data_1G8
#
_chem_comp.id 1G8
_chem_comp.name 4-(aminomethyl)-D-phenylalanine
_chem_comp.type "D-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C10 H14 N2 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2013-01-22
_chem_comp.pdbx_modified_date 2019-12-11
_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 194.230
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 1G8
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 4INU
_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
1G8 C25 C25 C 0 1 N N N N N N 11.199 -137.458 17.947 3.595 0.156 0.059 C25 1G8 1
1G8 O26 O26 O 0 1 N N N N N N 11.866 -136.443 17.796 4.296 -0.790 -0.213 O26 1G8 2
1G8 C15 C15 C 0 1 N N R N N N 10.064 -137.270 18.947 2.145 -0.056 0.408 C15 1G8 3
1G8 C16 C16 C 0 1 N N N N N N 8.904 -138.307 18.800 1.275 0.260 -0.810 C16 1G8 4
1G8 C17 C17 C 0 1 Y N N N N N 7.553 -137.861 19.382 -0.179 0.167 -0.427 C17 1G8 5
1G8 C22 C22 C 0 1 Y N N N N N 6.969 -138.558 20.452 -0.842 1.283 0.046 C22 1G8 6
1G8 C21 C21 C 0 1 Y N N N N N 5.736 -138.149 20.982 -2.177 1.198 0.398 C21 1G8 7
1G8 C20 C20 C 0 1 Y N N N N N 5.069 -137.039 20.441 -2.848 -0.004 0.276 C20 1G8 8
1G8 C23 C23 C 0 1 N N N N N N 3.718 -136.594 21.023 -4.302 -0.098 0.660 C23 1G8 9
1G8 N24 N24 N 0 1 N N N N N N 2.895 -137.760 21.440 -5.137 0.206 -0.510 N24 1G8 10
1G8 C19 C19 C 0 1 Y N N N N N 5.651 -136.342 19.369 -2.185 -1.121 -0.198 C19 1G8 11
1G8 C18 C18 C 0 1 Y N N N N N 6.883 -136.751 18.842 -0.852 -1.034 -0.554 C18 1G8 12
1G8 N14 N14 N 0 1 N N N N N N 10.456 -137.153 20.357 1.937 -1.454 0.809 N14 1G8 13
1G8 H32 H32 H 0 1 N N N N N N 9.609 -136.304 18.684 1.869 0.603 1.232 H32 1G8 14
1G8 H33 H33 H 0 1 N N N N N N 8.763 -138.511 17.728 1.494 1.268 -1.162 H33 1G8 15
1G8 H34 H34 H 0 1 N N N N N N 9.207 -139.232 19.312 1.488 -0.456 -1.604 H34 1G8 16
1G8 H35 H35 H 0 1 N N N N N N 7.473 -139.416 20.871 -0.318 2.223 0.142 H35 1G8 17
1G8 H36 H36 H 0 1 N N N N N N 5.299 -138.690 21.808 -2.694 2.070 0.768 H36 1G8 18
1G8 H37 H37 H 0 1 N N N N N N 3.899 -135.953 21.898 -4.521 -1.106 1.011 H37 1G8 19
1G8 H38 H38 H 0 1 N N N N N N 3.169 -136.024 20.259 -4.515 0.618 1.454 H38 1G8 20
1G8 H39 H39 H 0 1 N N N N N N 2.025 -137.438 21.813 -4.913 -0.403 -1.282 H39 1G8 21
1G8 H40 H40 H 0 1 N N N N N N 2.722 -138.346 20.648 -6.118 0.150 -0.278 H40 1G8 22
1G8 H42 H42 H 0 1 N N N N N N 5.145 -135.485 18.948 -2.710 -2.060 -0.294 H42 1G8 23
1G8 H43 H43 H 0 1 N N N N N N 7.320 -136.210 18.016 -0.334 -1.907 -0.925 H43 1G8 24
1G8 H44 H44 H 0 1 N N N N N N 9.639 -137.034 20.922 0.986 -1.607 1.110 H44 1G8 25
1G8 OXT OXT O 0 1 N Y N N N N ? ? ? 4.110 1.396 0.055 OXT 1G8 26
1G8 HXT HXT H 0 1 N Y N N N N ? ? ? 5.045 1.482 -0.176 HXT 1G8 27
1G8 H2 H2 H 0 1 N Y N N N N 10.938 -137.983 20.639 2.186 -2.085 0.062 H2 1G8 28
