data_4SQ
#
_chem_comp.id 4SQ
_chem_comp.name "tetraglycine phosphinate"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H16 N3 O6 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-05-21
_chem_comp.pdbx_modified_date 2015-10-16
_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 281.203
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 4SQ
_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 4ZYB
_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
4SQ C4 C1 C 0 1 N N N N N N 7.415 50.985 67.268 -6.179 -0.475 -0.152 C4 4SQ 1
4SQ N1 N1 N 0 1 N N N N N N 4.734 61.767 73.341 6.814 -1.022 -1.002 N1 4SQ 2
4SQ N2 N2 N 0 1 N N N N N N 6.410 60.293 71.355 4.024 0.661 0.738 N2 4SQ 3
4SQ C3 C2 C 0 1 N N N N N N 7.307 54.007 69.280 -2.621 0.534 -0.135 C3 4SQ 4
4SQ O42 O1 O 0 1 N N N N N N 7.483 49.726 67.300 -7.439 -0.112 -0.437 O42 4SQ 5
4SQ O41 O2 O 0 1 N N N N N N 7.170 51.596 66.193 -5.954 -1.576 0.294 O41 4SQ 6
4SQ CA4 C3 C 0 1 N N N N N N 7.645 51.771 68.549 -5.044 0.486 -0.394 CA4 4SQ 7
4SQ N4 N3 N 0 1 N N N N N N 6.867 52.971 68.575 -3.779 -0.144 -0.006 N4 4SQ 8
4SQ O3 O3 O 0 1 N N N N N N 8.361 53.953 69.891 -2.626 1.665 -0.574 O3 4SQ 9
4SQ CA3 C4 C 0 1 N N N N N N 6.458 55.279 69.306 -1.321 -0.114 0.264 CA3 4SQ 10
4SQ CN3 C5 C 0 1 N N N N N N 7.276 56.485 69.782 -0.168 0.862 0.018 CN3 4SQ 11
4SQ P P1 P 0 1 N N N N N N 6.234 57.770 70.460 1.405 0.079 0.502 P 4SQ 12
4SQ OP1 O4 O 0 1 N N N N N N 5.188 58.217 69.354 1.315 -0.386 1.904 OP1 4SQ 13
4SQ OP2 O5 O 0 1 N N N N N N 5.551 57.232 71.785 1.698 -1.177 -0.462 OP2 4SQ 14
4SQ CA2 C6 C 0 1 N N N N N N 7.221 59.200 70.896 2.759 1.290 0.350 CA2 4SQ 15
4SQ C1 C7 C 0 1 N N N N N N 6.828 61.188 72.247 4.827 0.127 -0.203 C1 4SQ 16
4SQ O1 O6 O 0 1 N N N N N N 7.945 61.118 72.732 4.504 0.167 -1.371 O1 4SQ 17
4SQ CA1 C8 C 0 1 N N N N N N 5.864 62.306 72.646 6.128 -0.521 0.197 CA1 4SQ 18
4SQ H1 H1 H 0 1 N N N N N N 4.113 62.509 73.595 7.690 -1.461 -0.760 H1 4SQ 19
4SQ H2 H2 H 0 1 N N N N N N 4.255 61.120 72.747 6.223 -1.655 -1.519 H2 4SQ 20
4SQ H4 H4 H 0 1 N N N N N N 5.485 60.386 70.986 4.282 0.628 1.672 H4 4SQ 21
4SQ H5 H5 H 0 1 N N N N N N 7.326 49.378 66.430 -8.133 -0.762 -0.265 H5 4SQ 22
4SQ H6 H6 H 0 1 N N N N N N 7.364 51.144 69.408 -5.009 0.748 -1.452 H6 4SQ 23
4SQ H7 H7 H 0 1 N N N N N N 8.711 52.034 68.620 -5.198 1.387 0.199 H7 4SQ 24
4SQ H8 H8 H 0 1 N N N N N N 6.006 53.029 68.070 -3.775 -1.048 0.345 H8 4SQ 25
4SQ H9 H9 H 0 1 N N N N N N 6.081 55.479 68.292 -1.355 -0.376 1.321 H9 4SQ 26
4SQ H10 H10 H 0 1 N N N N N N 5.609 55.129 69.990 -1.166 -1.015 -0.329 H10 4SQ 27
4SQ H11 H11 H 0 1 N N N N N N 7.981 56.153 70.558 -0.134 1.125 -1.039 H11 4SQ 28
4SQ H12 H12 H 0 1 N N N N N N 7.836 56.894 68.928 -0.323 1.764 0.612 H12 4SQ 29
4SQ H13 H13 H 0 1 N N N N N N 4.606 57.268 71.692 1.770 -0.946 -1.399 H13 4SQ 30
4SQ H14 H14 H 0 1 N N N N N N 7.922 58.918 71.695 2.561 2.141 1.002 H14 4SQ 31
4SQ H15 H15 H 0 1 N N N N N N 7.787 59.525 70.010 2.826 1.633 -0.683 H15 4SQ 32
4SQ H16 H16 H 0 1 N N N N N N 6.387 63.018 73.301 5.928 -1.351 0.874 H16 4SQ 33
