data_6DN
#
_chem_comp.id 6DN
_chem_comp.name "(2~{S})-2-azanyl-6-(2-hydroxy-2-oxoethylamino)hexanoic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C8 H16 N2 O4"
_chem_comp.mon_nstd_parent_comp_id LYS
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2016-03-30
_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 204.224
_chem_comp.one_letter_code K
_chem_comp.three_letter_code 6DN
_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 Y
_chem_comp.pdbx_model_coordinates_db_code 5J2S
_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
6DN O1 O1 O 0 1 N N N N N N -10.512 -29.428 1.755 ? ? ? O1 6DN 1
6DN O2 O2 O 0 1 N N N N N N -10.053 -28.142 0.042 ? ? ? O2 6DN 2
6DN CB C1 C 0 1 N N N N N N -14.629 -22.921 3.880 ? ? ? CB 6DN 3
6DN CA C2 C 0 1 N N S Y N N -14.600 -21.516 4.479 ? ? ? CA 6DN 4
6DN C C3 C 0 1 N N N Y N Y -15.961 -21.150 4.994 ? ? ? C 6DN 5
6DN O O3 O 0 1 N N N Y N Y -16.270 -21.443 6.167 ? ? ? O 6DN 6
6DN N N1 N 0 1 N N N Y Y N -13.796 -21.460 5.695 ? ? ? N 6DN 7
6DN CG C4 C 0 1 N N N N N N -13.376 -23.371 3.088 ? ? ? CG 6DN 8
6DN CD C5 C 0 1 N N N N N N -13.515 -24.805 2.528 ? ? ? CD 6DN 9
6DN CE C6 C 0 1 N N N N N N -12.717 -25.047 1.250 ? ? ? CE 6DN 10
6DN NZ N2 N 0 1 N N N N N N -12.268 -26.425 0.964 ? ? ? NZ 6DN 11
6DN CX1 C7 C 0 1 N N N N N N -11.308 -27.155 1.790 ? ? ? CX1 6DN 12
6DN CX2 C8 C 0 1 N N N N N N -10.577 -28.318 1.148 ? ? ? CX2 6DN 13
6DN OXT O4 O 0 1 N Y N Y N Y -16.741 -20.454 4.166 ? ? ? O3 6DN 14
6DN H1 H1 H 0 1 N N N N N N -10.019 -30.048 1.231 ? ? ? H1 6DN 15
6DN HB2 H2 H 0 1 N N N N N N -15.490 -22.974 3.198 ? ? ? H2 6DN 16
6DN HB3 H3 H 0 1 N N N N N N -14.773 -23.632 4.707 ? ? ? H3 6DN 17
6DN HA H4 H 0 1 N N N Y N N -14.254 -20.786 3.732 ? ? ? H4 6DN 18
6DN H H5 H 0 1 N N N Y Y N -13.801 -20.527 6.056 ? ? ? H5 6DN 19
6DN H2 H6 H 0 1 N Y N Y Y N -14.179 -22.083 6.377 ? ? ? H6 6DN 20
6DN HG2 H8 H 0 1 N N N N N N -12.504 -23.336 3.758 ? ? ? H8 6DN 21
6DN HG3 H9 H 0 1 N N N N N N -13.221 -22.678 2.248 ? ? ? H9 6DN 22
6DN HD2 H10 H 0 1 N N N N N N -14.578 -24.992 2.314 ? ? ? H10 6DN 23
6DN HD3 H11 H 0 1 N N N N N N -13.165 -25.512 3.295 ? ? ? H11 6DN 24
6DN HE2 H12 H 0 1 N N N N N N -11.819 -24.414 1.300 ? ? ? H12 6DN 25
6DN HE3 H13 H 0 1 N N N N N N -13.345 -24.726 0.406 ? ? ? H13 6DN 26
6DN HZ1 H14 H 0 1 N N N N N N -13.097 -26.984 0.952 ? ? ? H14 6DN 27
6DN H16 H16 H 0 1 N N N N N N -10.549 -26.434 2.128 ? ? ? H16 6DN 28
6DN H17 H17 H 0 1 N N N N N N -11.854 -27.548 2.660 ? ? ? H17 6DN 29
6DN HXT H18 H 0 1 N Y N Y N Y -17.550 -20.226 4.609 ? ? ? H18 6DN 30
#
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
6DN O2 CX2 DOUB N N 1
6DN NZ CE SING N N 2
6DN NZ CX1 SING N N 3
