data_DLE
#
_chem_comp.id DLE
_chem_comp.name D-LEUCINE
_chem_comp.type "D-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C6 H13 N O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_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 131.173
_chem_comp.one_letter_code L
_chem_comp.three_letter_code DLE
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1GMK
_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
DLE N N N 0 1 N N N Y Y N 13.228 -0.750 7.284 1.579 0.865 -0.459 N DLE 1
DLE CA CA C 0 1 N N R Y N N 12.726 -1.779 8.236 0.165 0.466 -0.464 CA DLE 2
DLE CB CB C 0 1 N N N N N N 11.198 -1.770 8.316 -0.068 -0.596 0.610 CB DLE 3
DLE CG CG C 0 1 N N N N N N 10.552 -0.587 9.017 0.176 0.012 1.992 CG DLE 4
DLE CD1 CD1 C 0 1 N N N N N N 9.440 0.069 8.179 -0.879 1.083 2.272 CD1 DLE 5
DLE CD2 CD2 C 0 1 N N N N N N 9.991 -1.069 10.349 0.086 -1.083 3.055 CD2 DLE 6
DLE C C C 0 1 N N N Y N Y 13.370 -1.627 9.629 -0.192 -0.096 -1.815 C DLE 7
DLE O O O 0 1 N N N Y N Y 13.261 -0.584 10.279 0.647 -0.660 -2.477 O DLE 8
DLE OXT OXT O 0 1 N Y N Y N Y 14.037 -2.675 10.093 -1.444 0.027 -2.284 OXT DLE 9
DLE H H H 0 1 N N N Y Y N 14.246 -0.756 7.230 1.708 1.485 -1.245 H DLE 10
DLE H2 HN2 H 0 1 N Y N Y Y N 12.871 0.177 7.514 2.115 0.033 -0.655 H2 DLE 11
DLE HA HA H 0 1 N N N Y N N 13.031 -2.775 7.839 -0.457 1.336 -0.256 HA DLE 12
DLE HB2 1HB H 0 1 N N N N N N 10.771 -1.873 7.291 0.617 -1.429 0.452 HB2 DLE 13
DLE HB3 2HB H 0 1 N N N N N N 10.844 -2.718 8.783 -1.095 -0.955 0.548 HB3 DLE 14
DLE HG HG H 0 1 N N N N N N 11.330 0.195 9.171 1.168 0.463 2.019 HG DLE 15
DLE HD11 1HD1 H 0 0 N N N N N N 8.965 0.937 8.693 -0.704 1.517 3.256 HD11 DLE 16
DLE HD12 2HD1 H 0 0 N N N N N N 9.818 0.360 7.171 -0.814 1.864 1.514 HD12 DLE 17
DLE HD13 3HD1 H 0 0 N N N N N N 8.673 -0.681 7.874 -1.871 0.631 2.244 HD13 DLE 18
DLE HD21 1HD2 H 0 0 N N N N N N 9.516 -0.200 10.863 -0.930 -1.475 3.088 HD21 DLE 19
DLE HD22 2HD2 H 0 0 N N N N N N 9.295 -1.932 10.234 0.777 -1.889 2.807 HD22 DLE 20
DLE HD23 3HD2 H 0 0 N N N N N N 10.758 -1.575 10.980 0.347 -0.668 4.028 HD23 DLE 21
DLE HXT HXT H 0 1 N Y N Y N Y 14.433 -2.581 10.951 -1.674 -0.334 -3.150 HXT DLE 22
#
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
DLE N CA SING N N 1
DLE N H SING N N 2
DLE N H2 SING N N 3
DLE CA CB SING N N 4
DLE CA C SING N N 5
DLE CA HA SING N N 6
DLE CB CG SING N N 7
DLE CB HB2 SING N N 8
DLE CB HB3 SING N N 9
DLE CG CD1 SING N N 10
DLE CG CD2 SING N N 11
DLE CG HG SING N N 12
DLE CD1 HD11 SING N N 13
DLE CD1 HD12 SING N N 14
DLE CD1 HD13 SING N N 15
DLE CD2 HD21 SING N N 16
DLE CD2 HD22 SING N N 17
DLE CD2 HD23 SING N N 18
DLE C O DOUB N N 19
DLE C OXT SING N N 20
DLE OXT HXT 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
DLE SMILES ACDLabs 10.04 O=C(O)C(N)CC(C)C
