data_L9Z
#
_chem_comp.id L9Z
_chem_comp.name "(1~{S},3~{S},4~{S},5~{R})-3-(aminomethyl)-3,4,5-tris(hydroxyl)cyclohexane-1-carboxylic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H15 N O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-08-01
_chem_comp.pdbx_modified_date 2020-04-10
_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 205.208
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code L9Z
_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 6SFE
_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
L9Z O16 O1 O 0 1 N N N N N N -17.088 -1.902 -14.662 -2.886 -1.401 0.710 O16 L9Z 1
L9Z C14 C1 C 0 1 N N N N N N -16.757 -0.853 -14.022 -2.689 -0.433 0.014 C14 L9Z 2
L9Z O15 O2 O 0 1 N N N N N N -16.368 0.199 -14.614 -3.725 0.292 -0.437 O15 L9Z 3
L9Z C5 C2 C 0 1 N N S N N N -16.802 -0.854 -12.520 -1.280 -0.036 -0.344 C5 L9Z 4
L9Z C6 C3 C 0 1 N N N N N N -15.393 -1.193 -12.027 -0.296 -1.017 0.297 C6 L9Z 5
L9Z C1 C4 C 0 1 N N S N N N -15.314 -1.237 -10.500 1.135 -0.614 -0.066 C1 L9Z 6
L9Z O28 O3 O 0 1 N N N N N N -15.399 0.084 -9.937 1.292 -0.642 -1.486 O28 L9Z 7
L9Z C21 C5 C 0 1 N N N N N N -13.987 -1.891 -10.173 2.119 -1.594 0.575 C21 L9Z 8
L9Z C4 C6 C 0 1 N N N N N N -17.824 -1.815 -11.927 -1.001 1.377 0.172 C4 L9Z 9
L9Z C3 C7 C 0 1 N N R N N N -17.781 -1.734 -10.405 0.429 1.780 -0.191 C3 L9Z 10
L9Z O19 O4 O 0 1 N N N N N N -18.791 -2.581 -9.839 0.689 3.099 0.292 O19 L9Z 11
L9Z C2 C8 C 0 1 N N S N N N -16.403 -2.123 -9.898 1.414 0.799 0.450 C2 L9Z 12
L9Z O17 O5 O 0 1 N N N N N N -16.331 -2.054 -8.466 2.750 1.176 0.111 O17 L9Z 13
L9Z H1 H1 H 0 1 N N N N N N -16.374 0.055 -15.553 -4.610 0.000 -0.177 H1 L9Z 14
L9Z H2 H2 H 0 1 N N N N N N -17.048 0.162 -12.179 -1.160 -0.058 -1.427 H2 L9Z 15
L9Z H3 H3 H 0 1 N N N N N N -15.105 -2.177 -12.426 -0.415 -0.996 1.380 H3 L9Z 16
L9Z H4 H4 H 0 1 N N N N N N -14.694 -0.428 -12.397 -0.494 -2.023 -0.071 H4 L9Z 17
L9Z H5 H5 H 0 1 N N N N N N -15.348 0.029 -8.990 1.130 -1.508 -1.883 H5 L9Z 18
L9Z H6 H6 H 0 1 N N N N N N -14.161 -2.595 -9.346 3.139 -1.307 0.317 H6 L9Z 19
L9Z H7 H7 H 0 1 N N N N N N -13.664 -2.447 -11.066 2.000 -1.573 1.658 H7 L9Z 20
L9Z H9 H9 H 0 1 N N N N N N -18.830 -1.543 -12.280 -1.702 2.075 -0.284 H9 L9Z 21
L9Z H10 H10 H 0 1 N N N N N N -17.589 -2.841 -12.246 -1.121 1.398 1.256 H10 L9Z 22
L9Z H11 H11 H 0 1 N N N N N N -17.974 -0.691 -10.112 0.549 1.758 -1.274 H11 L9Z 23
L9Z H12 H12 H 0 1 N N N N N N -18.757 -2.525 -8.891 0.101 3.775 -0.074 H12 L9Z 24
L9Z H13 H13 H 0 1 N N N N N N -16.207 -3.158 -10.216 1.294 0.821 1.534 H13 L9Z 25
L9Z H14 H14 H 0 1 N N N N N N -17.007 -2.604 -8.088 2.996 2.062 0.408 H14 L9Z 26
L9Z N1 N1 N 0 1 N Y N N N N -12.944 -1.063 -9.801 1.852 -2.951 0.079 N1 L9Z 27
