data_ZAE
#
_chem_comp.id ZAE
_chem_comp.name N-methyl-D-phenylalanine
_chem_comp.type 'D-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C10 H13 N O2'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2009-02-06
_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 179.216
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code ?
_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 ?
_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
ZAE N N N 0 1 N N N Y Y N 34.692 5.147 11.886 1.052 1.411 0.075 N1 ZAE 1
ZAE CA CA C 0 1 N N R Y N N 34.648 5.692 10.509 1.194 -0.023 -0.209 C1 ZAE 2
ZAE C C C 0 1 N N N Y N Y 33.882 7.017 10.467 2.619 -0.446 0.041 C2 ZAE 3
ZAE O O O 0 1 N N N Y N Y 33.561 7.596 11.514 3.432 0.364 0.418 O1 ZAE 4
ZAE OXT OXT O 0 1 N Y N Y N Y 33.600 7.485 9.254 2.985 -1.723 -0.154 O2 ZAE 5
ZAE CB CB C 0 1 N N N N N N 36.067 5.886 9.998 0.259 -0.819 0.703 C3 ZAE 6
ZAE CG CG C 0 1 Y N N N N N 36.930 6.703 10.909 -1.172 -0.486 0.367 C4 ZAE 7
ZAE CD1 CD1 C 0 1 Y N N N N N 37.767 6.083 11.827 -1.849 -1.225 -0.585 C5 ZAE 8
ZAE CD2 CD2 C 0 1 Y N N N N N 36.921 8.095 10.838 -1.811 0.554 1.016 C6 ZAE 9
ZAE CE1 CE1 C 0 1 Y N N N N N 38.584 6.833 12.661 -3.161 -0.920 -0.893 C7 ZAE 10
ZAE CE2 CE2 C 0 1 Y N N N N N 37.732 8.857 11.666 -3.123 0.859 0.708 C8 ZAE 11
ZAE CZ CZ C 0 1 Y N N N N N 38.566 8.224 12.578 -3.798 0.124 -0.248 C9 ZAE 12
ZAE C10 C10 C 0 1 N N N N N N 34.707 3.678 11.832 1.431 2.219 -1.092 C10 ZAE 13
ZAE H H H 0 1 N Y N Y Y N 35.518 5.472 12.347 0.114 1.628 0.376 H1 ZAE 14
ZAE HA HA H 0 1 N N N Y N N 34.119 4.977 9.862 0.937 -0.215 -1.251 H2 ZAE 15
ZAE HXT HXT H 0 1 N Y N Y N Y 33.129 8.306 9.333 3.909 -1.946 0.020 H3 ZAE 16
ZAE HB2 HB2 H 0 1 N N N N N N 36.529 4.894 9.889 0.428 -1.886 0.555 H4 ZAE 17
ZAE HB3 HB3 H 0 1 N N N N N N 35.996 6.431 9.045 0.458 -0.560 1.743 H5 ZAE 18
ZAE HD1 HD1 H 0 1 N N N N N N 37.782 5.005 11.893 -1.352 -2.041 -1.089 H6 ZAE 19
ZAE HD2 HD2 H 0 1 N N N N N N 36.273 8.587 10.128 -1.284 1.129 1.764 H7 ZAE 20
ZAE HE1 HE1 H 0 1 N N N N N N 39.231 6.341 13.372 -3.690 -1.497 -1.638 H8 ZAE 21
ZAE HE2 HE2 H 0 1 N N N N N N 37.715 9.935 11.602 -3.622 1.672 1.215 H9 ZAE 22
ZAE HZ HZ H 0 1 N N N N N N 39.202 8.811 13.224 -4.823 0.363 -0.489 H10 ZAE 23
ZAE H11 H11 H 0 1 N N N N N N 34.711 3.349 10.782 2.469 2.016 -1.354 H11 ZAE 24
ZAE H12 H12 H 0 1 N N N N N N 35.609 3.302 12.337 0.788 1.964 -1.935 H12 ZAE 25
ZAE H13 H13 H 0 1 N N N N N N 33.812 3.284 12.336 1.316 3.276 -0.855 H13 ZAE 26
#
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
ZAE N CA SING N N 1
ZAE N C10 SING N N 2
ZAE N H SING N N 3
ZAE CA C SING N N 4
ZAE CA CB SING N N 5