DLE SMILES_CANONICAL CACTVS 3.341 CC(C)C[C@@H](N)C(O)=O
DLE SMILES CACTVS 3.341 CC(C)C[CH](N)C(O)=O
DLE SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC(C)C[C@H](C(=O)O)N
DLE SMILES "OpenEye OEToolkits" 1.5.0 CC(C)CC(C(=O)O)N
DLE InChI InChI 1.03 InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t5-/m1/s1
DLE InChIKey InChI 1.03 ROHFNLRQFUQHCH-RXMQYKEDSA-N
#
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
DLE "SYSTEMATIC NAME" ACDLabs 10.04 D-leucine
DLE "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R)-2-amino-4-methyl-pentanoic 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
DLE 'Create component' 1999-07-08 RCSB
DLE 'Modify descriptor' 2011-06-04 RCSB
DLE 'Modify backbone' 2023-11-03 PDBE
#
_pdbe_chem_comp_drugbank_details.comp_id DLE
_pdbe_chem_comp_drugbank_details.drugbank_id DB01746
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name D-Leucine
_pdbe_chem_comp_drugbank_details.description
'An essential branched-chain amino acid important for hemoglobin formation. [PubChem]'
_pdbe_chem_comp_drugbank_details.cas_number 328-38-1
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
DLE '(2R)-2-amino-4-methylpentanoic acid' DrugBank ?
DLE '(R)-(−)-leucine' DrugBank ?
DLE (R)-leucine DrugBank ?
DLE 'D-2-Amino-4-methylvaleric acid' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id DLE
_pdbe_chem_comp_drugbank_classification.drugbank_id DB01746
_pdbe_chem_comp_drugbank_classification.parent 'Leucine and derivatives'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Carboxylic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as leucine and derivatives. These are compounds containing leucine or a derivative thereof resulting from reaction of leucine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.'
#
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
DLE N N 4.299 1.500 1
DLE CA C 5.598 0.750 2
DLE CB C 5.598 -0.750 3
DLE CG C 4.299 -1.500 4
DLE CD1 C 4.299 -3.000 5
DLE CD2 C 3.000 -0.750 6
DLE C C 6.897 1.500 7
DLE O O 8.196 0.750 8
DLE OXT O 6.897 3.000 9
#
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
DLE CA N SINGLE BEGINWEDGE 1
DLE CA CB SINGLE NONE 2
DLE CA C SINGLE NONE 3
DLE CB CG SINGLE NONE 4
DLE CG CD1 SINGLE NONE 5
DLE CG CD2 SINGLE NONE 6
DLE C O DOUBLE NONE 7
DLE C OXT SINGLE NONE 8
#
_pdbe_chem_comp_substructure.comp_id DLE
_pdbe_chem_comp_substructure.substructure_name peptide
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles NCC=O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2
_pdbe_chem_comp_substructure.substructure_inchikeys 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
DLE O F1 1
DLE C F1 1
DLE CA F1 1
DLE N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id DLE
_pdbe_chem_comp_rdkit_properties.exactmw 131.095
_pdbe_chem_comp_rdkit_properties.amw 131.175
