 0 1 N N N N N N 6.342 25.388 21.949 -2.747 1.583 0.488 OE2 G8M 3
G8M CG CG C 0 1 N N S N N N 6.257 27.135 20.269 -1.464 -0.503 0.801 CG G8M 4
G8M C C C 0 1 N N N N N N 7.686 25.409 17.604 2.190 0.497 -0.007 C G8M 5
G8M OXT OXT O 0 1 N Y N N N N 6.476 25.402 17.319 2.601 1.512 0.770 OXT G8M 6
G8M O O O 0 1 N N N N N N 8.550 25.225 16.724 2.998 -0.263 -0.486 O G8M 7
G8M CA CA C 0 1 N N S N N N 8.130 25.648 19.065 0.720 0.305 -0.280 CA G8M 8
G8M N N N 0 1 N N N N N N 9.598 25.485 19.145 0.550 -0.520 -1.484 N G8M 9
G8M CB CB C 0 1 N N R N N N 7.651 27.027 19.599 0.066 -0.394 0.913 CB G8M 10
G8M C6 C6 C 0 1 N N N N N N 8.268 27.635 20.875 0.103 -1.929 0.825 C6 G8M 11
G8M C7 C7 C 0 1 N N N N N N 6.868 28.111 21.299 -1.236 -1.840 0.075 C7 G8M 12
G8M HE2 HE2 H 0 1 N N N N N N 5.945 24.564 22.207 -3.130 2.237 -0.112 HE2 G8M 13
G8M HG2 HG2 H 0 1 N N N N N N 5.499 27.601 19.623 -1.967 -0.608 1.762 HG2 G8M 14
G8M HXT HXT H 0 1 N Y N N N N 6.370 25.243 16.388 3.553 1.594 0.916 HXT G8M 15
G8M HA H4A H 0 1 N N N N N N 7.660 24.872 19.686 0.250 1.276 -0.436 HA G8M 16
G8M H2 H2 H 0 1 N Y N N N N 9.900 25.637 20.086 0.917 -0.051 -2.299 H2 G8M 17
G8M H1 H1 H 0 1 N N N N N N 9.846 24.559 18.861 0.978 -1.426 -1.365 H1 G8M 18
G8M HB2 HB2 H 0 1 N N N N N N 7.713 27.764 18.785 0.406 -0.002 1.872 HB2 G8M 19
G8M H9 H9 H 0 1 N N N N N N 8.720 26.897 21.555 0.921 -2.311 0.215 H9 G8M 20
G8M H10 H10 H 0 1 N N N N N N 8.985 28.448 20.688 0.030 -2.423 1.794 H10 G8M 21
G8M H11 H11 H 0 1 N N N N N N 6.668 29.173 21.092 -1.947 -2.616 0.358 H11 G8M 22
G8M H12 H12 H 0 1 N N N N N N 6.610 27.887 22.345 -1.126 -1.737 -1.004 H12 G8M 23
#
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
G8M O C DOUB N N 1
G8M OXT C SING N N 2
G8M C CA SING N N 3
G8M CA N SING N N 4
G8M CA CB SING N N 5
G8M CB CG SING N N 6
G8M CB C6 SING N N 7
G8M CG CD SING N N 8
G8M CG C7 SING N N 9
G8M OE1 CD DOUB N N 10
G8M C6 C7 SING N N 11
G8M CD OE2 SING N N 12
G8M OE2 HE2 SING N N 13
G8M CG HG2 SING N N 14
G8M OXT HXT SING N N 15
G8M CA HA SING N N 16
G8M N H2 SING N N 17
G8M N H1 SING N N 18
G8M CB HB2 SING N N 19
G8M C6 H9 SING N N 20
G8M C6 H10 SING N N 21
G8M C7 H11 SING N N 22
G8M C7 H12 SING N N 23
#
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
G8M SMILES ACDLabs 12.01 O=C(O)C(N)C1CCC1C(=O)O
G8M InChI InChI 1.03 InChI=1S/C7H11NO4/c8-5(7(11)12)3-1-2-4(3)6(9)10/h3-5H,1-2,8H2,(H,9,10)(H,11,12)/t3-,4+,5+/m1/s1
G8M InChIKey InChI 1.03 SRAFHGOPGVYULO-WISUUJSJSA-N
G8M SMILES_CANONICAL CACTVS 3.370 N[C@@H]([C@@H]1CC[C@@H]1C(O)=O)C(O)=O
G8M SMILES CACTVS 3.370 N[CH]([CH]1CC[CH]1C(O)=O)C(O)=O
G8M SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C1C[C@@H]([C@@H]1[C@@H](C(=O)O)N)C(=O)O
G8M SMILES "OpenEye OEToolkits" 1.7.6 C1CC(C1C(C(=O)O)N)C(=O)O
#
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
G8M "SYSTEMATIC NAME" ACDLabs 12.01 "(1S,2R)-2-[(S)-amino(carboxy)methyl]cyclobutanecarboxylic acid"
G8M "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(1S,2R)-2-[(1S)-1-azanyl-2-oxidanyl-2-oxidanylidene-ethyl]cyclobutane-1-carboxylic 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
G8M 'Create component' 2012-07-30 RCSB
G8M 'Modify synonyms' 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id G8M
_pdbx_chem_comp_synonyms.name "(2S,1'R,2'S)-2-(2'-carboxycyclobutyl)glycine"
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id G8M
_pdbe_chem_comp_synonyms.name "(2S,1'R,2'S)-2-(2'-carboxycyclobutyl)glycine"
_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
G8M CD C 5.561 -2.461 1