L9Z H8 H8 H 0 1 N N N N N N -12.131 -1.614 -9.614 1.893 -2.982 -0.928 H8 L9Z 28
L9Z H15 H15 H 0 1 N N N N N N -12.748 -0.421 -10.542 2.490 -3.617 0.488 H15 L9Z 29
#
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
L9Z O16 C14 DOUB N N 1
L9Z O15 C14 SING N N 2
L9Z C14 C5 SING N N 3
L9Z C5 C6 SING N N 4
L9Z C5 C4 SING N N 5
L9Z C6 C1 SING N N 6
L9Z C4 C3 SING N N 7
L9Z C1 C21 SING N N 8
L9Z C1 O28 SING N N 9
L9Z C1 C2 SING N N 10
L9Z C3 C2 SING N N 11
L9Z C3 O19 SING N N 12
L9Z C2 O17 SING N N 13
L9Z O15 H1 SING N N 14
L9Z C5 H2 SING N N 15
L9Z C6 H3 SING N N 16
L9Z C6 H4 SING N N 17
L9Z O28 H5 SING N N 18
L9Z C21 H6 SING N N 19
L9Z C21 H7 SING N N 20
L9Z C4 H9 SING N N 21
L9Z C4 H10 SING N N 22
L9Z C3 H11 SING N N 23
L9Z O19 H12 SING N N 24
L9Z C2 H13 SING N N 25
L9Z O17 H14 SING N N 26
L9Z C21 N1 SING N N 27
L9Z N1 H8 SING N N 28
L9Z N1 H15 SING N N 29
#
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
L9Z InChI InChI 1.03 InChI=1S/C8H15NO5/c9-3-8(14)2-4(7(12)13)1-5(10)6(8)11/h4-6,10-11,14H,1-3,9H2,(H,12,13)/t4-,5+,6-,8-/m0/s1
L9Z InChIKey InChI 1.03 YNLZKDMNCIPLRS-GCJQMDKQSA-N
L9Z SMILES_CANONICAL CACTVS 3.385 NC[C@@]1(O)C[C@H](C[C@@H](O)[C@@H]1O)C(O)=O
L9Z SMILES CACTVS 3.385 NC[C]1(O)C[CH](C[CH](O)[CH]1O)C(O)=O
L9Z SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C1[C@@H](C[C@@]([C@H]([C@@H]1O)O)(CN)O)C(=O)O
L9Z SMILES "OpenEye OEToolkits" 2.0.7 C1C(CC(C(C1O)O)(CN)O)C(=O)O
#
_pdbx_chem_comp_identifier.comp_id L9Z
_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
"(1~{S},3~{S},4~{S},5~{R})-3-(aminomethyl)-3,4,5-tris(oxidanyl)cyclohexane-1-carboxylic 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
L9Z 'Create component' 2019-08-01 EBI
L9Z 'Initial release' 2020-04-15 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
L9Z O16 O 9.002 -3.070 1
L9Z C14 C 9.002 -1.570 2
L9Z O15 O 10.301 -0.820 3
L9Z C5 C 7.702 -0.820 4
L9Z C6 C 7.702 0.680 5
L9Z C1 C 6.404 1.430 6
L9Z O28 O 5.654 2.729 7
L9Z C21 C 7.154 2.729 8
L9Z C4 C 6.404 -1.570 9
L9Z C3 C 5.104 -0.820 10
L9Z O19 O 3.805 -1.570 11
L9Z C2 C 5.104 0.680 12
L9Z O17 O 3.805 1.430 13
L9Z N1 N 8.653 2.729 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
L9Z O16 C14 DOUBLE NONE 1
L9Z O15 C14 SINGLE NONE 2
L9Z C5 C14 SINGLE BEGINWEDGE 3
L9Z C5 C6 SINGLE NONE 4
L9Z C5 C4 SINGLE NONE 5
L9Z C6 C1 SINGLE NONE 6
L9Z C4 C3 SINGLE NONE 7
L9Z C1 C21 SINGLE NONE 8
L9Z C1 O28 SINGLE BEGINDASH 9
L9Z C1 C2 SINGLE NONE 10
L9Z C3 C2 SINGLE NONE 11
L9Z C3 O19 SINGLE BEGINWEDGE 12
L9Z C2 O17 SINGLE BEGINDASH 13
L9Z C21 N1 SINGLE NONE 14
#
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
L9Z MurckoScaffold S1 scaffold C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N
L9Z cyclohexane F1 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-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
