data_J8T
#
_chem_comp.id J8T
_chem_comp.name "[(3~{R})-4-azanyl-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H14 N O6 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-02-11
_chem_comp.pdbx_modified_date 2020-03-13
_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 227.152
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code J8T
_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 6QL6
_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
J8T C4 C1 C 0 1 N N N N N N 152.358 231.664 154.885 -0.095 -0.100 0.232 C4 J8T 1
J8T C5 C2 C 0 1 N N N N N N 153.319 232.021 156.047 -1.202 -0.966 -0.373 C5 J8T 2
J8T C6 C3 C 0 1 N N N N N N 153.477 230.766 156.934 -1.221 -0.782 -1.892 C6 J8T 3
J8T C7 C4 C 0 1 N N N N N N 154.707 232.343 155.449 -0.939 -2.436 -0.040 C7 J8T 4
J8T O3 O1 O 0 1 N N N N N N 151.995 233.619 151.444 2.548 1.743 -0.381 O3 J8T 5
J8T O4 O2 O 0 1 N N N N N N 150.229 232.474 152.966 2.717 0.155 1.573 O4 J8T 6
J8T O5 O3 O 0 1 N N N N N N 152.584 232.573 153.732 1.167 -0.493 -0.311 O5 J8T 7
J8T P1 P1 P 0 1 N N N N N N 151.631 232.528 152.424 2.556 0.208 0.103 P1 J8T 8
J8T O6 O4 O 0 1 N N N N N N 151.482 232.974 157.361 -2.581 -0.835 1.607 O6 J8T 9
J8T O7 O5 O 0 1 N N N N N N 154.310 234.741 158.062 -2.733 1.690 0.945 O7 J8T 10
J8T C8 C5 C 0 1 N N R N N N 152.815 233.234 156.904 -2.553 -0.545 0.208 C8 J8T 11
J8T C9 C6 C 0 1 N N N N N N 153.640 233.698 158.122 -2.752 0.934 -0.003 C9 J8T 12
J8T N2 N1 N 0 1 N N N N N N 153.570 232.957 159.225 -2.952 1.416 -1.245 N2 J8T 13
J8T H1 H1 H 0 1 N N N N N N 151.318 231.766 155.229 -0.282 0.947 -0.005 H1 J8T 14
J8T H2 H2 H 0 1 N N N N N N 152.540 230.626 154.570 -0.081 -0.231 1.314 H2 J8T 15
J8T H3 H3 H 0 1 N N N N N N 154.156 230.990 157.770 -0.305 -1.191 -2.318 H3 J8T 16
J8T H4 H4 H 0 1 N N N N N N 152.494 230.471 157.329 -2.081 -1.305 -2.310 H4 J8T 17
J8T H5 H5 H 0 1 N N N N N N 153.893 229.943 156.334 -1.290 0.279 -2.129 H5 J8T 18
J8T H6 H6 H 0 1 N N N N N N 155.405 232.600 156.259 -1.005 -2.582 1.038 H6 J8T 19
J8T H7 H7 H 0 1 N N N N N N 155.084 231.465 154.904 -1.681 -3.060 -0.538 H7 J8T 20
J8T H8 H8 H 0 1 N N N N N N 154.620 233.194 154.757 0.058 -2.713 -0.383 H8 J8T 21
J8T H9 H9 H 0 1 N N N N N N 151.237 234.169 151.286 2.446 1.854 -1.336 H9 J8T 22
J8T H11 H11 H 0 1 N N N N N N 151.176 233.708 157.880 -1.897 -0.379 2.117 H11 J8T 23
J8T H12 H12 H 0 1 N N N N N N 152.769 234.092 156.217 -3.351 -1.094 -0.292 H12 J8T 24
J8T H13 H13 H 0 1 N N N N N N 154.069 233.234 160.046 -3.009 2.374 -1.390 H13 J8T 25
