data_Y2Y
#
_chem_comp.id Y2Y
_chem_comp.name "(3S,4R)-3-amino-4-hydroxyheptanedioic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H13 N O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-06-02
_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 191.182
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code Y2Y
_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 6X8K
_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
Y2Y N N N 0 1 N N N Y Y N 40.368 17.631 11.561 -1.133 1.393 -0.758 N Y2Y 1
Y2Y C2 CA C 0 1 N N N N N N 39.458 15.833 15.481 2.607 -0.602 -0.322 CA Y2Y 2
Y2Y C3 C C 0 1 N N N N N N 39.625 16.364 16.674 3.828 0.208 0.030 C Y2Y 3
Y2Y O2 O O 0 1 N N N N N N 39.338 17.544 16.882 3.705 1.286 0.560 O Y2Y 4
Y2Y CB1 CB1 C 0 1 N N N N N N 38.342 17.033 10.720 -2.388 -0.664 -0.320 CB1 Y2Y 5
Y2Y CG1 CG1 C 0 1 N N N N N N 37.905 18.352 10.017 -3.627 0.090 0.091 CG1 Y2Y 6
Y2Y OD1 OD1 O 0 1 N N N N N N 38.228 19.446 10.516 -4.839 -0.442 -0.127 OD1 Y2Y 7
Y2Y OD2 OD2 O 0 1 N N N N N N 37.249 18.321 9.008 -3.528 1.174 0.615 OD2 Y2Y 8
Y2Y C1 C01 C 0 1 N N N N N N 39.660 16.821 14.381 1.349 0.163 0.094 C01 Y2Y 9
Y2Y C C2 C 0 1 N N R Y N Y 39.054 16.369 12.953 0.110 -0.659 -0.264 C2 Y2Y 10
Y2Y CA CA1 C 0 1 N N S Y N N 39.213 17.387 11.897 -1.148 0.158 0.038 CA1 Y2Y 11
Y2Y O O1 O 0 1 N N N Y N Y 37.999 16.133 13.094 0.095 -1.860 0.511 O1 Y2Y 12
Y2Y H H1 H 0 1 N N N Y Y N 40.910 17.860 12.370 -1.111 1.186 -1.745 H1 Y2Y 13
Y2Y H2 H2 H 0 1 N Y N Y Y N 40.761 16.828 11.113 -1.921 1.980 -0.529 H2 Y2Y 14
Y2Y H4 H4 H 0 1 N N N N N N 38.435 15.434 15.413 2.586 -0.778 -1.398 H4 Y2Y 15
Y2Y H5 H5 H 0 1 N N N N N N 40.181 15.013 15.356 2.641 -1.558 0.201 H5 Y2Y 16
Y2Y H7 H7 H 0 1 N N N N N N 37.454 16.485 11.067 -2.354 -1.620 0.204 H7 Y2Y 17
Y2Y H8 H8 H 0 1 N N N N N N 38.907 16.406 10.015 -2.409 -0.840 -1.395 H8 Y2Y 18
Y2Y H9 H9 H 0 1 N N N N N N 37.881 20.152 9.984 -5.604 0.079 0.154 H9 Y2Y 19
Y2Y H10 H10 H 0 1 N N N N N N 40.741 16.983 14.259 1.371 0.339 1.169 H10 Y2Y 20
Y2Y H11 H11 H 0 1 N N N N N N 39.178 17.765 14.675 1.315 1.119 -0.430 H11 Y2Y 21
Y2Y H12 H12 H 0 1 N Y N Y N Y 39.652 15.498 12.647 0.134 -0.910 -1.324 H12 Y2Y 22
Y2Y HA H13 H 0 1 N N N Y N N 38.770 18.305 12.311 -1.173 0.410 1.098 H13 Y2Y 23
Y2Y H14 H14 H 0 1 N N N Y N Y 37.909 15.477 13.775 0.073 -1.712 1.466 H14 Y2Y 24
Y2Y O1 OXT O 0 1 N N N N N N 39.477 15.503 17.691 5.052 -0.269 -0.245 OXT Y2Y 25