6DN CX2 O1 SING N N 4
6DN CX2 CX1 SING N N 5
6DN CE CD SING N N 6
6DN CD CG SING N N 7
6DN CG CB SING N N 8
6DN CB CA SING N N 9
6DN CA C SING N N 10
6DN CA N SING N N 11
6DN C O DOUB N N 12
6DN C OXT SING N N 13
6DN O1 H1 SING N N 14
6DN CB HB2 SING N N 15
6DN CB HB3 SING N N 16
6DN CA HA SING N N 17
6DN N H SING N N 18
6DN N H2 SING N N 19
6DN CG HG2 SING N N 20
6DN CG HG3 SING N N 21
6DN CD HD2 SING N N 22
6DN CD HD3 SING N N 23
6DN CE HE2 SING N N 24
6DN CE HE3 SING N N 25
6DN NZ HZ1 SING N N 26
6DN CX1 H16 SING N N 27
6DN CX1 H17 SING N N 28
6DN OXT HXT 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
6DN InChI InChI 1.03 InChI=1S/C8H16N2O4/c9-6(8(13)14)3-1-2-4-10-5-7(11)12/h6,10H,1-5,9H2,(H,11,12)(H,13,14)/t6-/m0/s1
6DN InChIKey InChI 1.03 NUXSIDPKKIEIMI-LURJTMIESA-N
6DN SMILES_CANONICAL CACTVS 3.385 N[C@@H](CCCCNCC(O)=O)C(O)=O
6DN SMILES CACTVS 3.385 N[CH](CCCCNCC(O)=O)C(O)=O
6DN SMILES_CANONICAL "OpenEye OEToolkits" 2.0.5 C(CCNCC(=O)O)C[C@@H](C(=O)O)N
6DN SMILES "OpenEye OEToolkits" 2.0.5 C(CCNCC(=O)O)CC(C(=O)O)N
#
_pdbx_chem_comp_identifier.comp_id 6DN
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.5
_pdbx_chem_comp_identifier.identifier "(2~{S})-2-azanyl-6-(2-hydroxy-2-oxoethylamino)hexanoic 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
6DN 'Create component' 2016-03-30 EBI
6DN 'Modify parent residue' 2016-03-30 EBI
6DN 'Initial release' 2017-10-11 RCSB
6DN 'Other modification' 2019-04-16 EBI
6DN '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
6DN O1 O 10.301 -3.750 1
6DN O2 O 9.002 -6.000 2
6DN CB C 5.104 2.250 3
6DN CA C 5.104 3.750 4
6DN C C 6.404 4.500 5
6DN O O 7.702 3.750 6
6DN N N 3.805 4.500 7
6DN CG C 6.404 1.500 8
6DN CD C 6.404 0.000 9
6DN CE C 7.702 -0.750 10
6DN NZ N 7.702 -2.250 11
6DN CX1 C 7.702 -3.750 12
6DN CX2 C 9.002 -4.500 13
6DN OXT O 6.404 6.000 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
6DN O2 CX2 DOUBLE NONE 1
6DN NZ CE SINGLE NONE 2
6DN NZ CX1 SINGLE NONE 3
6DN CX2 O1 SINGLE NONE 4
6DN CX2 CX1 SINGLE NONE 5
6DN CE CD SINGLE NONE 6
6DN CD CG SINGLE NONE 7
6DN CG CB SINGLE NONE 8
6DN CB CA SINGLE NONE 9
6DN CA C SINGLE NONE 10
6DN CA N SINGLE BEGINDASH 11
6DN C O DOUBLE NONE 12
6DN C OXT SINGLE NONE 13
#
_pdbe_chem_comp_substructure.comp_id 6DN
_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
6DN O2 F1 1
6DN CX2 F1 1
6DN CX1 F1 1
6DN NZ F1 1
6DN O F1 2
6DN C F1 2
6DN CA F1 2
6DN N F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id 6DN
_pdbe_chem_comp_rdkit_properties.exactmw 204.111
_pdbe_chem_comp_rdkit_properties.amw 204.226
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 30
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.750