J8T H14 H14 H 0 1 N N N N N N 153.019 232.123 159.233 -3.040 0.806 -1.994 H14 J8T 26
J8T O1 O6 O 0 1 N Y N N N N 152.015 231.092 151.797 3.780 -0.569 -0.599 O1 J8T 27
J8T H10 H10 H 0 1 N N N N N N 151.281 230.497 151.894 4.649 -0.201 -0.393 H10 J8T 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
J8T O3 P1 SING N N 1
J8T P1 O4 DOUB N N 2
J8T P1 O5 SING N N 3
J8T O5 C4 SING N N 4
J8T C4 C5 SING N N 5
J8T C7 C5 SING N N 6
J8T C5 C8 SING N N 7
J8T C5 C6 SING N N 8
J8T C8 O6 SING N N 9
J8T C8 C9 SING N N 10
J8T O7 C9 DOUB N N 11
J8T C9 N2 SING N N 12
J8T C4 H1 SING N N 13
J8T C4 H2 SING N N 14
J8T C6 H3 SING N N 15
J8T C6 H4 SING N N 16
J8T C6 H5 SING N N 17
J8T C7 H6 SING N N 18
J8T C7 H7 SING N N 19
J8T C7 H8 SING N N 20
J8T O3 H9 SING N N 21
J8T O6 H11 SING N N 22
J8T C8 H12 SING N N 23
J8T N2 H13 SING N N 24
J8T N2 H14 SING N N 25
J8T P1 O1 SING N N 26
J8T O1 H10 SING N N 27
#
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
J8T InChI InChI 1.03 InChI=1S/C6H14NO6P/c1-6(2,4(8)5(7)9)3-13-14(10,11)12/h4,8H,3H2,1-2H3,(H2,7,9)(H2,10,11,12)/t4-/m0/s1
J8T InChIKey InChI 1.03 UUMQHJQLVJSTLV-BYPYZUCNSA-N
J8T SMILES_CANONICAL CACTVS 3.385 CC(C)(CO[P](O)(O)=O)[C@@H](O)C(N)=O
J8T SMILES CACTVS 3.385 CC(C)(CO[P](O)(O)=O)[CH](O)C(N)=O
J8T SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CC(C)(COP(=O)(O)O)[C@H](C(=O)N)O
J8T SMILES "OpenEye OEToolkits" 2.0.7 CC(C)(COP(=O)(O)O)C(C(=O)N)O
#
_pdbx_chem_comp_identifier.comp_id J8T
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier
"[(3~{R})-4-azanyl-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
J8T 'Create component' 2019-02-11 RCSB
J8T 'Initial release' 2020-03-18 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
J8T C4 C 7.702 -1.083 1
J8T C5 C 9.002 -0.333 2
J8T C6 C 9.752 -1.632 3
J8T C7 C 8.252 0.966 4
J8T O3 O 3.805 -1.833 5
J8T O4 O 4.354 0.216 6
J8T O5 O 6.404 -0.333 7
J8T P1 P 5.104 -1.083 8
J8T O6 O 10.301 1.917 9
J8T O7 O 11.600 -1.833 10
J8T C8 C 10.301 0.417 11
J8T C9 C 11.600 -0.333 12
J8T N2 N 12.899 0.417 13
J8T O1 O 5.854 -2.382 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
J8T O3 P1 SINGLE NONE 1
J8T P1 O4 DOUBLE NONE 2
J8T P1 O5 SINGLE NONE 3
J8T O5 C4 SINGLE NONE 4
J8T C4 C5 SINGLE NONE 5
J8T C7 C5 SINGLE NONE 6
J8T C5 C8 SINGLE NONE 7
J8T C5 C6 SINGLE NONE 8
J8T C8 O6 SINGLE BEGINWEDGE 9
J8T C8 C9 SINGLE NONE 10
J8T O7 C9 DOUBLE NONE 11
J8T C9 N2 SINGLE NONE 12
J8T P1 O1 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
J8T amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
J8T 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
