data_3YM
#
_chem_comp.id 3YM
_chem_comp.name 3-methoxy-L-tyrosine
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C10 H13 N O4'
_chem_comp.mon_nstd_parent_comp_id TYR
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2012-10-29
_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 211.215
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 3YM
_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 4HPW
_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
3YM CAN CAN C 0 1 N N N N N N 17.416 -3.942 32.195 -2.597 2.795 -0.169 CAN 3YM 1
3YM OAM OAM O 0 1 N N N N N N 17.899 -2.943 31.308 -3.140 1.474 -0.227 OAM 3YM 2
3YM CAJ CAJ C 0 1 Y N N N N N 16.997 -2.784 30.299 -2.287 0.445 0.020 CAJ 3YM 3
3YM CD2 CD2 C 0 1 Y N N N N N 15.978 -1.843 30.418 -0.956 0.700 0.312 CD2 3YM 4
3YM CAK CAK C 0 1 Y N N N N N 17.087 -3.561 29.146 -2.749 -0.867 -0.014 CAK 3YM 5
3YM OAL OAL O 0 1 N N N N N N 18.074 -4.489 29.018 -4.053 -1.123 -0.301 OAL 3YM 6
3YM CAI CAI C 0 1 Y N N N N N 16.165 -3.389 28.120 -1.877 -1.913 0.244 CAI 3YM 7
3YM CD1 CD1 C 0 1 Y N N N N N 15.148 -2.447 28.242 -0.551 -1.651 0.535 CD1 3YM 8
3YM CG CG C 0 1 Y N N N N N 15.052 -1.668 29.388 -0.090 -0.348 0.563 CG 3YM 9
3YM CB CB C 0 1 N N N N N N 13.933 -0.627 29.552 1.356 -0.068 0.881 CB 3YM 10
3YM CA CA C 0 1 N N S Y N N 14.226 0.718 28.877 2.170 -0.058 -0.415 CA 3YM 11
3YM C C C 0 1 N N N Y N Y 13.067 1.668 29.192 3.591 0.342 -0.113 C 3YM 12
3YM O O O 0 1 N N N Y N Y 12.382 2.173 28.303 4.449 -0.503 -0.021 O 3YM 13
3YM N N N 0 1 N N N Y Y N 15.451 1.308 29.419 2.155 -1.399 -1.014 N 3YM 14
3YM H1 H1 H 0 1 N N N N N N 18.134 -4.082 33.016 -2.196 2.980 0.828 H1 3YM 15
3YM H11 H11 H 0 1 N N N N N N 16.445 -3.628 32.607 -1.799 2.893 -0.905 H2 3YM 16
3YM H3 H3 H 0 1 N N N N N N 17.294 -4.889 31.649 -3.381 3.520 -0.385 H3 3YM 17
3YM H4 H4 H 0 1 N N N N N N 15.903 -1.244 31.314 -0.596 1.718 0.344 H4 3YM 18
3YM H5 H5 H 0 1 N N N N N N 18.617 -4.484 29.798 -4.232 -1.244 -1.243 H5 3YM 19
3YM H6 H6 H 0 1 N N N N N N 16.238 -3.989 27.225 -2.234 -2.932 0.223 H6 3YM 20
3YM H7 H7 H 0 1 N N N N N N 14.432 -2.321 27.444 0.128 -2.467 0.736 H7 3YM 21
3YM H8 H8 H 0 1 N N N N N N 13.782 -0.449 30.627 1.440 0.902 1.370 H8 3YM 22
3YM H9 H9 H 0 1 N N N N N N 13.011 -1.039 29.116 1.739 -0.844 1.544 H9 3YM 23
3YM HA H10 H 0 1 N N N Y N N 14.309 0.578 27.789 1.732 0.656 -1.113 H10 3YM 24
3YM H H H 0 1 N N N Y Y N 16.225 0.705 29.226 2.556 -2.079 -0.386 H12 3YM 25
3YM H2 H2 H 0 1 N Y N Y Y N 15.608 2.199 28.993 1.220 -1.664 -1.285 H13 3YM 26
3YM OXT OXT O 0 1 N Y N Y N Y ? ? ? 3.902 1.637 0.054 OXT 3YM 27
3YM HXT HXT H 0 1 N Y N Y N Y ? ? ? 4.827 1.845 0.246 H11 3YM 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
3YM CAI CD1 DOUB Y N 1
3YM CAI CAK SING Y N 2
3YM CD1 CG SING Y N 3
3YM O C DOUB N N 4
3YM CA C SING N N 5
3YM CA N SING N N 6
3YM CA CB SING N N 7
3YM OAL CAK SING N N 8
3YM CAK CAJ DOUB Y N 9
3YM CG CB SING N N 10