#
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
1G8 O26 C25 DOUB N N 1
1G8 C25 C15 SING N N 2
1G8 C16 C15 SING N N 3
1G8 C16 C17 SING N N 4
1G8 C18 C19 DOUB Y N 5
1G8 C18 C17 SING Y N 6
1G8 C15 N14 SING N N 7
1G8 C19 C20 SING Y N 8
1G8 C17 C22 DOUB Y N 9
1G8 C20 C21 DOUB Y N 10
1G8 C20 C23 SING N N 11
1G8 C22 C21 SING Y N 12
1G8 C23 N24 SING N N 13
1G8 C15 H32 SING N N 14
1G8 C16 H33 SING N N 15
1G8 C16 H34 SING N N 16
1G8 C22 H35 SING N N 17
1G8 C21 H36 SING N N 18
1G8 C23 H37 SING N N 19
1G8 C23 H38 SING N N 20
1G8 N24 H39 SING N N 21
1G8 N24 H40 SING N N 22
1G8 C19 H42 SING N N 23
1G8 C18 H43 SING N N 24
1G8 N14 H44 SING N N 25
1G8 C25 OXT SING N N 26
1G8 OXT HXT SING N N 27
1G8 N14 H2 SING N N 28
#
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
1G8 SMILES ACDLabs 12.01 O=C(O)C(N)Cc1ccc(cc1)CN
1G8 InChI InChI 1.03 InChI=1S/C10H14N2O2/c11-6-8-3-1-7(2-4-8)5-9(12)10(13)14/h1-4,9H,5-6,11-12H2,(H,13,14)/t9-/m1/s1
1G8 InChIKey InChI 1.03 GNVNKFUEUXUWDV-SECBINFHSA-N
1G8 SMILES_CANONICAL CACTVS 3.370 NCc1ccc(C[C@@H](N)C(O)=O)cc1
1G8 SMILES CACTVS 3.370 NCc1ccc(C[CH](N)C(O)=O)cc1
1G8 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 c1cc(ccc1C[C@H](C(=O)O)N)CN
1G8 SMILES "OpenEye OEToolkits" 1.7.6 c1cc(ccc1CC(C(=O)O)N)CN
#
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
1G8 "SYSTEMATIC NAME" ACDLabs 12.01 4-(aminomethyl)-D-phenylalanine
1G8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2R)-3-[4-(aminomethyl)phenyl]-2-azanyl-propanoic 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
1G8 'Create component' 2013-01-22 RCSB
1G8 'Initial release' 2013-01-25 RCSB
1G8 'Other modification' 2019-12-11 RCSB
#
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
1G8 C25 C 6.404 4.125 1
1G8 O26 O 7.702 4.875 2
1G8 C15 C 6.404 2.625 3
1G8 C16 C 5.104 1.875 4
1G8 C17 C 5.104 0.375 5
1G8 C22 C 6.404 -0.375 6
1G8 C21 C 6.404 -1.875 7
1G8 C20 C 5.104 -2.625 8
1G8 C23 C 5.104 -4.125 9
1G8 N24 N 3.805 -4.875 10
1G8 C19 C 3.805 -1.875 11
1G8 C18 C 3.805 -0.375 12
1G8 N14 N 7.702 1.875 13
1G8 OXT O 5.104 4.875 14
#
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
1G8 O26 C25 DOUBLE NONE 1
1G8 C25 C15 SINGLE NONE 2
1G8 C16 C15 SINGLE NONE 3
1G8 C16 C17 SINGLE NONE 4
1G8 C18 C19 SINGLE NONE 5
1G8 C18 C17 DOUBLE NONE 6
1G8 C15 N14 SINGLE BEGINDASH 7
1G8 C19 C20 DOUBLE NONE 8
1G8 C17 C22 SINGLE NONE 9
1G8 C20 C21 SINGLE NONE 10
1G8 C20 C23 SINGLE NONE 11
1G8 C22 C21 DOUBLE NONE 12
1G8 C23 N24 SINGLE NONE 13
1G8 C25 OXT SINGLE NONE 14
#
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
1G8 MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
1G8 peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
1G8 phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-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