ZAE CA HA SING N N 6
ZAE C O DOUB N N 7
ZAE C OXT SING N N 8
ZAE OXT HXT SING N N 9
ZAE CB CG SING N N 10
ZAE CB HB2 SING N N 11
ZAE CB HB3 SING N N 12
ZAE CG CD1 DOUB Y N 13
ZAE CG CD2 SING Y N 14
ZAE CD1 CE1 SING Y N 15
ZAE CD1 HD1 SING N N 16
ZAE CD2 CE2 DOUB Y N 17
ZAE CD2 HD2 SING N N 18
ZAE CE1 CZ DOUB Y N 19
ZAE CE1 HE1 SING N N 20
ZAE CE2 CZ SING Y N 21
ZAE CE2 HE2 SING N N 22
ZAE CZ HZ SING N N 23
ZAE C10 H11 SING N N 24
ZAE C10 H12 SING N N 25
ZAE C10 H13 SING N N 26
#
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
ZAE SMILES ACDLabs 10.04 'O=C(O)C(NC)Cc1ccccc1'
ZAE SMILES_CANONICAL CACTVS 3.341 'CN[C@H](Cc1ccccc1)C(O)=O'
ZAE SMILES CACTVS 3.341 'CN[CH](Cc1ccccc1)C(O)=O'
ZAE SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'CN[C@H](Cc1ccccc1)C(=O)O'
ZAE SMILES 'OpenEye OEToolkits' 1.5.0 'CNC(Cc1ccccc1)C(=O)O'
ZAE InChI InChI 1.03 'InChI=1S/C10H13NO2/c1-11-9(10(12)13)7-8-5-3-2-4-6-8/h2-6,9,11H,7H2,1H3,(H,12,13)/t9-/m1/s1'
ZAE InChIKey InChI 1.03 SCIFESDRCALIIM-SECBINFHSA-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
ZAE 'SYSTEMATIC NAME' ACDLabs 10.04 N-methyl-D-phenylalanine
ZAE 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2R)-2-methylamino-3-phenyl-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
ZAE 'Create component' 2009-02-06 RCSB
ZAE 'Modify descriptor' 2011-06-04 RCSB
ZAE 'Modify leaving atom flag' 2021-09-07 RCSB
ZAE 'Modify backbone' 2023-11-03 PDBE
ZAE 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id ZAE
_pdbx_chem_comp_pcm.modified_residue_id DPN
_pdbx_chem_comp_pcm.type Methylation
_pdbx_chem_comp_pcm.category 'Named protein modification'
_pdbx_chem_comp_pcm.position 'Amino-acid backbone'
_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 ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
ZAE N N 6.897 0.285 1
ZAE CA C 5.598 1.035 2
ZAE C C 5.598 2.535 3
ZAE O O 6.897 3.285 4
ZAE OXT O 4.299 3.285 5
ZAE CB C 4.299 0.285 6
ZAE CG C 4.299 -1.215 7
ZAE CD1 C 3.000 -1.965 8
ZAE CD2 C 5.598 -1.965 9
ZAE CE1 C 3.000 -3.465 10
ZAE CE2 C 5.598 -3.465 11
ZAE CZ C 4.299 -4.215 12
ZAE C10 C 8.196 1.035 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
ZAE N CA SINGLE NONE 1
ZAE N C10 SINGLE NONE 2
ZAE CA C SINGLE NONE 3
ZAE CA CB SINGLE BEGINDASH 4
ZAE C O DOUBLE NONE 5
ZAE C OXT SINGLE NONE 6
ZAE CB CG SINGLE NONE 7
ZAE CG CD1 DOUBLE NONE 8
ZAE CG CD2 SINGLE NONE 9
ZAE CD1 CE1 SINGLE NONE 10
ZAE CD2 CE2 DOUBLE NONE 11
ZAE CE1 CZ DOUBLE NONE 12
ZAE CE2 CZ SINGLE NONE 13
#
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
ZAE MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
ZAE peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