3YM CG CD2 DOUB Y N 11
3YM CAJ CD2 SING Y N 12
3YM CAJ OAM SING N N 13
3YM OAM CAN SING N N 14
3YM CAN H1 SING N N 15
3YM CAN H11 SING N N 16
3YM CAN H3 SING N N 17
3YM CD2 H4 SING N N 18
3YM OAL H5 SING N N 19
3YM CAI H6 SING N N 20
3YM CD1 H7 SING N N 21
3YM CB H8 SING N N 22
3YM CB H9 SING N N 23
3YM CA HA SING N N 24
3YM N H SING N N 25
3YM N H2 SING N N 26
3YM C OXT SING N N 27
3YM OXT HXT 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
3YM SMILES ACDLabs 12.01 'O=C(O)C(N)Cc1cc(OC)c(O)cc1'
3YM InChI InChI 1.03 'InChI=1S/C10H13NO4/c1-15-9-5-6(2-3-8(9)12)4-7(11)10(13)14/h2-3,5,7,12H,4,11H2,1H3,(H,13,14)/t7-/m0/s1'
3YM InChIKey InChI 1.03 PFDUUKDQEHURQC-ZETCQYMHSA-N
3YM SMILES_CANONICAL CACTVS 3.370 'COc1cc(C[C@H](N)C(O)=O)ccc1O'
3YM SMILES CACTVS 3.370 'COc1cc(C[CH](N)C(O)=O)ccc1O'
3YM SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.6 'COc1cc(ccc1O)C[C@@H](C(=O)O)N'
3YM SMILES 'OpenEye OEToolkits' 1.7.6 'COc1cc(ccc1O)CC(C(=O)O)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
3YM 'SYSTEMATIC NAME' ACDLabs 12.01 3-methoxy-L-tyrosine
3YM 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.7.6 '(2S)-2-azanyl-3-(3-methoxy-4-oxidanyl-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
3YM 'Create component' 2012-10-29 RCSB
3YM 'Initial release' 2013-10-30 RCSB
3YM 'Modify backbone' 2023-11-03 PDBE
3YM 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id 3YM
_pdbx_chem_comp_pcm.modified_residue_id TYR
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Non-standard residue'
_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 ?
_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
3YM CAN C 3.000 -2.107 1
3YM OAM O 4.299 -2.857 2
3YM CAJ C 5.598 -2.107 3
3YM CD2 C 5.598 -0.608 4
3YM CAK C 6.897 -2.857 5
3YM OAL O 6.897 -4.357 6
3YM CAI C 8.196 -2.107 7
3YM CD1 C 8.196 -0.608 8
3YM CG C 6.897 0.142 9
3YM CB C 6.897 1.643 10
3YM CA C 8.196 2.393 11
3YM C C 9.495 1.643 12
3YM O O 10.794 2.393 13
3YM N N 8.196 3.893 14
3YM OXT O 9.495 0.142 15
#
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
3YM CAI CD1 DOUBLE NONE 1
3YM CAI CAK SINGLE NONE 2
3YM CD1 CG SINGLE NONE 3
3YM O C DOUBLE NONE 4
3YM CA C SINGLE NONE 5
3YM CA N SINGLE BEGINDASH 6
3YM CA CB SINGLE NONE 7
3YM OAL CAK SINGLE NONE 8
3YM CAK CAJ DOUBLE NONE 9
3YM CG CB SINGLE NONE 10
3YM CG CD2 DOUBLE NONE 11
3YM CAJ CD2 SINGLE NONE 12
3YM CAJ OAM SINGLE NONE 13
3YM OAM CAN SINGLE NONE 14
3YM C OXT SINGLE NONE 15
#
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
3YM MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
3YM peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
3YM 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
3YM CAJ S1 1
3YM CD2 S1 1
3YM CAK S1 1
3YM CAI S1 1
3YM CD1 S1 1
3YM CG S1 1
3YM O F1 1
3YM C F1 1
3YM CA F1 1
3YM N F1 1
3YM CAJ F2 1
3YM CAK F2 1
3YM CAI F2 1
3YM CD1 F2 1
3YM CG F2 1
3YM CD2 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 3YM
