data_TPO
#
_chem_comp.id TPO
_chem_comp.name PHOSPHOTHREONINE
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C4 H10 N O6 P"
_chem_comp.mon_nstd_parent_comp_id THR
_chem_comp.pdbx_synonyms PHOSPHONOTHREONINE
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2023-11-03
_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 199.099
_chem_comp.one_letter_code T
_chem_comp.three_letter_code TPO
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1FMO
_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
TPO N N N 0 1 N N N Y Y N 21.891 2.133 -14.748 1.153 -1.040 2.377 N TPO 1
TPO CA CA C 0 1 N N S Y N N 22.318 2.994 -13.673 0.572 0.199 1.844 CA TPO 2
TPO CB CB C 0 1 N N R N N N 21.313 4.075 -13.361 1.111 0.449 0.434 CB TPO 3
TPO CG2 CG2 C 0 1 N N N N N N 21.837 5.045 -12.302 2.634 0.580 0.485 CG2 TPO 4
TPO OG1 OG1 O 0 1 N N N N N N 20.898 4.716 -14.523 0.755 -0.645 -0.412 OG1 TPO 5
TPO P P P 0 1 N N N N N N 19.424 4.424 -14.993 -0.142 -0.039 -1.603 P TPO 6
TPO O1P O1P O 0 1 N N N N N N 19.358 5.014 -16.321 0.644 0.968 -2.350 O1P TPO 7
TPO O2P O2P O 0 1 N N N N N N 19.243 2.986 -14.834 -0.580 -1.224 -2.601 O2P TPO 8
TPO O3P O3P O 0 1 N N N N N N 18.506 5.082 -14.021 -1.456 0.656 -0.985 O3P TPO 9
TPO C C C 0 1 N N N Y N Y 22.539 2.278 -12.384 -0.927 0.070 1.794 C TPO 10
TPO O O O 0 1 N N N Y N Y 21.778 1.390 -12.005 -1.435 -1.012 1.626 O TPO 11
TPO OXT OXT O 0 1 N Y N Y N Y 23.582 2.721 -11.720 -1.700 1.159 1.935 OXT TPO 12
TPO H H H 0 1 N N N Y Y N 22.570 1.402 -14.958 2.154 -0.949 2.296 H TPO 13
TPO H2 2HN H 0 1 N Y N Y Y N 21.663 2.673 -15.582 0.877 -1.782 1.751 H2 TPO 14
TPO HA HA H 0 1 N N N Y N N 23.275 3.418 -14.056 0.844 1.034 2.490 HA TPO 15
TPO HB HB H 0 1 N N N N N N 20.410 3.593 -12.916 0.680 1.369 0.039 HB TPO 16
TPO HG21 1HG2 H 0 0 N N N N N N 21.094 5.844 -12.071 3.065 -0.339 0.881 HG21 TPO 17
TPO HG22 2HG2 H 0 0 N N N N N N 22.154 4.506 -11.378 3.018 0.758 -0.518 HG22 TPO 18
TPO HG23 3HG2 H 0 0 N N N N N N 22.821 5.477 -12.598 2.906 1.415 1.131 HG23 TPO 19
TPO HOP2 2HOP H 0 0 N N N N N N 18.353 2.809 -15.117 -1.114 -0.819 -3.298 HOP2 TPO 20
TPO HOP3 3HOP H 0 0 N N N N N N 17.616 4.905 -14.304 -1.938 -0.033 -0.509 HOP3 TPO 21
TPO HXT HXT H 0 1 N Y N Y N Y 23.722 2.264 -10.898 -2.662 1.076 1.902 HXT TPO 22
#
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
TPO N CA SING N N 1
TPO N H SING N N 2
TPO N H2 SING N N 3
TPO CA CB SING N N 4
TPO CA C SING N N 5
TPO CA HA SING N N 6
TPO CB CG2 SING N N 7
TPO CB OG1 SING N N 8
TPO CB HB SING N N 9
TPO CG2 HG21 SING N N 10
TPO CG2 HG22 SING N N 11
TPO CG2 HG23 SING N N 12
TPO OG1 P SING N N 13
TPO P O1P DOUB N N 14
TPO P O2P SING N N 15
TPO P O3P SING N N 16
TPO O2P HOP2 SING N N 17
TPO O3P HOP3 SING N N 18
TPO C O DOUB N N 19
TPO C OXT SING N N 20
TPO OXT HXT SING N N 21
#
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
TPO SMILES ACDLabs 10.04 O=P(O)(O)OC(C(N)C(=O)O)C
TPO SMILES_CANONICAL CACTVS 3.341 C[C@@H](O[P](O)(O)=O)[C@H](N)C(O)=O
TPO SMILES CACTVS 3.341 C[CH](O[P](O)(O)=O)[CH](N)C(O)=O
TPO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[C@H]([C@@H](C(=O)O)N)OP(=O)(O)O
TPO SMILES "OpenEye OEToolkits" 1.5.0 CC(C(C(=O)O)N)OP(=O)(O)O
TPO InChI InChI 1.03 InChI=1S/C4H10NO6P/c1-2(3(5)4(6)7)11-12(8,9)10/h2-3H,5H2,1H3,(H,6,7)(H2,8,9,10)/t2-,3+/m1/s1
TPO InChIKey InChI 1.03 USRGIUJOYOXOQJ-GBXIJSLDSA-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
TPO "SYSTEMATIC NAME" ACDLabs 10.04 O-phosphono-L-threonine
TPO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S,3R)-2-amino-3-phosphonooxy-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
TPO 'Create component' 1999-07-08 EBI
TPO 'Modify descriptor' 2011-06-04 RCSB
TPO 'Modify synonyms' 2020-06-05 PDBE
TPO 'Modify backbone' 2023-11-03 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id TPO
_pdbx_chem_comp_synonyms.name PHOSPHONOTHREONINE
