data_XDT
#
_chem_comp.id XDT
_chem_comp.name O-methyl-D-allothreonine
_chem_comp.type "D-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C5 H11 N O3"
_chem_comp.mon_nstd_parent_comp_id DTH
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2013-06-06
_chem_comp.pdbx_modified_date 2018-01-16
_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 133.146
_chem_comp.one_letter_code T
_chem_comp.three_letter_code XDT
_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 3ZOI
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
XDT N N N 0 1 N N N N N N 7.408 38.107 4.672 -1.024 1.967 -0.067 N XDT 1
XDT CA CA C 0 1 N N R N N N 6.601 36.849 4.461 -0.478 0.700 0.438 CA XDT 2
XDT C C C 0 1 N N N N N N 5.322 36.964 5.293 -1.395 -0.432 0.054 C XDT 3
XDT O O O 0 1 N N N N N N 5.238 38.003 5.978 -2.181 -0.291 -0.854 O XDT 4
XDT CB CB C 0 1 N N R N N N 6.389 36.970 2.967 0.907 0.464 -0.169 CB XDT 5
XDT OG1 OG1 O 0 1 N N N N N N 5.240 37.676 2.547 1.438 -0.768 0.323 OG1 XDT 6
XDT CG2 CG2 C 0 1 N N N N N N 7.420 36.265 2.069 1.838 1.613 0.222 CG2 XDT 7
XDT CD1 CD1 C 0 1 N N N N N N 4.333 37.121 1.576 2.317 -1.428 -0.590 CD1 XDT 8
XDT OXT OXT O 0 1 N Y N N N N 4.458 36.041 5.233 -1.339 -1.596 0.719 OXT XDT 9
XDT H H H 0 1 N N N N N N 8.251 38.056 4.137 -1.110 1.948 -1.072 H XDT 10
XDT H2 H2 H 0 1 N Y N N N N 6.874 38.899 4.377 -1.910 2.178 0.368 H2 XDT 11
XDT HCA HCA H 0 1 N N N N N N 7.173 35.946 4.721 -0.395 0.748 1.524 HCA XDT 12
XDT HB HB H 0 1 N N N N N N 6.983 37.896 2.944 0.824 0.416 -1.254 HB XDT 13
XDT HG21 HG21 H 0 0 N N N N N N 7.158 36.426 1.013 1.433 2.553 -0.153 HG21 XDT 14
XDT HG22 HG22 H 0 0 N N N N N N 8.420 36.678 2.265 1.921 1.661 1.308 HG22 XDT 15
XDT HG23 HG23 H 0 0 N N N N N N 7.419 35.187 2.287 2.824 1.445 -0.210 HG23 XDT 16
XDT HD11 HD11 H 0 0 N N N N N N 3.512 37.830 1.393 1.781 -1.654 -1.512 HD11 XDT 17
XDT HD12 HD12 H 0 0 N N N N N N 4.872 36.934 0.636 3.164 -0.778 -0.813 HD12 XDT 18
XDT HD13 HD13 H 0 0 N N N N N N 3.922 36.174 1.957 2.678 -2.354 -0.143 HD13 XDT 19
XDT HXT HXT H 0 1 N Y N N N N 3.723 36.257 5.795 -1.947 -2.293 0.436 HXT XDT 20
#
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
XDT N CA SING N N 1
XDT N H SING N N 2
XDT N H2 SING N N 3
XDT CA C SING N N 4
XDT CA CB SING N N 5
XDT CA HCA SING N N 6
XDT C O DOUB N N 7
XDT C OXT SING N N 8
XDT CB OG1 SING N N 9
XDT CB CG2 SING N N 10
XDT CB HB SING N N 11
XDT OG1 CD1 SING N N 12
XDT CG2 HG21 SING N N 13
XDT CG2 HG22 SING N N 14
XDT CG2 HG23 SING N N 15
XDT CD1 HD11 SING N N 16
XDT CD1 HD12 SING N N 17
XDT CD1 HD13 SING N N 18
XDT OXT HXT SING N N 19
#
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
XDT SMILES ACDLabs 12.01 NC(C(=O)O)C(OC)C
XDT InChI InChI 1.03 InChI=1S/C5H11NO3/c1-3(9-2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t3-,4-/m1/s1
XDT InChIKey InChI 1.03 FYCWLJLGIAUCCL-QWWZWVQMSA-N
XDT SMILES_CANONICAL CACTVS 3.385 CO[C@H](C)[C@@H](N)C(O)=O
XDT SMILES CACTVS 3.385 CO[CH](C)[CH](N)C(O)=O
XDT SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 CC([C@H](C(=O)O)N)OC
XDT SMILES "OpenEye OEToolkits" 2.0.6 CC(C(C(=O)O)N)OC
#
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
XDT "SYSTEMATIC NAME" ACDLabs 12.01 O-methyl-D-allothreonine