G8M OE1 O 5.173 -3.910 2
G8M OE2 O 7.010 -2.073 3
G8M CG C 4.500 -1.401 4
G8M C C 5.173 2.609 5
G8M OXT O 3.724 2.997 6
G8M O O 6.233 3.669 7
G8M CA C 5.561 1.160 8
G8M N N 7.010 0.772 9
G8M CB C 4.500 0.099 10
G8M C6 C 3.000 0.099 11
G8M C7 C 3.000 -1.401 12
#
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
G8M O C DOUBLE NONE 1
G8M OXT C SINGLE NONE 2
G8M C CA SINGLE NONE 3
G8M CA N SINGLE BEGINWEDGE 4
G8M CA CB SINGLE NONE 5
G8M CB CG SINGLE NONE 6
G8M CB C6 SINGLE BEGINWEDGE 7
G8M CG CD SINGLE BEGINWEDGE 8
G8M CG C7 SINGLE NONE 9
G8M OE1 CD DOUBLE NONE 10
G8M C6 C7 SINGLE NONE 11
G8M CD OE2 SINGLE NONE 12
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
G8M MurckoScaffold S1 scaffold C1CCC1 InChI=1S/C4H8/c1-2-4-3-1/h1-4H2 PMPVIKIVABFJJI-UHFFFAOYSA-N
G8M cyclobutane F1 fragment C1CCC1 InChI=1S/C4H8/c1-2-4-3-1/h1-4H2 PMPVIKIVABFJJI-UHFFFAOYSA-N
G8M peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 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
G8M CG S1 1
G8M CB S1 1
G8M C6 S1 1
G8M C7 S1 1
G8M CG F1 1
G8M CB F1 1
G8M C6 F1 1
G8M C7 F1 1
G8M O F2 1
G8M C F2 1
G8M CA F2 1
G8M N F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id G8M
_pdbe_chem_comp_rdkit_properties.exactmw 173.069
_pdbe_chem_comp_rdkit_properties.amw 173.168
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 23
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.714
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_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 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 84.919
_pdbe_chem_comp_rdkit_properties.tpsa 100.620
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.491
_pdbe_chem_comp_rdkit_properties.CrippenMR 39.461
_pdbe_chem_comp_rdkit_properties.chi0v 5.580
_pdbe_chem_comp_rdkit_properties.chi1v 2.790
_pdbe_chem_comp_rdkit_properties.chi2v 1.197
_pdbe_chem_comp_rdkit_properties.chi3v 1.197
_pdbe_chem_comp_rdkit_properties.chi4v 0.620
_pdbe_chem_comp_rdkit_properties.chi0n 16.580
_pdbe_chem_comp_rdkit_properties.chi1n 8.001
_pdbe_chem_comp_rdkit_properties.chi2n 1.197
_pdbe_chem_comp_rdkit_properties.chi3n 1.197
_pdbe_chem_comp_rdkit_properties.chi4n 0.620
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.100
_pdbe_chem_comp_rdkit_properties.kappa1 2.227
_pdbe_chem_comp_rdkit_properties.kappa2 3.102
_pdbe_chem_comp_rdkit_properties.kappa3 1.403
_pdbe_chem_comp_rdkit_properties.Phi 0.576
#
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
G8M UniChem ChEMBL CHEMBL384474
G8M UniChem PDBe G8M
G8M UniChem PubChem 44417425
G8M UniChem BindingDb 50197103
#
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
G8M CD 1.438 1.320 0.452 ETKDGv3 1
G8M OE1 1.266 2.557 0.614 ETKDGv3 2
G8M OE2 2.048 0.572 1.456 ETKDGv3 3
G8M CG 0.946 0.664 -0.815 ETKDGv3 4
G8M C -1.593 0.891 1.127 ETKDGv3 5
G8M OXT -2.442 1.577 0.263 ETKDGv3 6
G8M O -1.378 1.342 2.284 ETKDGv3 7
G8M CA -0.964 -0.404 0.696 ETKDGv3 8
G8M N -1.999 -1.439 0.667 ETKDGv3 9
G8M CB -0.288 -0.253 -0.695 ETKDGv3 10
G8M C6 0.579 -1.449 -1.099 ETKDGv3 11
G8M C7 1.787 -0.534 -1.258 ETKDGv3 12
G8M HE2 2.363 1.012 2.313 ETKDGv3 13
G8M HG2 0.828 1.402 -1.641 ETKDGv3 14
G8M HXT -2.879 2.446 0.545 ETKDGv3 15
G8M HA -0.202 -0.700 1.452 ETKDGv3 16
G8M H2 -1.549 -2.369 0.506 ETKDGv3 17
G8M H1 -2.649 -1.263 -0.134 ETKDGv3 18
G8M HB2 -1.032 -0.019 -1.491 ETKDGv3 19
G8M H9 0.734 -2.195 -0.289 ETKDGv3 20
G8M H10 0.259 -1.902 -2.063 ETKDGv3 21
G8M H11 2.618 -0.808 -0.571 ETKDGv3 22
G8M H12 2.111 -0.450 -2.318 ETKDGv3 23
#