4SQ H17 H17 H 0 1 N N N N N N 5.518 62.826 71.741 6.760 0.212 0.698 H17 4SQ 34
#
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
4SQ O41 C4 DOUB N N 1
4SQ C4 O42 SING N N 2
4SQ C4 CA4 SING N N 3
4SQ CA4 N4 SING N N 4
4SQ N4 C3 SING N N 5
4SQ C3 CA3 SING N N 6
4SQ C3 O3 DOUB N N 7
4SQ CA3 CN3 SING N N 8
4SQ OP1 P DOUB N N 9
4SQ CN3 P SING N N 10
4SQ P CA2 SING N N 11
4SQ P OP2 SING N N 12
4SQ CA2 N2 SING N N 13
4SQ N2 C1 SING N N 14
4SQ C1 CA1 SING N N 15
4SQ C1 O1 DOUB N N 16
4SQ CA1 N1 SING N N 17
4SQ N1 H1 SING N N 18
4SQ N1 H2 SING N N 19
4SQ N2 H4 SING N N 20
4SQ O42 H5 SING N N 21
4SQ CA4 H6 SING N N 22
4SQ CA4 H7 SING N N 23
4SQ N4 H8 SING N N 24
4SQ CA3 H9 SING N N 25
4SQ CA3 H10 SING N N 26
4SQ CN3 H11 SING N N 27
4SQ CN3 H12 SING N N 28
4SQ OP2 H13 SING N N 29
4SQ CA2 H14 SING N N 30
4SQ CA2 H15 SING N N 31
4SQ CA1 H16 SING N N 32
4SQ CA1 H17 SING N N 33
#
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
4SQ SMILES ACDLabs 12.01 C(O)(CNC(CCP(CNC(CN)=O)(O)=O)=O)=O
4SQ InChI InChI 1.03 InChI=1S/C8H16N3O6P/c9-3-7(13)11-5-18(16,17)2-1-6(12)10-4-8(14)15/h1-5,9H2,(H,10,12)(H,11,13)(H,14,15)(H,16,17)
4SQ InChIKey InChI 1.03 UENGEQFXYOYUEI-UHFFFAOYSA-N
4SQ SMILES_CANONICAL CACTVS 3.385 NCC(=O)NC[P](O)(=O)CCC(=O)NCC(O)=O
4SQ SMILES CACTVS 3.385 NCC(=O)NC[P](O)(=O)CCC(=O)NCC(O)=O
4SQ SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 C(CP(=O)(CNC(=O)CN)O)C(=O)NCC(=O)O
4SQ SMILES "OpenEye OEToolkits" 1.9.2 C(CP(=O)(CNC(=O)CN)O)C(=O)NCC(=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
4SQ "SYSTEMATIC NAME" ACDLabs 12.01 N-{3-[(R)-[(glycylamino)methyl](hydroxy)phosphoryl]propanoyl}glycine
4SQ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "2-[3-[(2-azanylethanoylamino)methyl-oxidanyl-phosphoryl]propanoylamino]ethanoic 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
4SQ 'Create component' 2015-05-21 EBI
4SQ 'Initial release' 2015-10-21 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
4SQ C4 C 18.095 0.000 1
4SQ N1 N 3.805 -0.750 2
4SQ N2 N 7.702 0.000 3
4SQ C3 C 14.198 0.750 4
4SQ O42 O 18.095 -1.500 5
4SQ O41 O 19.394 0.750 6
4SQ CA4 C 16.796 0.750 7
4SQ N4 N 15.497 0.000 8
4SQ O3 O 14.198 2.250 9
4SQ CA3 C 12.899 0.000 10
4SQ CN3 C 11.600 0.750 11
4SQ P P 10.301 0.000 12
4SQ OP1 O 9.551 1.299 13
4SQ OP2 O 11.051 -1.299 14
4SQ CA2 C 9.002 -0.750 15
4SQ C1 C 6.404 -0.750 16
4SQ O1 O 6.404 -2.250 17
4SQ CA1 C 5.104 0.000 18
#
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
4SQ O41 C4 DOUBLE NONE 1
4SQ C4 O42 SINGLE NONE 2
4SQ C4 CA4 SINGLE NONE 3
4SQ CA4 N4 SINGLE NONE 4
4SQ N4 C3 SINGLE NONE 5
4SQ C3 CA3 SINGLE NONE 6
4SQ C3 O3 DOUBLE NONE 7
4SQ CA3 CN3 SINGLE NONE 8
4SQ OP1 P DOUBLE NONE 9
4SQ CN3 P SINGLE NONE 10
4SQ P CA2 SINGLE NONE 11
4SQ P OP2 SINGLE BEGINDASH 12
4SQ CA2 N2 SINGLE NONE 13
4SQ N2 C1 SINGLE NONE 14
4SQ C1 CA1 SINGLE NONE 15
4SQ C1 O1 DOUBLE NONE 16
4SQ CA1 N1 SINGLE NONE 17
#
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
4SQ amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
4SQ peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 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
