data_2KY
#
_chem_comp.id 2KY
_chem_comp.name "(2S)-amino(cyclopentyl)ethanoic acid"
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C7 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 2013-11-22
_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 143.184
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 2KY
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 2M8Q
_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
2KY C C5 C 0 1 N N N Y N Y 124.203 -9.566 6.793 1.842 -0.313 0.032 C5 2KY 1
2KY CA C6 C 0 1 N N S Y N N 125.333 -10.346 7.563 0.711 0.587 0.459 C6 2KY 2
2KY N N7 N 0 1 N N N Y Y N 126.641 -10.008 6.945 1.073 1.986 0.196 N7 2KY 3
2KY O O32 O 0 1 N N N Y N Y 124.450 -8.502 6.228 2.672 0.089 -0.748 O32 2KY 4
2KY C33 C33 C 0 1 N N N N N N 125.289 -9.935 9.071 -0.551 0.229 -0.329 C33 2KY 5
2KY C34 C34 C 0 1 N N N N N N 126.568 -10.271 9.860 -1.725 1.138 0.090 C34 2KY 6
2KY C35 C35 C 0 1 N N N N N N 126.146 -10.261 11.330 -2.986 0.256 0.089 C35 2KY 7
2KY C36 C36 C 0 1 N N N N N N 124.624 -10.368 11.336 -2.534 -1.158 -0.331 C36 2KY 8
2KY C37 C37 C 0 1 N N N N N N 124.236 -10.681 9.900 -1.028 -1.199 0.032 C37 2KY 9
2KY HA H6 H 0 1 N N N Y N N 125.142 -11.426 7.479 0.524 0.454 1.525 H6 2KY 10
2KY H H7 H 0 1 N N N Y Y N 127.372 -10.496 7.423 1.251 2.135 -0.786 H7 2KY 11
2KY H33 H33 H 0 1 N N N N N N 125.100 -8.853 9.137 -0.367 0.313 -1.400 H33 2KY 12
2KY H341 H341 H 0 0 N N N N N N 126.948 -11.263 9.574 -1.550 1.537 1.089 1H34 2KY 13
2KY H342 H342 H 0 0 N N N N N N 127.345 -9.514 9.676 -1.839 1.954 -0.623 2H34 2KY 14
2KY H352 H352 H 0 0 N N N N N N 126.591 -11.116 11.860 -3.422 0.227 1.088 2H35 2KY 15
2KY H351 H351 H 0 0 N N N N N N 126.464 -9.325 11.812 -3.712 0.643 -0.625 1H35 2KY 16
2KY H361 H361 H 0 0 N N N N N N 124.173 -9.418 11.658 -3.082 -1.916 0.229 1H36 2KY 17
2KY H362 H362 H 0 0 N N N N N N 124.298 -11.176 12.008 -2.674 -1.301 -1.403 2H36 2KY 18
2KY H371 H371 H 0 0 N N N N N N 123.225 -10.310 9.677 -0.507 -1.944 -0.569 1H37 2KY 19
2KY H372 H372 H 0 0 N N N N N N 124.280 -11.763 9.708 -0.892 -1.395 1.095 2H37 2KY 20
2KY H2 H2 H 0 1 N Y N Y Y N 126.634 -10.278 5.982 0.358 2.614 0.532 H2 2KY 21
2KY OXT OXT O 0 1 N Y N Y N Y ? ? ? 1.929 -1.559 0.522 OXT 2KY 22
2KY HXT HXT H 0 1 N Y N Y N Y ? ? ? 2.672 -2.099 0.219 HXT 2KY 23
#
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
2KY O C DOUB N N 1
2KY C CA SING N N 2
2KY N CA SING N N 3
2KY CA C33 SING N N 4
2KY C33 C34 SING N N 5
2KY C33 C37 SING N N 6
2KY C34 C35 SING N N 7
2KY C37 C36 SING N N 8
2KY C35 C36 SING N N 9
2KY CA HA SING N N 10
2KY N H SING N N 11
2KY C33 H33 SING N N 12
2KY C34 H341 SING N N 13
2KY C34 H342 SING N N 14
2KY C35 H352 SING N N 15
2KY C35 H351 SING N N 16
2KY C36 H361 SING N N 17
2KY C36 H362 SING N N 18
2KY C37 H371 SING N N 19
2KY C37 H372 SING N N 20
2KY N H2 SING N N 21
2KY C OXT SING N N 22
2KY OXT HXT SING N N 23
#
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
2KY SMILES ACDLabs 12.01 O=C(O)C(N)C1CCCC1
2KY InChI InChI 1.03 InChI=1S/C7H13NO2/c8-6(7(9)10)5-3-1-2-4-5/h5-6H,1-4,8H2,(H,9,10)/t6-/m0/s1
2KY InChIKey InChI 1.03 XBPKRVHTESHFAA-LURJTMIESA-N
2KY SMILES_CANONICAL CACTVS 3.385 N[C@@H](C1CCCC1)C(O)=O
2KY SMILES CACTVS 3.385 N[CH](C1CCCC1)C(O)=O
2KY SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C1CCC(C1)[C@@H](C(=O)O)N
2KY SMILES "OpenEye OEToolkits" 1.7.6 C1CCC(C1)C(C(=O)O)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
2KY "SYSTEMATIC NAME" ACDLabs 12.01 "(2S)-amino(cyclopentyl)ethanoic acid"
2KY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2S)-2-azanyl-2-cyclopentyl-ethanoic 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
2KY 'Create component' 2013-11-22 RCSB