_pdbe_chem_comp_rdkit_properties.exactmw 211.084
_pdbe_chem_comp_rdkit_properties.amw 211.217
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_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 105.649
_pdbe_chem_comp_rdkit_properties.tpsa 92.780
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.624
_pdbe_chem_comp_rdkit_properties.CrippenMR 52.488
_pdbe_chem_comp_rdkit_properties.chi0v 7.080
_pdbe_chem_comp_rdkit_properties.chi1v 3.494
_pdbe_chem_comp_rdkit_properties.chi2v 1.285
_pdbe_chem_comp_rdkit_properties.chi3v 1.285
_pdbe_chem_comp_rdkit_properties.chi4v 0.681
_pdbe_chem_comp_rdkit_properties.chi0n 20.080
_pdbe_chem_comp_rdkit_properties.chi1n 9.705
_pdbe_chem_comp_rdkit_properties.chi2n 1.285
_pdbe_chem_comp_rdkit_properties.chi3n 1.285
_pdbe_chem_comp_rdkit_properties.chi4n 0.681
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.750
_pdbe_chem_comp_rdkit_properties.kappa1 2.886
_pdbe_chem_comp_rdkit_properties.kappa2 4.655
_pdbe_chem_comp_rdkit_properties.kappa3 2.850
_pdbe_chem_comp_rdkit_properties.Phi 0.895
#
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
3YM UniChem ChEBI 133668
3YM UniChem ChEBI 82913
3YM UniChem ZINC ZINC000000085742
3YM UniChem eMolecules 591924
3YM UniChem fdasrs V3O7J20DWN
3YM UniChem HMDB HMDB0060747
3YM UniChem 'PubChem TPHARMA' 15121188
3YM UniChem MetaboLights MTBLC133668
3YM UniChem MetaboLights MTBLC82913
3YM UniChem BRENDA 120734
3YM UniChem BRENDA 158400
3YM UniChem BRENDA 207386
3YM UniChem BRENDA 228969
3YM UniChem BRENDA 43336
3YM UniChem BRENDA 6273
3YM UniChem ChemicalBook CB9183320
3YM UniChem MedChemExpress HY-113468A
3YM UniChem 'Probes And Drugs' PD053041
3YM UniChem Nikkaji J5.475E
3YM UniChem SureChEMBL SCHEMBL180104
3YM UniChem PubChem 25273143
3YM UniChem PubChem 9307
3YM UniChem ACTor 300-48-1
#
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
3YM CAN -2.977 1.726 1.343 ETKDGv3 1
3YM OAM -3.052 0.395 0.846 ETKDGv3 2
3YM CAJ -2.033 -0.226 0.108 ETKDGv3 3
3YM CD2 -0.766 0.480 -0.231 ETKDGv3 4
3YM CAK -2.210 -1.493 -0.301 ETKDGv3 5
3YM OAL -3.391 -2.164 0.008 ETKDGv3 6
3YM CAI -1.152 -2.177 -1.079 ETKDGv3 7
3YM CD1 -0.016 -1.540 -1.379 ETKDGv3 8
3YM CG 0.195 -0.141 -0.939 ETKDGv3 9
3YM CB 1.494 0.560 -1.258 ETKDGv3 10
3YM CA 2.588 0.313 -0.198 ETKDGv3 11
3YM C 2.200 0.909 1.129 ETKDGv3 12
3YM O 1.584 0.218 1.986 ETKDGv3 13
3YM N 2.871 -1.118 -0.060 ETKDGv3 14
3YM H1 -2.868 2.442 0.501 ETKDGv3 15
3YM H11 -2.120 1.826 2.042 ETKDGv3 16
3YM H3 -3.912 1.962 1.891 ETKDGv3 17
3YM H4 -0.611 1.499 0.100 ETKDGv3 18
3YM H5 -3.545 -3.120 -0.289 ETKDGv3 19
3YM H6 -1.298 -3.199 -1.405 ETKDGv3 20
3YM H7 0.750 -2.052 -1.947 ETKDGv3 21
3YM H8 1.323 1.654 -1.364 ETKDGv3 22
3YM H9 1.863 0.208 -2.246 ETKDGv3 23
3YM HA 3.514 0.827 -0.542 ETKDGv3 24
3YM H 3.669 -1.232 0.608 ETKDGv3 25
3YM H2 3.214 -1.475 -0.981 ETKDGv3 26
3YM OXT 2.479 2.246 1.390 ETKDGv3 27
3YM HXT 2.207 2.672 2.268 ETKDGv3 28
#