Y2Y H3 H3 H 0 1 N N N N N N 39.155 15.967 18.455 5.805 0.286 -0.001 H3 Y2Y 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
Y2Y OD2 CG1 DOUB N N 1
Y2Y CG1 OD1 SING N N 2
Y2Y CG1 CB1 SING N N 3
Y2Y CB1 CA SING N N 4
Y2Y N CA SING N N 5
Y2Y CA C SING N N 6
Y2Y C O SING N N 7
Y2Y C C1 SING N N 8
Y2Y C1 C2 SING N N 9
Y2Y C2 C3 SING N N 10
Y2Y C3 O2 DOUB N N 11
Y2Y N H SING N N 12
Y2Y N H2 SING N N 13
Y2Y C2 H4 SING N N 14
Y2Y C2 H5 SING N N 15
Y2Y CB1 H7 SING N N 16
Y2Y CB1 H8 SING N N 17
Y2Y OD1 H9 SING N N 18
Y2Y C1 H10 SING N N 19
Y2Y C1 H11 SING N N 20
Y2Y C H12 SING N N 21
Y2Y CA HA SING N N 22
Y2Y O H14 SING N N 23
Y2Y C3 O1 SING N N 24
Y2Y O1 H3 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
Y2Y SMILES ACDLabs 12.01 NC(CC(O)=O)C(CCC(=O)O)O
Y2Y InChI InChI 1.03 InChI=1S/C7H13NO5/c8-4(3-7(12)13)5(9)1-2-6(10)11/h4-5,9H,1-3,8H2,(H,10,11)(H,12,13)/t4-,5+/m0/s1
Y2Y InChIKey InChI 1.03 XBEFTDYWKMUVOR-CRCLSJGQSA-N
Y2Y SMILES_CANONICAL CACTVS 3.385 N[C@@H](CC(O)=O)[C@H](O)CCC(O)=O
Y2Y SMILES CACTVS 3.385 N[CH](CC(O)=O)[CH](O)CCC(O)=O
Y2Y SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C(CC(=O)O)[C@H]([C@H](CC(=O)O)N)O
Y2Y SMILES "OpenEye OEToolkits" 2.0.7 C(CC(=O)O)C(C(CC(=O)O)N)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
Y2Y "SYSTEMATIC NAME" ACDLabs 12.01 "(3S,4R)-3-amino-4-hydroxyheptanedioic acid"
Y2Y "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(3~{S},4~{R})-3-azanyl-4-oxidanyl-heptanedioic 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
Y2Y 'Create component' 2020-06-02 RCSB
Y2Y 'Initial release' 2021-06-02 RCSB
Y2Y 'Modify backbone' 2023-11-03 PDBE
#
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
Y2Y N N 7.702 -1.875 1
Y2Y C2 C 11.600 0.375 2
Y2Y C3 C 12.899 -0.375 3
Y2Y O2 O 14.198 0.375 4
Y2Y CB1 C 6.404 0.375 5
Y2Y CG1 C 5.104 -0.375 6
Y2Y OD1 O 5.104 -1.875 7
Y2Y OD2 O 3.805 0.375 8
Y2Y C1 C 10.301 -0.375 9
Y2Y C C 9.002 0.375 10
Y2Y CA C 7.702 -0.375 11
Y2Y O O 9.002 1.875 12
Y2Y O1 O 12.899 -1.875 13
#
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
Y2Y OD2 CG1 DOUBLE NONE 1
Y2Y CG1 OD1 SINGLE NONE 2
Y2Y CG1 CB1 SINGLE NONE 3
Y2Y CB1 CA SINGLE NONE 4
Y2Y CA N SINGLE BEGINWEDGE 5
Y2Y CA C SINGLE NONE 6
Y2Y C O SINGLE BEGINDASH 7
Y2Y C C1 SINGLE NONE 8
Y2Y C1 C2 SINGLE NONE 9
Y2Y C2 C3 SINGLE NONE 10
Y2Y C3 O2 DOUBLE NONE 11
Y2Y C3 O1 SINGLE NONE 12
