data_ZS8
#
_chem_comp.id ZS8
_chem_comp.name '(2S)-2-amino-2-methyldec-8-ynoic acid'
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C11 H19 N O2'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2016-04-06
_chem_comp.pdbx_modified_date 2024-09-27
_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 197.274
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code ZS8
_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 5J31
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
_chem_comp.pdbx_pcm Y
#
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
ZS8 N N N 0 1 N N N Y Y N -14.100 9.222 -13.803 -2.486 1.445 0.935 N ZS8 1
ZS8 CA CA C 0 1 N N S Y N N -13.602 7.989 -14.314 -2.628 0.423 -0.111 CA ZS8 2
ZS8 C C C 0 1 N N N Y N Y -12.280 7.864 -14.099 -3.941 -0.295 0.064 C ZS8 3
ZS8 O O O 0 1 N N N Y N Y -11.768 6.681 -14.060 -4.024 -1.473 -0.191 O ZS8 4
ZS8 CB2 CB2 C 0 1 N N N N N N -14.409 6.882 -13.681 -2.591 1.091 -1.486 CB2 ZS8 5
ZS8 CB1 CB1 C 0 1 N N N N N N -13.919 8.007 -15.796 -1.479 -0.582 -0.000 CB1 ZS8 6
ZS8 CG1 CG1 C 0 1 N N N N N N -13.225 6.950 -16.606 -0.144 0.163 -0.053 CG1 ZS8 7
ZS8 CD1 CD1 C 0 1 N N N N N N -12.974 7.451 -17.959 1.005 -0.841 0.058 CD1 ZS8 8
ZS8 CZ1 CZ1 C 0 1 N N N N N N -11.898 8.441 -17.963 2.341 -0.097 0.005 CZ1 ZS8 9
ZS8 CE1 CE1 C 0 1 N N N N N N -11.176 8.353 -19.259 3.489 -1.101 0.115 CE1 ZS8 10
ZS8 CT1 CT1 C 0 1 N N N N N N -10.867 9.574 -19.694 4.774 -0.385 0.065 CT1 ZS8 11
ZS8 CI1 CI1 C 0 1 N N N N N N -10.616 10.613 -20.063 5.799 0.187 0.025 CI1 ZS8 12
ZS8 CK1 CK1 C 0 1 N N N N N N -10.355 11.832 -20.487 7.084 0.903 -0.025 CK1 ZS8 13
ZS8 H H1 H 0 1 N N N Y Y N -13.921 9.273 -12.821 -2.508 1.029 1.853 H1 ZS8 14
ZS8 H2 H2 H 0 1 N Y N Y Y N -13.644 9.983 -14.265 -1.643 1.984 0.802 H2 ZS8 15
ZS8 H7 H7 H 0 1 N N N N N N -14.199 6.845 -12.602 -3.409 1.807 -1.565 H7 ZS8 16
ZS8 H8 H8 H 0 1 N N N N N N -15.481 7.073 -13.839 -1.641 1.610 -1.612 H8 ZS8 17
ZS8 H9 H9 H 0 1 N N N N N N -14.136 5.921 -14.141 -2.696 0.333 -2.262 H9 ZS8 18
ZS8 H10 H10 H 0 1 N N N N N N -13.627 8.990 -16.195 -1.558 -1.121 0.943 H10 ZS8 19
ZS8 H11 H11 H 0 1 N N N N N N -15.004 7.870 -15.915 -1.534 -1.288 -0.829 H11 ZS8 20
ZS8 H12 H12 H 0 1 N N N N N N -13.861 6.054 -16.660 -0.065 0.703 -0.996 H12 ZS8 21
ZS8 H13 H13 H 0 1 N N N N N N -12.268 6.692 -16.128 -0.089 0.870 0.775 H13 ZS8 22
ZS8 H14 H14 H 0 1 N N N N N N -13.892 7.917 -18.346 0.927 -1.381 1.001 H14 ZS8 23
ZS8 H15 H15 H 0 1 N N N N N N -12.690 6.609 -18.607 0.951 -1.548 -0.771 H15 ZS8 24
ZS8 H16 H16 H 0 1 N N N N N N -11.202 8.235 -17.137 2.419 0.443 -0.938 H16 ZS8 25
ZS8 H17 H17 H 0 1 N N N N N N -12.322 9.449 -17.843 2.395 0.610 0.833 H17 ZS8 26
ZS8 H18 H18 H 0 1 N N N N N N -11.818 7.854 -20.000 3.411 -1.641 1.059 H18 ZS8 27
ZS8 H19 H19 H 0 1 N N N N N N -10.253 7.771 -19.123 3.435 -1.808 -0.713 H19 ZS8 28