XDT "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(2~{R})-2-azanyl-3-methoxy-butanoic 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
XDT 'Create component' 2013-06-06 EBI
XDT 'Other modification' 2013-06-12 EBI
XDT 'Modify descriptor' 2014-09-05 RCSB
XDT 'Modify name' 2018-01-16 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
XDT N N 6.404 -1.643 1
XDT CA C 6.404 -0.142 2
XDT C C 5.104 0.608 3
XDT O O 3.805 -0.142 4
XDT CB C 7.702 0.608 5
XDT OG1 O 9.002 -0.142 6
XDT CG2 C 7.702 2.107 7
XDT CD1 C 10.301 0.608 8
XDT OXT O 5.104 2.107 9
#
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
XDT CA N SINGLE BEGINWEDGE 1
XDT CA C SINGLE NONE 2
XDT CA CB SINGLE NONE 3
XDT C O DOUBLE NONE 4
XDT C OXT SINGLE NONE 5
XDT CB OG1 SINGLE NONE 6
XDT CB CG2 SINGLE BEGINWEDGE 7
XDT OG1 CD1 SINGLE NONE 8
#
_pdbe_chem_comp_substructure.comp_id XDT
_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
XDT O F1 1
XDT C F1 1
XDT CA F1 1
XDT N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id XDT
_pdbe_chem_comp_rdkit_properties.exactmw 133.074
_pdbe_chem_comp_rdkit_properties.amw 133.147
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 9
_pdbe_chem_comp_rdkit_properties.NumAtoms 20
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.800
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 69.266
_pdbe_chem_comp_rdkit_properties.tpsa 72.550
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.567
_pdbe_chem_comp_rdkit_properties.CrippenMR 32.082
_pdbe_chem_comp_rdkit_properties.chi0v 4.172
_pdbe_chem_comp_rdkit_properties.chi1v 1.790
_pdbe_chem_comp_rdkit_properties.chi2v 0.510
_pdbe_chem_comp_rdkit_properties.chi3v 0.510
_pdbe_chem_comp_rdkit_properties.chi4v 0.141
_pdbe_chem_comp_rdkit_properties.chi0n 15.172
_pdbe_chem_comp_rdkit_properties.chi1n 7.093
_pdbe_chem_comp_rdkit_properties.chi2n 0.510
_pdbe_chem_comp_rdkit_properties.chi3n 0.510
_pdbe_chem_comp_rdkit_properties.chi4n 0.141
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.610
_pdbe_chem_comp_rdkit_properties.kappa1 1.355
_pdbe_chem_comp_rdkit_properties.kappa2 3.422
_pdbe_chem_comp_rdkit_properties.kappa3 2.435
_pdbe_chem_comp_rdkit_properties.Phi 0.515
#
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
XDT UniChem PDBe XDT
XDT UniChem ZINC ZINC000001700278
XDT UniChem ChemicalBook CB51011954
XDT UniChem SureChEMBL SCHEMBL6186621
XDT UniChem PubChem 45789850
XDT UniChem 'EPA CompTox Dashboard' DTXSID70672071
#
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
XDT N -1.226 -0.474 -1.536 ETKDGv3 1
XDT CA -0.699 0.380 -0.466 ETKDGv3 2
XDT C -1.766 0.765 0.530 ETKDGv3 3
XDT O -2.718 -0.019 0.793 ETKDGv3 4
XDT CB 0.532 -0.265 0.221 ETKDGv3 5
XDT OG1 1.532 -0.526 -0.752 ETKDGv3 6
XDT CG2 0.201 -1.585 0.928 ETKDGv3 7
XDT CD1 2.517 0.484 -0.746 ETKDGv3 8
XDT OXT -1.671 1.981 1.199 ETKDGv3 9
XDT H -1.945 0.068 -2.069 ETKDGv3 10
XDT H2 -1.711 -1.306 -1.131 ETKDGv3 11
XDT HCA -0.349 1.326 -0.937 ETKDGv3 12
XDT HB 0.882 0.431 1.024 ETKDGv3 13
XDT HG21 -0.123 -2.358 0.200 ETKDGv3 14
XDT HG22 1.108 -1.962 1.445 ETKDGv3 15
XDT HG23 -0.591 -1.441 1.692 ETKDGv3 16
XDT HD11 3.092 0.466 0.207 ETKDGv3 17
XDT HD12 3.229 0.290 -1.573 ETKDGv3 18
XDT HD13 2.071 1.490 -0.911 ETKDGv3 19
XDT HXT -2.365 2.254 1.884 ETKDGv3 20
#