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id Y2Y
_pdbe_chem_comp_rdkit_properties.exactmw 191.079
_pdbe_chem_comp_rdkit_properties.amw 191.183
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_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 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_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 0.714
_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 93.615
_pdbe_chem_comp_rdkit_properties.tpsa 120.850
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.986
_pdbe_chem_comp_rdkit_properties.CrippenMR 43.105
_pdbe_chem_comp_rdkit_properties.chi0v 5.988
_pdbe_chem_comp_rdkit_properties.chi1v 2.744
_pdbe_chem_comp_rdkit_properties.chi2v 0.714
_pdbe_chem_comp_rdkit_properties.chi3v 0.714
_pdbe_chem_comp_rdkit_properties.chi4v 0.320
_pdbe_chem_comp_rdkit_properties.chi0n 18.988
_pdbe_chem_comp_rdkit_properties.chi1n 8.863
_pdbe_chem_comp_rdkit_properties.chi2n 0.714
_pdbe_chem_comp_rdkit_properties.chi3n 0.714
_pdbe_chem_comp_rdkit_properties.chi4n 0.320
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.140
_pdbe_chem_comp_rdkit_properties.kappa1 2.457
_pdbe_chem_comp_rdkit_properties.kappa2 5.496
_pdbe_chem_comp_rdkit_properties.kappa3 6.061
_pdbe_chem_comp_rdkit_properties.Phi 1.039
#
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
Y2Y UniChem PDBe Y2Y
Y2Y UniChem PubChem 155923779
#
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
Y2Y N -1.309 -0.571 -2.030 ETKDGv3 1
Y2Y C2 2.603 0.220 0.985 ETKDGv3 2
Y2Y C3 3.449 0.696 -0.156 ETKDGv3 3
Y2Y O2 3.707 1.923 -0.282 ETKDGv3 4
Y2Y CB1 -1.976 -0.219 0.342 ETKDGv3 5
Y2Y CG1 -3.315 0.364 0.011 ETKDGv3 6
Y2Y OD1 -4.310 -0.446 -0.528 ETKDGv3 7
Y2Y OD2 -3.531 1.592 0.192 ETKDGv3 8
Y2Y C1 1.112 0.508 0.753 ETKDGv3 9
Y2Y C 0.508 -0.347 -0.390 ETKDGv3 10
Y2Y CA -0.936 0.079 -0.768 ETKDGv3 11
Y2Y O 0.576 -1.723 -0.101 ETKDGv3 12
Y2Y H -1.526 -1.579 -1.856 ETKDGv3 13
Y2Y H2 -2.174 -0.120 -2.407 ETKDGv3 14
Y2Y H4 2.764 -0.867 1.146 ETKDGv3 15
Y2Y H5 2.930 0.743 1.910 ETKDGv3 16
Y2Y H7 -2.086 -1.316 0.486 ETKDGv3 17
Y2Y H8 -1.647 0.216 1.308 ETKDGv3 18
Y2Y H9 -5.217 -0.063 -0.770 ETKDGv3 19
Y2Y H10 0.578 0.302 1.704 ETKDGv3 20
Y2Y H11 0.980 1.589 0.526 ETKDGv3 21
Y2Y H12 1.129 -0.170 -1.294 ETKDGv3 22
Y2Y HA -0.920 1.179 -0.942 ETKDGv3 23
Y2Y H14 0.196 -1.866 0.804 ETKDGv3 24
Y2Y O1 3.925 -0.215 -1.094 ETKDGv3 25
Y2Y H3 4.488 0.092 -1.878 ETKDGv3 26
#