data_2D8
#
_chem_comp.id 2D8
_chem_comp.name "(2R)-3-[(R)-[(1S)-1-aminoethyl](hydroxy)phosphoryl]-2-methylpropanoic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H14 N O4 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2013-09-25
_chem_comp.pdbx_modified_date 2013-10-04
_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 195.153
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 2D8
_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 4MUQ
_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
2D8 C4 C4 C 0 1 N N N N N N 19.874 -0.455 6.269 0.450 -0.589 -0.065 C4 2D8 1
2D8 C5 C5 C 0 1 N N R N N N 20.544 -1.255 7.340 1.631 0.377 0.051 C5 2D8 2
2D8 C6 C6 C 0 1 N N N N N N 20.209 -2.730 7.175 2.912 -0.407 0.174 C6 2D8 3
2D8 C7 C7 C 0 1 N N N N N N 22.037 -0.994 7.260 1.692 1.260 -1.197 C7 2D8 4
2D8 N1 N1 N 0 1 N N N N N N 16.019 0.717 5.206 -2.570 -1.545 -1.056 N1 2D8 5
2D8 P P P 0 1 N N N N N N 18.124 -0.096 6.586 -1.105 0.315 0.233 P 2D8 6
2D8 C1 C1 C 0 1 N N N N N N 17.412 -1.030 4.230 -3.804 -0.103 0.491 C1 2D8 7
2D8 C2 C2 C 0 1 N N S N N N 17.338 0.278 4.993 -2.498 -0.861 0.242 C2 2D8 8
2D8 O31 O31 O 0 1 N N N N N N 17.493 -1.349 7.236 -1.033 1.004 1.540 O31 2D8 9
2D8 O32 O32 O 0 1 N N N N N N 17.882 1.093 7.571 -1.327 1.401 -0.935 O32 2D8 10
2D8 O61 O61 O 0 1 N N N N N N 20.143 -3.395 8.195 4.084 0.235 0.289 O61 2D8 11
2D8 O62 O62 O 0 1 N N N N N N 20.060 -3.189 6.055 2.883 -1.615 0.170 O62 2D8 12
2D8 H1 H1 H 0 1 N N N N N N 19.945 -1.016 5.325 0.433 -1.023 -1.064 H1 2D8 13
2D8 H2 H2 H 0 1 N N N N N N 20.409 0.501 6.168 0.556 -1.383 0.674 H2 2D8 14
2D8 H3 H3 H 0 1 N N N N N N 20.178 -0.918 8.321 1.503 1.004 0.934 H3 2D8 15
2D8 H4 H4 H 0 1 N N N N N N 22.553 -1.573 8.040 0.766 1.828 -1.286 H4 2D8 16
2D8 H5 H5 H 0 1 N N N N N N 22.410 -1.298 6.271 2.534 1.949 -1.114 H5 2D8 17
2D8 H6 H6 H 0 1 N N N N N N 22.230 0.078 7.411 1.821 0.634 -2.079 H6 2D8 18
2D8 H7 H7 H 0 1 N N N N N N 16.032 1.580 5.711 -2.709 -0.885 -1.806 H7 2D8 19
2D8 H8 H8 H 0 1 N N N N N N 15.567 0.854 4.325 -1.746 -2.105 -1.216 H8 2D8 20
2D8 H10 H10 H 0 1 N N N N N N 18.465 -1.318 4.096 -4.637 -0.805 0.496 H10 2D8 21
2D8 H11 H11 H 0 1 N N N N N N 16.886 -1.814 4.795 -3.751 0.405 1.454 H11 2D8 22
2D8 H12 H12 H 0 1 N N N N N N 16.938 -0.907 3.245 -3.954 0.633 -0.300 H12 2D8 23
2D8 H13 H13 H 0 1 N N N N N N 17.956 1.045 4.502 -2.348 -1.596 1.032 H13 2D8 24
2D8 H14 H14 H 0 1 N N N N N N 17.409 0.782 8.334 -1.383 1.019 -1.822 H14 2D8 25