1G8 C17 S1 1
1G8 C22 S1 1
1G8 C21 S1 1
1G8 C20 S1 1
1G8 C19 S1 1
1G8 C18 S1 1
1G8 O26 F1 1
1G8 C25 F1 1
1G8 C15 F1 1
1G8 N14 F1 1
1G8 C17 F2 1
1G8 C18 F2 1
1G8 C19 F2 1
1G8 C20 F2 1
1G8 C21 F2 1
1G8 C22 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 1G8
_pdbe_chem_comp_rdkit_properties.exactmw 194.106
_pdbe_chem_comp_rdkit_properties.amw 194.234
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.300
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_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 102.515
_pdbe_chem_comp_rdkit_properties.tpsa 89.340
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.010
_pdbe_chem_comp_rdkit_properties.CrippenMR 53.117
_pdbe_chem_comp_rdkit_properties.chi0v 6.711
_pdbe_chem_comp_rdkit_properties.chi1v 3.355
_pdbe_chem_comp_rdkit_properties.chi2v 1.174
_pdbe_chem_comp_rdkit_properties.chi3v 1.174
_pdbe_chem_comp_rdkit_properties.chi4v 0.600
_pdbe_chem_comp_rdkit_properties.chi0n 20.711
_pdbe_chem_comp_rdkit_properties.chi1n 10.053
_pdbe_chem_comp_rdkit_properties.chi2n 1.174
_pdbe_chem_comp_rdkit_properties.chi3n 1.174
_pdbe_chem_comp_rdkit_properties.chi4n 0.600
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.390
_pdbe_chem_comp_rdkit_properties.kappa1 2.400
_pdbe_chem_comp_rdkit_properties.kappa2 4.737
_pdbe_chem_comp_rdkit_properties.kappa3 2.829
_pdbe_chem_comp_rdkit_properties.Phi 0.812
#
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
1G8 UniChem PDBe 1G8
1G8 UniChem ZINC ZINC000071257747
1G8 UniChem eMolecules 26947849
1G8 UniChem 'EPA CompTox Dashboard' DTXSID10426934
1G8 UniChem SureChEMBL SCHEMBL662103
1G8 UniChem PubChem 7018015
#
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
1G8 C25 -4.041 0.276 -0.301 ETKDGv3 1
1G8 O26 -4.718 0.890 -1.168 ETKDGv3 2
1G8 C15 -2.599 -0.065 -0.572 ETKDGv3 3
1G8 C16 -1.686 0.618 0.461 ETKDGv3 4
1G8 C17 -0.231 0.393 0.141 ETKDGv3 5
1G8 C22 0.502 -0.731 0.773 ETKDGv3 6
1G8 C21 1.785 -0.959 0.467 ETKDGv3 7
1G8 C20 2.485 -0.095 -0.514 ETKDGv3 8
1G8 C23 3.942 -0.333 -0.818 ETKDGv3 9
1G8 N24 4.798 0.417 0.097 ETKDGv3 10
1G8 C19 1.824 0.930 -1.080 ETKDGv3 11
1G8 C18 0.405 1.175 -0.749 ETKDGv3 12
1G8 N14 -2.401 -1.516 -0.556 ETKDGv3 13
1G8 H32 -2.329 0.316 -1.583 ETKDGv3 14
1G8 H33 -1.895 1.711 0.478 ETKDGv3 15
1G8 H34 -1.909 0.231 1.480 ETKDGv3 16
1G8 H35 -0.000 -1.373 1.486 ETKDGv3 17
1G8 H36 2.310 -1.779 0.939 ETKDGv3 18
1G8 H37 4.173 -1.416 -0.729 ETKDGv3 19
1G8 H38 4.174 -0.036 -1.864 ETKDGv3 20
1G8 H39 4.575 0.130 1.079 ETKDGv3 21
1G8 H40 4.578 1.436 0.007 ETKDGv3 22
1G8 H42 2.320 1.587 -1.783 ETKDGv3 23
1G8 H43 -0.114 1.993 -1.235 ETKDGv3 24
1G8 H44 -2.713 -1.903 0.365 ETKDGv3 25
1G8 OXT -4.629 -0.087 0.908 ETKDGv3 26
1G8 HXT -5.598 0.136 1.102 ETKDGv3 27
1G8 H2 -3.003 -1.945 -1.296 ETKDGv3 28
#