J8T N2 F1 1
J8T C9 F1 1
J8T O7 F1 1
J8T C8 F1 1
J8T O3 F2 1
J8T P1 F2 1
J8T O4 F2 1
J8T O5 F2 1
J8T H1 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id J8T
_pdbe_chem_comp_rdkit_properties.exactmw 227.056
_pdbe_chem_comp_rdkit_properties.amw 227.153
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 10
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.833
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 101.157
_pdbe_chem_comp_rdkit_properties.tpsa 130.080
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.032
_pdbe_chem_comp_rdkit_properties.CrippenMR 46.978
_pdbe_chem_comp_rdkit_properties.chi0v 7.238
_pdbe_chem_comp_rdkit_properties.chi1v 4.277
_pdbe_chem_comp_rdkit_properties.chi2v 1.160
_pdbe_chem_comp_rdkit_properties.chi3v 1.160
_pdbe_chem_comp_rdkit_properties.chi4v 0.580
_pdbe_chem_comp_rdkit_properties.chi0n 20.344
_pdbe_chem_comp_rdkit_properties.chi1n 9.435
_pdbe_chem_comp_rdkit_properties.chi2n 0.845
_pdbe_chem_comp_rdkit_properties.chi3n 0.845
_pdbe_chem_comp_rdkit_properties.chi4n 0.331
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.460
_pdbe_chem_comp_rdkit_properties.kappa1 3.023
_pdbe_chem_comp_rdkit_properties.kappa2 4.374
_pdbe_chem_comp_rdkit_properties.kappa3 4.686
_pdbe_chem_comp_rdkit_properties.Phi 0.944
#
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
J8T UniChem PDBe J8T
J8T UniChem SureChEMBL SCHEMBL21033367
J8T UniChem PubChem 131750124
#
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
J8T C4 0.848 0.337 -0.349 ETKDGv3 1
J8T C5 -0.304 -0.448 -1.039 ETKDGv3 2
J8T C6 -0.172 -0.228 -2.564 ETKDGv3 3
J8T C7 -0.138 -1.961 -0.756 ETKDGv3 4
J8T O3 2.263 0.556 3.374 ETKDGv3 5
J8T O4 1.593 2.476 1.742 ETKDGv3 6
J8T O5 0.907 0.032 1.027 ETKDGv3 7
J8T P1 2.068 1.040 1.765 ETKDGv3 8
J8T O6 -2.761 -0.460 -1.321 ETKDGv3 9
J8T O7 -2.367 -1.148 1.381 ETKDGv3 10
J8T C8 -1.704 0.097 -0.574 ETKDGv3 11
J8T C9 -1.972 -0.048 0.910 ETKDGv3 12
J8T N2 -1.771 1.058 1.791 ETKDGv3 13
J8T H1 0.682 1.427 -0.512 ETKDGv3 14
J8T H2 1.813 0.053 -0.828 ETKDGv3 15
J8T H3 -0.279 0.849 -2.817 ETKDGv3 16
J8T H4 -0.951 -0.795 -3.118 ETKDGv3 17
J8T H5 0.819 -0.572 -2.931 ETKDGv3 18
J8T H6 0.872 -2.303 -1.070 ETKDGv3 19
J8T H7 -0.882 -2.562 -1.319 ETKDGv3 20
J8T H8 -0.247 -2.187 0.324 ETKDGv3 21
J8T H9 2.541 -0.393 3.318 ETKDGv3 22
J8T H11 -2.838 -1.420 -1.086 ETKDGv3 23
J8T H12 -1.719 1.187 -0.797 ETKDGv3 24
J8T H13 -1.428 1.976 1.431 ETKDGv3 25
J8T H14 -1.948 0.954 2.815 ETKDGv3 26
J8T O1 3.560 0.914 0.971 ETKDGv3 27
J8T H10 3.516 1.569 0.230 ETKDGv3 28
#