2D8 H15 H15 H 0 1 N N N N N N 19.962 -4.300 7.972 4.879 -0.311 0.366 H15 2D8 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
2D8 C1 C2 SING N N 1
2D8 C2 N1 SING N N 2
2D8 C2 P SING N N 3
2D8 O62 C6 DOUB N N 4
2D8 C4 P SING N N 5
2D8 C4 C5 SING N N 6
2D8 P O31 DOUB N N 7
2D8 P O32 SING N N 8
2D8 C6 C5 SING N N 9
2D8 C6 O61 SING N N 10
2D8 C7 C5 SING N N 11
2D8 C4 H1 SING N N 12
2D8 C4 H2 SING N N 13
2D8 C5 H3 SING N N 14
2D8 C7 H4 SING N N 15
2D8 C7 H5 SING N N 16
2D8 C7 H6 SING N N 17
2D8 N1 H7 SING N N 18
2D8 N1 H8 SING N N 19
2D8 C1 H10 SING N N 20
2D8 C1 H11 SING N N 21
2D8 C1 H12 SING N N 22
2D8 C2 H13 SING N N 23
2D8 O32 H14 SING N N 24
2D8 O61 H15 SING N N 25
#
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
2D8 SMILES ACDLabs 12.01 O=P(O)(C(N)C)CC(C(=O)O)C
2D8 InChI InChI 1.03 InChI=1S/C6H14NO4P/c1-4(6(8)9)3-12(10,11)5(2)7/h4-5H,3,7H2,1-2H3,(H,8,9)(H,10,11)/t4-,5-/m0/s1
2D8 InChIKey InChI 1.03 XXVGIEKADYFHOF-WHFBIAKZSA-N
2D8 SMILES_CANONICAL CACTVS 3.385 C[C@@H](N)[P](O)(=O)C[C@H](C)C(O)=O
2D8 SMILES CACTVS 3.385 C[CH](N)[P](O)(=O)C[CH](C)C(O)=O
2D8 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C[C@@H](CP(=O)([C@@H](C)N)O)C(=O)O
2D8 SMILES "OpenEye OEToolkits" 1.7.6 CC(CP(=O)(C(C)N)O)C(=O)O
#
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
2D8 "SYSTEMATIC NAME" ACDLabs 12.01 "(2R)-3-[(R)-[(1S)-1-aminoethyl](hydroxy)phosphoryl]-2-methylpropanoic acid"
2D8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2R)-3-[[(1S)-1-azanylethyl]-oxidanyl-phosphoryl]-2-methyl-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
2D8 'Create component' 2013-09-25 RCSB
2D8 'Initial release' 2013-10-09 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
2D8 C4 C 7.702 0.750 1
2D8 C5 C 9.002 0.000 2
2D8 C6 C 10.301 0.750 3
2D8 C7 C 9.002 -1.500 4
2D8 N1 N 5.104 -2.250 5
2D8 P P 6.404 0.000 6
2D8 C1 C 3.805 0.000 7
2D8 C2 C 5.104 -0.750 8
2D8 O31 O 5.654 1.299 9
2D8 O32 O 7.154 -1.299 10
2D8 O61 O 10.301 2.250 11
2D8 O62 O 11.600 0.000 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
2D8 C2 C1 SINGLE BEGINDASH 1
2D8 C2 N1 SINGLE NONE 2
2D8 C2 P SINGLE NONE 3
2D8 O62 C6 DOUBLE NONE 4
2D8 C4 P SINGLE NONE 5
2D8 C4 C5 SINGLE NONE 6
2D8 P O31 DOUBLE NONE 7
2D8 P O32 SINGLE BEGINDASH 8
2D8 C6 C5 SINGLE NONE 9
2D8 C6 O61 SINGLE NONE 10
2D8 C5 C7 SINGLE BEGINWEDGE 11
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id 2D8
_pdbe_chem_comp_rdkit_properties.exactmw 195.066
