data_41K
#
_chem_comp.id 41K
_chem_comp.name "(2R,4R)-2-methyl-1,3-thiazolidine-2,4-dicarboxylic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H9 N O4 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-01-13
_chem_comp.pdbx_modified_date 2015-02-06
_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 191.205
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 41K
_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 4XKR
_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
41K OAA O1 O 0 1 N N N N N N 39.427 61.793 13.443 -3.415 -0.323 0.244 OAA 41K 1
41K CAE C1 C 0 1 N N N N N N 39.012 61.092 12.491 -2.141 -0.748 0.235 CAE 41K 2
41K OAD O2 O 0 1 N N N N N N 39.524 61.056 11.360 -1.846 -1.783 0.784 OAD 41K 3
41K CAF C2 C 0 1 N N R N N N 37.806 60.173 12.728 -1.081 0.066 -0.460 CAF 41K 4
41K CAB C3 C 0 1 N N N N N N 36.617 60.700 11.918 -1.502 0.375 -1.898 CAB 41K 5
41K N N1 N 0 1 N N N N N N 37.349 60.052 14.136 0.215 -0.651 -0.443 N 41K 6
41K SAK S1 S 0 1 N N N N N N 38.283 58.508 12.249 -0.759 1.618 0.463 SAK 41K 7
41K CB C4 C 0 1 N N N N N N 37.891 57.744 13.811 1.033 1.320 0.741 CB 41K 8
41K CA C5 C 0 1 N N R N N N 37.995 58.921 14.828 1.342 0.299 -0.389 CA 41K 9
41K C C6 C 0 1 N N N N N N 39.424 59.092 15.347 2.619 -0.438 -0.078 C 41K 10
41K O O3 O 0 1 N N N N N N 40.060 58.029 15.539 2.602 -1.635 0.084 O 41K 11
41K OXT O4 O 0 1 N N N N N N 39.814 60.257 15.606 3.776 0.236 0.019 OXT 41K 12
41K H1 H1 H 0 1 N N N N N N 40.189 62.288 13.164 -4.060 -0.879 0.702 H1 41K 13
41K H2 H2 H 0 1 N N N N N N 36.368 61.718 12.251 -2.441 0.928 -1.890 H2 41K 14
41K H3 H3 H 0 1 N N N N N N 36.880 60.717 10.850 -0.731 0.974 -2.382 H3 41K 15
41K H4 H4 H 0 1 N N N N N N 35.749 60.042 12.071 -1.635 -0.558 -2.445 H4 41K 16
41K H5 H5 H 0 1 N N N N N N 37.571 60.898 14.622 0.256 -1.305 0.324 H5 41K 17
41K H7 H7 H 0 1 N N N N N N 36.875 57.323 13.799 1.608 2.237 0.610 H7 41K 18
41K H8 H8 H 0 1 N N N N N N 38.613 56.950 14.053 1.211 0.884 1.724 H8 41K 19
41K H9 H9 H 0 1 N N N N N N 37.367 58.652 15.690 1.435 0.819 -1.343 H9 41K 20
41K H10 H10 H 0 1 N N N N N N 40.687 60.223 15.980 4.569 -0.280 0.220 H10 41K 21
#
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
41K OAD CAE DOUB N N 1
41K CAB CAF SING N N 2
41K SAK CAF SING N N 3
41K SAK CB SING N N 4
41K CAE CAF SING N N 5
41K CAE OAA SING N N 6
41K CAF N SING N N 7
41K CB CA SING N N 8
41K N CA SING N N 9
41K CA C SING N N 10
41K C O DOUB N N 11
41K C OXT SING N N 12
41K OAA H1 SING N N 13
41K CAB H2 SING N N 14
41K CAB H3 SING N N 15
41K CAB H4 SING N N 16
41K N H5 SING N N 17
41K CB H7 SING N N 18
41K CB H8 SING N N 19
41K CA H9 SING N N 20
41K OXT H10 SING N N 21
#
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
41K SMILES ACDLabs 12.01 O=C(O)C1(SCC(C(=O)O)N1)C
41K InChI InChI 1.03 InChI=1S/C6H9NO4S/c1-6(5(10)11)7-3(2-12-6)4(8)9/h3,7H,2H2,1H3,(H,8,9)(H,10,11)/t3-,6+/m0/s1
41K InChIKey InChI 1.03 JCAKCGQZNBEITC-BBIVZNJYSA-N
41K SMILES_CANONICAL CACTVS 3.385 C[C@]1(N[C@@H](CS1)C(O)=O)C(O)=O
41K SMILES CACTVS 3.385 C[C]1(N[CH](CS1)C(O)=O)C(O)=O
41K SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 C[C@]1(N[C@@H](CS1)C(=O)O)C(=O)O
41K SMILES "OpenEye OEToolkits" 1.9.2 CC1(NC(CS1)C(=O)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
41K "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,4R)-2-methyl-1,3-thiazolidine-2,4-dicarboxylic acid"
41K "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "(2R,4R)-2-methyl-1,3-thiazolidine-2,4-dicarboxylic 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