ZAE 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
ZAE CG S1 1
ZAE CD1 S1 1
ZAE CD2 S1 1
ZAE CE1 S1 1
ZAE CE2 S1 1
ZAE CZ S1 1
ZAE O F1 1
ZAE C F1 1
ZAE CA F1 1
ZAE N F1 1
ZAE CG F2 1
ZAE CD1 F2 1
ZAE CE1 F2 1
ZAE CZ F2 1
ZAE CE2 F2 1
ZAE CD2 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id ZAE
_pdbe_chem_comp_rdkit_properties.exactmw 179.095
_pdbe_chem_comp_rdkit_properties.amw 179.219
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 26
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_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 95.806
_pdbe_chem_comp_rdkit_properties.tpsa 49.330
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.847
_pdbe_chem_comp_rdkit_properties.CrippenMR 50.364
_pdbe_chem_comp_rdkit_properties.chi0v 6.264
_pdbe_chem_comp_rdkit_properties.chi1v 3.105
_pdbe_chem_comp_rdkit_properties.chi2v 1.049
_pdbe_chem_comp_rdkit_properties.chi3v 1.049
_pdbe_chem_comp_rdkit_properties.chi4v 0.556
_pdbe_chem_comp_rdkit_properties.chi0n 19.264
_pdbe_chem_comp_rdkit_properties.chi1n 9.461
_pdbe_chem_comp_rdkit_properties.chi2n 1.049
_pdbe_chem_comp_rdkit_properties.chi3n 1.049
_pdbe_chem_comp_rdkit_properties.chi4n 0.556
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.350
_pdbe_chem_comp_rdkit_properties.kappa1 2.175
_pdbe_chem_comp_rdkit_properties.kappa2 4.621
_pdbe_chem_comp_rdkit_properties.kappa3 2.874
_pdbe_chem_comp_rdkit_properties.Phi 0.773
#
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
ZAE UniChem SureChEMBL 161255
ZAE UniChem fdasrs 8O2G4R6S29
ZAE UniChem PubChem 6427037
ZAE UniChem PubChem 86306363
#
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
ZAE N -1.428 0.091 0.796 ETKDGv3 1
ZAE CA -1.251 -0.720 -0.428 ETKDGv3 2
ZAE C -2.551 -0.945 -1.162 ETKDGv3 3
ZAE O -2.907 -0.174 -2.095 ETKDGv3 4
ZAE OXT -3.387 -1.985 -0.771 ETKDGv3 5
ZAE CB -0.148 -0.152 -1.349 ETKDGv3 6
ZAE CG 1.167 -0.024 -0.623 ETKDGv3 7
ZAE CD1 1.964 -1.096 -0.454 ETKDGv3 8
ZAE CD2 1.572 1.281 -0.043 ETKDGv3 9
ZAE CE1 3.236 -0.969 0.287 ETKDGv3 10
ZAE CE2 2.724 1.391 0.630 ETKDGv3 11
ZAE CZ 3.597 0.212 0.802 ETKDGv3 12
ZAE C10 -2.115 1.371 0.579 ETKDGv3 13
ZAE H -1.995 -0.463 1.480 ETKDGv3 14
ZAE HA -0.899 -1.727 -0.109 ETKDGv3 15
ZAE HXT -4.273 -2.144 -1.237 ETKDGv3 16
ZAE HB2 -0.446 0.833 -1.766 ETKDGv3 17
ZAE HB3 -0.018 -0.830 -2.221 ETKDGv3 18
ZAE HD1 1.682 -2.062 -0.854 ETKDGv3 19
ZAE HD2 0.939 2.151 -0.163 ETKDGv3 20
ZAE HE1 3.873 -1.834 0.413 ETKDGv3 21
ZAE HE2 3.018 2.344 1.052 ETKDGv3 22
ZAE HZ 4.528 0.306 1.346 ETKDGv3 23
ZAE H11 -2.098 1.953 1.524 ETKDGv3 24
ZAE H12 -1.606 1.977 -0.195 ETKDGv3 25
ZAE H13 -3.178 1.211 0.298 ETKDGv3 26
#