_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 104.922
_pdbe_chem_comp_rdkit_properties.tpsa 112.650
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.757
_pdbe_chem_comp_rdkit_properties.CrippenMR 49.968
_pdbe_chem_comp_rdkit_properties.chi0v 6.527
_pdbe_chem_comp_rdkit_properties.chi1v 2.987
_pdbe_chem_comp_rdkit_properties.chi2v 0.696
_pdbe_chem_comp_rdkit_properties.chi3v 0.696
_pdbe_chem_comp_rdkit_properties.chi4v 0.271
_pdbe_chem_comp_rdkit_properties.chi0n 22.527
_pdbe_chem_comp_rdkit_properties.chi1n 10.645
_pdbe_chem_comp_rdkit_properties.chi2n 0.696
_pdbe_chem_comp_rdkit_properties.chi3n 0.696
_pdbe_chem_comp_rdkit_properties.chi4n 0.271
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.140
_pdbe_chem_comp_rdkit_properties.kappa1 2.330
_pdbe_chem_comp_rdkit_properties.kappa2 7.281
_pdbe_chem_comp_rdkit_properties.kappa3 7.506
_pdbe_chem_comp_rdkit_properties.Phi 1.212
#
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
6DN UniChem PDBe 6DN
6DN UniChem ChEBI 53014
6DN UniChem ZINC ZINC000002599098
6DN UniChem fdasrs 70YDX3Z2O7
6DN UniChem SureChEMBL SCHEMBL43621
6DN UniChem HMDB HMDB0240347
6DN UniChem 'PubChem TPHARMA' 16349930
6DN UniChem PubChem 40430212
6DN UniChem NMRShiftDB 70074823
6DN UniChem Nikkaji J437.648J
6DN UniChem MetaboLights MTBLC53014
6DN UniChem BRENDA 260032
6DN UniChem ChemicalBook CB7410316
6DN UniChem 'Probes And Drugs' PD018338
6DN UniChem eMolecules 10479975
6DN UniChem PubChem 123800
6DN UniChem ACTor 5746-04-3
#
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
6DN O1 5.684 0.696 0.183 ETKDGv3 1
6DN O2 4.452 -0.723 -1.138 ETKDGv3 2
6DN CB -1.932 -0.397 0.043 ETKDGv3 3
6DN CA -3.053 -0.247 -1.002 ETKDGv3 4
6DN C -4.219 -1.132 -0.647 ETKDGv3 5
6DN O -4.595 -2.030 -1.448 ETKDGv3 6
6DN N -3.482 1.150 -1.102 ETKDGv3 7
6DN CG -0.664 0.367 -0.366 ETKDGv3 8
6DN CD 0.451 0.177 0.669 ETKDGv3 9
6DN CE 1.717 0.939 0.264 ETKDGv3 10
6DN NZ 2.754 0.793 1.298 ETKDGv3 11
6DN CX1 3.611 -0.384 1.080 ETKDGv3 12
6DN CX2 4.604 -0.156 -0.023 ETKDGv3 13
6DN OXT -4.886 -0.960 0.563 ETKDGv3 14
6DN H1 6.359 0.866 -0.553 ETKDGv3 15
6DN HB2 -2.286 -0.025 1.030 ETKDGv3 16
6DN HB3 -1.681 -1.476 0.151 ETKDGv3 17
6DN HA -2.654 -0.565 -1.991 ETKDGv3 18
6DN H -4.209 1.225 -1.850 ETKDGv3 19
6DN H2 -3.926 1.446 -0.202 ETKDGv3 20
6DN HG2 -0.897 1.450 -0.458 ETKDGv3 21
6DN HG3 -0.314 -0.004 -1.355 ETKDGv3 22
6DN HD2 0.681 -0.906 0.763 ETKDGv3 23
6DN HD3 0.105 0.549 1.658 ETKDGv3 24
6DN HE2 2.075 0.591 -0.731 ETKDGv3 25
6DN HE3 1.459 2.017 0.160 ETKDGv3 26
6DN HZ1 3.350 1.655 1.308 ETKDGv3 27
6DN H16 4.171 -0.589 2.016 ETKDGv3 28
6DN H17 2.999 -1.287 0.869 ETKDGv3 29
6DN HXT -5.671 -1.549 0.812 ETKDGv3 30
#