41K 'Create component' 2015-01-13 EBI
41K 'Initial release' 2015-02-11 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
41K OAA O 9.124 -2.005 1
41K CAE C 9.735 -0.635 2
41K OAD O 11.226 -0.478 3
41K CAF C 8.853 0.579 4
41K CAB C 10.280 1.042 5
41K N N 7.639 -0.303 6
41K SAK S 8.389 2.005 7
41K CB C 6.889 2.005 8
41K CA C 6.426 0.579 9
41K C C 4.999 0.115 10
41K O O 3.884 1.119 11
41K OXT O 4.687 -1.352 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
41K OAD CAE DOUBLE NONE 1
41K CAF CAB SINGLE BEGINWEDGE 2
41K SAK CAF SINGLE NONE 3
41K SAK CB SINGLE NONE 4
41K CAE CAF SINGLE NONE 5
41K CAE OAA SINGLE NONE 6
41K CAF N SINGLE NONE 7
41K CB CA SINGLE NONE 8
41K N CA SINGLE NONE 9
41K CA C SINGLE BEGINDASH 10
41K C O DOUBLE NONE 11
41K C OXT SINGLE NONE 12
#
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
41K MurckoScaffold S1 scaffold C1CSCN1 InChI=1S/C3H7NS/c1-2-5-3-4-1/h4H,1-3H2 OGYGFUAIIOPWQD-UHFFFAOYSA-N
41K peptide F1 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
41K CAF S1 1
41K N S1 1
41K SAK S1 1
41K CB S1 1
41K CA S1 1
41K OAD F1 1
41K CAE F1 1
41K CAF F1 1
41K N F1 1
41K O F1 2
41K C F1 2
41K CA F1 2
41K N F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id 41K
_pdbe_chem_comp_rdkit_properties.exactmw 191.025
_pdbe_chem_comp_rdkit_properties.amw 191.208
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 21
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.667
_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 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_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 86.019
_pdbe_chem_comp_rdkit_properties.tpsa 86.630
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.423
_pdbe_chem_comp_rdkit_properties.CrippenMR 43.058
_pdbe_chem_comp_rdkit_properties.chi0v 6.305
_pdbe_chem_comp_rdkit_properties.chi1v 3.488
_pdbe_chem_comp_rdkit_properties.chi2v 1.883
_pdbe_chem_comp_rdkit_properties.chi3v 1.883
_pdbe_chem_comp_rdkit_properties.chi4v 1.094
_pdbe_chem_comp_rdkit_properties.chi0n 14.488
_pdbe_chem_comp_rdkit_properties.chi1n 6.936
_pdbe_chem_comp_rdkit_properties.chi2n 1.035
_pdbe_chem_comp_rdkit_properties.chi3n 1.035
_pdbe_chem_comp_rdkit_properties.chi4n 0.500
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.750
_pdbe_chem_comp_rdkit_properties.kappa1 2.882
_pdbe_chem_comp_rdkit_properties.kappa2 2.947
_pdbe_chem_comp_rdkit_properties.kappa3 1.535
_pdbe_chem_comp_rdkit_properties.Phi 0.708
#
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
41K UniChem PDBe 41K
41K UniChem ZINC ZINC000001701053
41K UniChem SureChEMBL SCHEMBL3127120
41K UniChem 'PubChem TPHARMA' 15188852
41K UniChem PubChem 10192618
#
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
41K OAA 2.384 -0.030 1.587 ETKDGv3 1
41K CAE 2.273 -0.272 0.220 ETKDGv3 2
41K OAD 3.250 -0.769 -0.404 ETKDGv3 3
41K CAF 1.010 0.089 -0.517 ETKDGv3 4
41K CAB 1.289 1.270 -1.465 ETKDGv3 5
41K N -0.045 0.426 0.455 ETKDGv3 6
41K SAK 0.469 -1.350 -1.514 ETKDGv3 7
41K CB -1.144 -1.368 -0.703 ETKDGv3 8
41K CA -1.333 0.002 -0.082 ETKDGv3 9
41K C -2.362 -0.043 1.008 ETKDGv3 10
41K O -3.533 0.365 0.786 ETKDGv3 11
41K OXT -2.036 -0.571 2.255 ETKDGv3 12
41K H1 3.234 -0.259 2.088 ETKDGv3 13
41K H2 1.656 2.150 -0.894 ETKDGv3 14
41K H3 2.059 0.993 -2.217 ETKDGv3 15
41K H4 0.364 1.561 -2.006 ETKDGv3 16
41K H5 -0.070 1.456 0.648 ETKDGv3 17
41K H7 -1.132 -2.163 0.075 ETKDGv3 18
41K H8 -1.944 -1.584 -1.443 ETKDGv3 19
41K H9 -1.663 0.717 -0.871 ETKDGv3 20
41K H10 -2.725 -0.620 2.995 ETKDGv3 21
#