_pdbe_chem_comp_rdkit_properties.amw 195.155
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 26
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_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 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 90.989
_pdbe_chem_comp_rdkit_properties.tpsa 100.620
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.282
_pdbe_chem_comp_rdkit_properties.CrippenMR 45.142
_pdbe_chem_comp_rdkit_properties.chi0v 6.422
_pdbe_chem_comp_rdkit_properties.chi1v 4.069
_pdbe_chem_comp_rdkit_properties.chi2v 1.818
_pdbe_chem_comp_rdkit_properties.chi3v 1.818
_pdbe_chem_comp_rdkit_properties.chi4v 0.737
_pdbe_chem_comp_rdkit_properties.chi0n 19.527
_pdbe_chem_comp_rdkit_properties.chi1n 9.155
_pdbe_chem_comp_rdkit_properties.chi2n 0.742
_pdbe_chem_comp_rdkit_properties.chi3n 0.742
_pdbe_chem_comp_rdkit_properties.chi4n 0.246
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.380
_pdbe_chem_comp_rdkit_properties.kappa1 2.162
_pdbe_chem_comp_rdkit_properties.kappa2 4.028
_pdbe_chem_comp_rdkit_properties.kappa3 3.344
_pdbe_chem_comp_rdkit_properties.Phi 0.726
#
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
2D8 UniChem ChEMBL CHEMBL3350233
2D8 UniChem PDBe 2D8
2D8 UniChem ZINC ZINC000000024584
2D8 UniChem 'PubChem TPHARMA' 15463043
2D8 UniChem PubChem 10442640
2D8 UniChem BRENDA 53920
2D8 UniChem BRENDA 90346
2D8 UniChem BindingDb 50227637
#
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
2D8 C4 0.600 -1.062 0.327 ETKDGv3 1
2D8 C5 1.451 -0.273 -0.687 ETKDGv3 2
2D8 C6 2.137 0.898 -0.039 ETKDGv3 3
2D8 C7 2.496 -1.188 -1.333 ETKDGv3 4
2D8 N1 -2.958 1.368 0.209 ETKDGv3 5
2D8 P -0.793 -0.083 0.996 ETKDGv3 6
2D8 C1 -2.382 -0.522 -1.235 ETKDGv3 7
2D8 C2 -1.844 0.598 -0.345 ETKDGv3 8
2D8 O31 -1.628 -0.985 1.877 ETKDGv3 9
2D8 O32 -0.179 1.188 1.931 ETKDGv3 10
2D8 O61 3.002 0.697 1.034 ETKDGv3 11
2D8 O62 1.934 2.065 -0.470 ETKDGv3 12
2D8 H1 0.176 -1.963 -0.166 ETKDGv3 13
2D8 H2 1.231 -1.407 1.174 ETKDGv3 14
2D8 H3 0.789 0.095 -1.502 ETKDGv3 15
2D8 H4 1.995 -2.022 -1.869 ETKDGv3 16
2D8 H5 3.176 -1.615 -0.564 ETKDGv3 17
2D8 H6 3.100 -0.618 -2.071 ETKDGv3 18
2D8 H7 -2.572 2.192 0.724 ETKDGv3 19
2D8 H8 -3.479 0.780 0.900 ETKDGv3 20
2D8 H10 -2.977 -1.245 -0.637 ETKDGv3 21
2D8 H11 -3.032 -0.093 -2.026 ETKDGv3 22
2D8 H12 -1.546 -1.059 -1.729 ETKDGv3 23
2D8 H13 -1.223 1.275 -0.970 ETKDGv3 24
2D8 H14 -0.943 1.497 2.481 ETKDGv3 25
2D8 H15 3.468 1.479 1.478 ETKDGv3 26
#