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id TPO
_pdbe_chem_comp_synonyms.name PHOSPHONOTHREONINE
_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
TPO N N 9.002 1.643 1
TPO CA C 9.002 0.142 2
TPO CB C 7.702 -0.608 3
TPO CG2 C 7.702 -2.107 4
TPO OG1 O 6.404 0.142 5
TPO P P 5.104 -0.608 6
TPO O1P O 3.805 -1.357 7
TPO O2P O 4.354 0.692 8
TPO O3P O 5.854 -1.907 9
TPO C C 10.301 -0.608 10
TPO O O 11.600 0.142 11
TPO OXT O 10.301 -2.107 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
TPO CA N SINGLE BEGINDASH 1
TPO CA CB SINGLE NONE 2
TPO CA C SINGLE NONE 3
TPO CB CG2 SINGLE BEGINWEDGE 4
TPO CB OG1 SINGLE NONE 5
TPO OG1 P SINGLE NONE 6
TPO P O1P DOUBLE NONE 7
TPO P O2P SINGLE NONE 8
TPO P O3P SINGLE NONE 9
TPO C O DOUBLE NONE 10
TPO C OXT SINGLE NONE 11
#
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
TPO peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
TPO phosphate F2 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-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
TPO O F1 1
TPO C F1 1
TPO CA F1 1
TPO N F1 1
TPO OG1 F2 1
TPO P F2 1
TPO O1P F2 1
TPO O2P F2 1
TPO O3P F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id TPO
_pdbe_chem_comp_rdkit_properties.exactmw 199.025
_pdbe_chem_comp_rdkit_properties.amw 199.099
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.750
_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 82.807
_pdbe_chem_comp_rdkit_properties.tpsa 130.080
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.104
_pdbe_chem_comp_rdkit_properties.CrippenMR 38.202
_pdbe_chem_comp_rdkit_properties.chi0v 6.238
_pdbe_chem_comp_rdkit_properties.chi1v 3.777
_pdbe_chem_comp_rdkit_properties.chi2v 1.018
_pdbe_chem_comp_rdkit_properties.chi3v 1.018
_pdbe_chem_comp_rdkit_properties.chi4v 0.558
_pdbe_chem_comp_rdkit_properties.chi0n 15.344
_pdbe_chem_comp_rdkit_properties.chi1n 6.935
_pdbe_chem_comp_rdkit_properties.chi2n 0.612
_pdbe_chem_comp_rdkit_properties.chi3n 0.612
_pdbe_chem_comp_rdkit_properties.chi4n 0.248
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.460
_pdbe_chem_comp_rdkit_properties.kappa1 3.039
_pdbe_chem_comp_rdkit_properties.kappa2 3.972
_pdbe_chem_comp_rdkit_properties.kappa3 4.425
_pdbe_chem_comp_rdkit_properties.Phi 1.006
#
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
TPO UniChem PDBe TPO
TPO UniChem 'KEGG LIGAND' C12147
TPO UniChem ChEBI 37525
TPO UniChem ZINC ZINC000001532464
TPO UniChem eMolecules 530922
TPO UniChem fdasrs 3L4WX7B1EI
TPO UniChem HMDB HMDB0011185
TPO UniChem 'PubChem TPHARMA' 24710793
TPO UniChem NMRShiftDB 60028223
TPO UniChem MetaboLights MTBLC37525
TPO UniChem BRENDA 119318
TPO UniChem BRENDA 130034
TPO UniChem BRENDA 18453
TPO UniChem BRENDA 30348
TPO UniChem BRENDA 33187
TPO UniChem BRENDA 4927
TPO UniChem BRENDA 94765
TPO UniChem ChemicalBook CB6336732
TPO UniChem 'Probes And Drugs' PD163941
TPO UniChem Nikkaji J203.332A
TPO UniChem SureChEMBL SCHEMBL42675
TPO UniChem PubChem 139055008
TPO UniChem PubChem 3246323
#
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
TPO N -2.288 0.378 -0.808 ETKDGv3 1
TPO CA -1.543 -0.409 0.181 ETKDGv3 2
TPO CB -0.098 -0.684 -0.296 ETKDGv3 3
TPO CG2 -0.101 -1.522 -1.580 ETKDGv3 4
TPO OG1 0.560 0.545 -0.548 ETKDGv3 5
TPO P 2.118 0.539 0.152 ETKDGv3 6
TPO O1P 2.002 0.520 1.660 ETKDGv3 7
TPO O2P 2.988 -0.817 -0.367 ETKDGv3 8
TPO O3P 2.941 1.939 -0.324 ETKDGv3 9
TPO C -1.536 0.280 1.522 ETKDGv3 10
TPO O -1.833 -0.366 2.562 ETKDGv3 11
TPO OXT -1.169 1.619 1.622 ETKDGv3 12
TPO H -1.885 1.341 -0.875 ETKDGv3 13
TPO H2 -3.276 0.476 -0.479 ETKDGv3 14
TPO HA -2.059 -1.389 0.300 ETKDGv3 15
TPO HB 0.384 -1.305 0.498 ETKDGv3 16
TPO HG21 0.940 -1.761 -1.878 ETKDGv3 17
TPO HG22 -0.644 -2.478 -1.418 ETKDGv3 18
TPO HG23 -0.585 -0.966 -2.411 ETKDGv3 19
TPO HOP2 3.888 -0.708 0.032 ETKDGv3 20
TPO HOP3 2.341 2.684 -0.067 ETKDGv3 21
TPO HXT -1.146 2.086 2.521 ETKDGv3 22
#