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 9
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 73.327
_pdbe_chem_comp_rdkit_properties.tpsa 63.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.444
_pdbe_chem_comp_rdkit_properties.CrippenMR 35.066
_pdbe_chem_comp_rdkit_properties.chi0v 4.264
_pdbe_chem_comp_rdkit_properties.chi1v 1.882
_pdbe_chem_comp_rdkit_properties.chi2v 0.437
_pdbe_chem_comp_rdkit_properties.chi3v 0.437
_pdbe_chem_comp_rdkit_properties.chi4v 0.169
_pdbe_chem_comp_rdkit_properties.chi0n 17.264
_pdbe_chem_comp_rdkit_properties.chi1n 8.185
_pdbe_chem_comp_rdkit_properties.chi2n 0.437
_pdbe_chem_comp_rdkit_properties.chi3n 0.437
_pdbe_chem_comp_rdkit_properties.chi4n 0.169
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.570
_pdbe_chem_comp_rdkit_properties.kappa1 1.115
_pdbe_chem_comp_rdkit_properties.kappa2 3.455
_pdbe_chem_comp_rdkit_properties.kappa3 3.968
_pdbe_chem_comp_rdkit_properties.Phi 0.428
#
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
DLE UniChem ChEMBL CHEMBL1232258
DLE UniChem DrugBank DB01746
DLE UniChem PDBe DLE
DLE UniChem 'KEGG LIGAND' C01570
DLE UniChem ChEBI 143079
DLE UniChem ChEBI 28225
DLE UniChem ZINC ZINC000000388396
DLE UniChem fdasrs 965COD96YA
DLE UniChem HMDB HMDB0013773
DLE UniChem NMRShiftDB 60059655
DLE UniChem BindingDb 50463213
DLE UniChem 'EPA CompTox Dashboard' DTXSID6046347
DLE UniChem MetaboLights MTBLC143079
DLE UniChem MetaboLights MTBLC28225
DLE UniChem BRENDA 1717
DLE UniChem BRENDA 2480
DLE UniChem Rhea 143079
DLE UniChem ChemicalBook CB6677228
DLE UniChem MedChemExpress HY-Y0378
DLE UniChem 'Probes And Drugs' PD016144
DLE UniChem Nikkaji J1.197E
DLE UniChem eMolecules 514646
DLE UniChem SureChEMBL SCHEMBL42012
DLE UniChem 'PubChem TPHARMA' 15237770
DLE UniChem PubChem 439524
DLE UniChem PubChem 6950207
DLE UniChem Mcule MCULE-3041792060
DLE UniChem Mcule MCULE-8280206722
#
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
DLE N 1.672 2.099 -0.218 ETKDGv3 1
DLE CA 0.843 0.912 -0.440 ETKDGv3 2
DLE CB -0.018 0.606 0.815 ETKDGv3 3
DLE CG -1.205 -0.373 0.616 ETKDGv3 4
DLE CD1 -2.231 0.136 -0.406 ETKDGv3 5
DLE CD2 -0.762 -1.803 0.284 ETKDGv3 6
DLE C 1.742 -0.235 -0.804 ETKDGv3 7
DLE O 1.758 -0.673 -1.986 ETKDGv3 8
DLE OXT 2.587 -0.794 0.151 ETKDGv3 9
DLE H 2.206 1.990 0.675 ETKDGv3 10
DLE H2 1.047 2.931 -0.109 ETKDGv3 11
DLE HA 0.176 1.129 -1.301 ETKDGv3 12
DLE HB2 0.633 0.227 1.633 ETKDGv3 13
DLE HB3 -0.444 1.564 1.189 ETKDGv3 14
DLE HG -1.730 -0.424 1.596 ETKDGv3 15
DLE HD11 -2.502 1.191 -0.191 ETKDGv3 16
DLE HD12 -3.155 -0.477 -0.347 ETKDGv3 17
DLE HD13 -1.838 0.065 -1.442 ETKDGv3 18
DLE HD21 -1.623 -2.497 0.391 ETKDGv3 19
DLE HD22 -0.393 -1.878 -0.760 ETKDGv3 20
DLE HD23 0.036 -2.135 0.981 ETKDGv3 21
DLE HXT 3.203 -1.562 -0.086 ETKDGv3 22
#