2KY 'Initial release' 2018-02-28 RCSB
2KY '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
2KY C C 6.404 1.297 1
2KY CA C 5.104 0.547 2
2KY N N 3.805 1.297 3
2KY O O 6.404 2.797 4
2KY C33 C 5.104 -0.953 5
2KY C34 C 3.891 -1.835 6
2KY C35 C 4.354 -3.262 7
2KY C36 C 5.854 -3.262 8
2KY C37 C 6.318 -1.835 9
2KY OXT O 7.702 0.547 10
#
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
2KY O C DOUBLE NONE 1
2KY C CA SINGLE NONE 2
2KY CA N SINGLE BEGINDASH 3
2KY CA C33 SINGLE NONE 4
2KY C33 C34 SINGLE NONE 5
2KY C33 C37 SINGLE NONE 6
2KY C34 C35 SINGLE NONE 7
2KY C37 C36 SINGLE NONE 8
2KY C35 C36 SINGLE NONE 9
2KY C OXT SINGLE NONE 10
#
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
2KY MurckoScaffold S1 scaffold C1CCCC1 InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2 RGSFGYAAUTVSQA-UHFFFAOYSA-N
2KY cyclopentane F1 fragment C1CCCC1 InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2 RGSFGYAAUTVSQA-UHFFFAOYSA-N
2KY peptide F2 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
2KY C33 S1 1
2KY C34 S1 1
2KY C35 S1 1
2KY C36 S1 1
2KY C37 S1 1
2KY C33 F1 1
2KY C34 F1 1
2KY C35 F1 1
2KY C36 F1 1
2KY C37 F1 1
2KY O F2 1
2KY C F2 1
2KY CA F2 1
2KY N F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 2KY
_pdbe_chem_comp_rdkit_properties.exactmw 143.095
_pdbe_chem_comp_rdkit_properties.amw 143.186
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 23
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.857
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 78.686
_pdbe_chem_comp_rdkit_properties.tpsa 63.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.588
_pdbe_chem_comp_rdkit_properties.CrippenMR 37.569
_pdbe_chem_comp_rdkit_properties.chi0v 4.764
_pdbe_chem_comp_rdkit_properties.chi1v 2.382
_pdbe_chem_comp_rdkit_properties.chi2v 0.868
_pdbe_chem_comp_rdkit_properties.chi3v 0.868
_pdbe_chem_comp_rdkit_properties.chi4v 0.439
_pdbe_chem_comp_rdkit_properties.chi0n 17.764
_pdbe_chem_comp_rdkit_properties.chi1n 8.685
_pdbe_chem_comp_rdkit_properties.chi2n 0.868
_pdbe_chem_comp_rdkit_properties.chi3n 0.868
_pdbe_chem_comp_rdkit_properties.chi4n 0.439
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.570
_pdbe_chem_comp_rdkit_properties.kappa1 1.332
_pdbe_chem_comp_rdkit_properties.kappa2 3.012
_pdbe_chem_comp_rdkit_properties.kappa3 1.475
_pdbe_chem_comp_rdkit_properties.Phi 0.401
#
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
2KY UniChem PDBe 2KY
2KY UniChem ZINC ZINC000002042759
2KY UniChem eMolecules 4360535
2KY UniChem SureChEMBL SCHEMBL1053865
2KY UniChem 'PubChem TPHARMA' 15388485
2KY UniChem PubChem 10374564
2KY UniChem ACTor 2521-84-8
2KY UniChem 'EPA CompTox Dashboard' DTXSID20438806
2KY UniChem ChemicalBook CB5436815
2KY UniChem Nikkaji J516.949F
2KY UniChem PubChem 38989116
#
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
2KY C 2.245 -0.514 0.943 ETKDGv3 1
2KY CA 1.377 0.551 0.332 ETKDGv3 2
2KY N 2.139 1.239 -0.714 ETKDGv3 3
2KY O 2.493 -0.494 2.178 ETKDGv3 4
2KY C33 0.065 -0.063 -0.227 ETKDGv3 5
2KY C34 -0.772 -0.758 0.844 ETKDGv3 6
2KY C35 -2.207 -0.727 0.333 ETKDGv3 7
2KY C36 -2.274 0.372 -0.726 ETKDGv3 8
2KY C37 -0.880 0.980 -0.819 ETKDGv3 9
2KY HA 1.122 1.293 1.123 ETKDGv3 10
2KY H 2.210 0.627 -1.560 ETKDGv3 11
2KY H33 0.309 -0.807 -1.021 ETKDGv3 12
2KY H341 -0.427 -1.802 1.011 ETKDGv3 13
2KY H342 -0.715 -0.200 1.806 ETKDGv3 14
2KY H352 -2.467 -1.708 -0.123 ETKDGv3 15
2KY H351 -2.914 -0.521 1.166 ETKDGv3 16
2KY H361 -2.561 -0.066 -1.707 ETKDGv3 17
2KY H362 -3.021 1.147 -0.448 ETKDGv3 18
2KY H371 -0.851 1.916 -0.218 ETKDGv3 19
2KY H372 -0.614 1.213 -1.872 ETKDGv3 20
2KY H2 1.629 2.107 -0.995 ETKDGv3 21
2KY OXT 2.767 -1.530 0.147 ETKDGv3 22
2KY HXT 3.348 -2.256 0.547 ETKDGv3 23
#