L9Z C5 S1 1
L9Z C6 S1 1
L9Z C1 S1 1
L9Z C4 S1 1
L9Z C3 S1 1
L9Z C2 S1 1
L9Z C5 F1 1
L9Z C6 F1 1
L9Z C1 F1 1
L9Z C2 F1 1
L9Z C3 F1 1
L9Z C4 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id L9Z
_pdbe_chem_comp_rdkit_properties.exactmw 205.095
_pdbe_chem_comp_rdkit_properties.amw 205.210
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 29
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.875
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_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 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 102.504
_pdbe_chem_comp_rdkit_properties.tpsa 124.010
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.107
_pdbe_chem_comp_rdkit_properties.CrippenMR 46.378
_pdbe_chem_comp_rdkit_properties.chi0v 6.488
_pdbe_chem_comp_rdkit_properties.chi1v 3.244
_pdbe_chem_comp_rdkit_properties.chi2v 1.427
_pdbe_chem_comp_rdkit_properties.chi3v 1.427
_pdbe_chem_comp_rdkit_properties.chi4v 0.775
_pdbe_chem_comp_rdkit_properties.chi0n 21.488
_pdbe_chem_comp_rdkit_properties.chi1n 10.272
_pdbe_chem_comp_rdkit_properties.chi2n 1.427
_pdbe_chem_comp_rdkit_properties.chi3n 1.427
_pdbe_chem_comp_rdkit_properties.chi4n 0.775
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.690
_pdbe_chem_comp_rdkit_properties.kappa1 2.517
_pdbe_chem_comp_rdkit_properties.kappa2 3.817
_pdbe_chem_comp_rdkit_properties.kappa3 1.877
_pdbe_chem_comp_rdkit_properties.Phi 0.686
#
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
L9Z UniChem PDBe L9Z
L9Z UniChem PubChem 138753606
#
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
L9Z O16 -3.692 -0.933 -1.535 ETKDGv3 1
L9Z C14 -2.991 -0.671 -0.521 ETKDGv3 2
L9Z O15 -3.499 -0.915 0.753 ETKDGv3 3
L9Z C5 -1.611 -0.098 -0.688 ETKDGv3 4
L9Z C6 -0.560 -1.045 -0.083 ETKDGv3 5
L9Z C1 0.883 -0.489 -0.235 ETKDGv3 6
L9Z O28 1.212 -0.385 -1.603 ETKDGv3 7
L9Z C21 1.865 -1.464 0.472 ETKDGv3 8
L9Z C4 -1.526 1.287 -0.028 ETKDGv3 9
L9Z C3 -0.114 1.876 -0.178 ETKDGv3 10
L9Z O19 -0.049 3.143 0.429 ETKDGv3 11
L9Z C2 0.960 0.927 0.410 ETKDGv3 12
L9Z O17 2.233 1.482 0.190 ETKDGv3 13
L9Z H1 -4.427 -1.301 0.877 ETKDGv3 14
L9Z H2 -1.406 0.015 -1.777 ETKDGv3 15
L9Z H3 -0.635 -2.036 -0.584 ETKDGv3 16
L9Z H4 -0.783 -1.203 0.997 ETKDGv3 17
L9Z H5 1.153 -1.293 -2.002 ETKDGv3 18
L9Z H6 1.702 -2.503 0.103 ETKDGv3 19
L9Z H7 1.664 -1.468 1.566 ETKDGv3 20
L9Z H9 -1.786 1.210 1.051 ETKDGv3 21
L9Z H10 -2.258 1.972 -0.511 ETKDGv3 22
L9Z H11 0.092 2.016 -1.262 ETKDGv3 23
L9Z H12 -0.219 3.021 1.400 ETKDGv3 24
L9Z H13 0.780 0.820 1.508 ETKDGv3 25
L9Z H14 2.389 2.148 0.909 ETKDGv3 26
L9Z N1 3.259 -1.090 0.242 ETKDGv3 27
L9Z H8 3.506 -1.324 -0.747 ETKDGv3 28
L9Z H15 3.857 -1.699 0.846 ETKDGv3 29
#