4SQ N2 F1 1
4SQ C1 F1 1
4SQ O1 F1 1
4SQ CA1 F1 1
4SQ N4 F1 2
4SQ C3 F1 2
4SQ O3 F1 2
4SQ CA3 F1 2
4SQ O41 F2 1
4SQ C4 F2 1
4SQ CA4 F2 1
4SQ N4 F2 1
4SQ O1 F2 2
4SQ C1 F2 2
4SQ CA1 F2 2
4SQ N1 F2 2
#
_pdbe_chem_comp_rdkit_properties.comp_id 4SQ
_pdbe_chem_comp_rdkit_properties.exactmw 281.078
_pdbe_chem_comp_rdkit_properties.amw 281.205
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 9
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 10
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 34
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 10
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.625
_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 126.068
_pdbe_chem_comp_rdkit_properties.tpsa 158.820
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.120
_pdbe_chem_comp_rdkit_properties.CrippenMR 62.019
_pdbe_chem_comp_rdkit_properties.chi0v 9.133
_pdbe_chem_comp_rdkit_properties.chi1v 5.372
_pdbe_chem_comp_rdkit_properties.chi2v 1.707
_pdbe_chem_comp_rdkit_properties.chi3v 1.707
_pdbe_chem_comp_rdkit_properties.chi4v 0.922
_pdbe_chem_comp_rdkit_properties.chi0n 24.238
_pdbe_chem_comp_rdkit_properties.chi1n 11.352
_pdbe_chem_comp_rdkit_properties.chi2n 0.938
_pdbe_chem_comp_rdkit_properties.chi3n 0.938
_pdbe_chem_comp_rdkit_properties.chi4n 0.407
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.440
_pdbe_chem_comp_rdkit_properties.kappa1 4.025
_pdbe_chem_comp_rdkit_properties.kappa2 7.803
_pdbe_chem_comp_rdkit_properties.kappa3 8.682
_pdbe_chem_comp_rdkit_properties.Phi 1.745
#
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
4SQ UniChem PDBe 4SQ
4SQ UniChem ZINC ZINC000263621084
4SQ UniChem PubChem 91971261
#
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
4SQ C4 -4.596 1.015 1.308 ETKDGv3 1
4SQ N1 2.345 -0.030 2.137 ETKDGv3 2
4SQ N2 1.609 -1.977 -0.206 ETKDGv3 3
4SQ C3 -1.169 1.797 -0.110 ETKDGv3 4
4SQ O42 -4.638 0.696 2.661 ETKDGv3 5
4SQ O41 -5.431 0.505 0.514 ETKDGv3 6
4SQ CA4 -3.526 1.922 0.789 ETKDGv3 7
4SQ N4 -2.339 1.155 0.413 ETKDGv3 8
4SQ O3 -1.150 3.048 -0.275 ETKDGv3 9
4SQ CA3 0.023 0.981 -0.506 ETKDGv3 10
4SQ CN3 -0.167 0.411 -1.913 ETKDGv3 11
4SQ P 1.305 -0.512 -2.469 ETKDGv3 12
4SQ OP1 1.184 -0.749 -3.958 ETKDGv3 13
4SQ OP2 2.701 0.397 -2.172 ETKDGv3 14
4SQ CA2 1.423 -2.135 -1.645 ETKDGv3 15
4SQ C1 2.866 -1.608 0.379 ETKDGv3 16
4SQ O1 3.897 -1.498 -0.338 ETKDGv3 17
4SQ CA1 2.953 -1.324 1.846 ETKDGv3 18
4SQ H1 2.948 0.716 1.719 ETKDGv3 19
4SQ H2 2.373 0.110 3.173 ETKDGv3 20
4SQ H4 0.804 -2.194 0.425 ETKDGv3 21
4SQ H5 -5.345 0.070 3.026 ETKDGv3 22
4SQ H6 -3.257 2.657 1.577 ETKDGv3 23
4SQ H7 -3.906 2.477 -0.096 ETKDGv3 24
4SQ H8 -2.333 0.114 0.518 ETKDGv3 25
4SQ H9 0.150 0.160 0.226 ETKDGv3 26
4SQ H10 0.933 1.618 -0.473 ETKDGv3 27
4SQ H11 -0.343 1.245 -2.627 ETKDGv3 28
4SQ H12 -1.047 -0.267 -1.937 ETKDGv3 29
4SQ H13 2.557 1.250 -2.654 ETKDGv3 30
4SQ H14 2.265 -2.717 -2.077 ETKDGv3 31
4SQ H15 0.483 -2.693 -1.836 ETKDGv3 32
4SQ H16 2.413 -2.119 2.404 ETKDGv3 33
4SQ H17 4.016 -1.328 2.178 ETKDGv3 34
#