ZS8 H20 H20 H 0 1 N N N N N N -9.299 11.898 -20.788 7.902 0.188 0.053 H20 ZS8 29
ZS8 H21 H21 H 0 1 N N N N N N -10.997 12.065 -21.349 7.162 1.443 -0.969 H21 ZS8 30
ZS8 H22 H22 H 0 1 N Y N N N N -10.551 12.551 -19.678 7.138 1.610 0.803 H22 ZS8 31
ZS8 OXT OXT O 0 1 N Y N Y N Y ? ? ? -5.019 0.374 0.502 OXT ZS8 32
ZS8 HXT H3 H 0 1 N Y N Y N Y ? ? ? -5.839 -0.129 0.599 H3 ZS8 33
#
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
ZS8 CK1 CI1 SING N N 1
ZS8 CI1 CT1 TRIP N N 2
ZS8 CT1 CE1 SING N N 3
ZS8 CE1 CZ1 SING N N 4
ZS8 CZ1 CD1 SING N N 5
ZS8 CD1 CG1 SING N N 6
ZS8 CG1 CB1 SING N N 7
ZS8 CB1 CA SING N N 8
ZS8 CA C SING N N 9
ZS8 CA N SING N N 10
ZS8 CA CB2 SING N N 11
ZS8 C O DOUB N N 12
ZS8 N H SING N N 13
ZS8 N H2 SING N N 14
ZS8 CB2 H7 SING N N 15
ZS8 CB2 H8 SING N N 16
ZS8 CB2 H9 SING N N 17
ZS8 CB1 H10 SING N N 18
ZS8 CB1 H11 SING N N 19
ZS8 CG1 H12 SING N N 20
ZS8 CG1 H13 SING N N 21
ZS8 CD1 H14 SING N N 22
ZS8 CD1 H15 SING N N 23
ZS8 CZ1 H16 SING N N 24
ZS8 CZ1 H17 SING N N 25
ZS8 CE1 H18 SING N N 26
ZS8 CE1 H19 SING N N 27
ZS8 CK1 H20 SING N N 28
ZS8 CK1 H21 SING N N 29
ZS8 CK1 H22 SING N N 30
ZS8 C OXT SING N N 31
ZS8 OXT HXT SING N N 32
#
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
ZS8 SMILES ACDLabs 12.01 'NC(C(=O)O)(C)CCCCCC#CC'
ZS8 InChI InChI 1.03 'InChI=1S/C11H19NO2/c1-3-4-5-6-7-8-9-11(2,12)10(13)14/h5-9,12H2,1-2H3,(H,13,14)/t11-/m0/s1'
ZS8 InChIKey InChI 1.03 IEDCXEQAWYUWSL-NSHDSACASA-N
ZS8 SMILES_CANONICAL CACTVS 3.385 'CC#CCCCCC[C@](C)(N)C(O)=O'
ZS8 SMILES CACTVS 3.385 'CC#CCCCCC[C](C)(N)C(O)=O'
ZS8 SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.4 'CC#CCCCCC[C@@](C)(C(=O)O)N'
ZS8 SMILES 'OpenEye OEToolkits' 2.0.4 'CC#CCCCCCC(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
ZS8 'SYSTEMATIC NAME' ACDLabs 12.01 '(2S)-2-amino-2-methyldec-8-ynoic acid'
ZS8 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 2.0.4 '(2~{S})-2-azanyl-2-methyl-dec-8-ynoic 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
ZS8 'Create component' 2016-04-06 EBI
ZS8 'Initial release' 2016-10-19 RCSB
ZS8 'Modify backbone' 2023-11-03 PDBE
ZS8 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id ZS8
_pdbx_chem_comp_pcm.modified_residue_id ?
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Non-standard residue'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain and backbone'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom ?
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom ?
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 '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
ZS8 N N 11.451 -1.859 1
ZS8 CA C 12.750 -1.109 2
ZS8 C C 14.049 -0.358 3
ZS8 O O 15.348 -1.109 4
ZS8 CB2 C 13.500 -2.408 5
ZS8 CB1 C 12.000 0.191 6
ZS8 CG1 C 10.500 0.191 7
ZS8 CD1 C 9.750 1.490 8
ZS8 CZ1 C 8.250 1.490 9
ZS8 CE1 C 7.500 2.788 10
ZS8 CT1 C 6.000 2.788 11
ZS8 CI1 C 4.500 2.788 12
ZS8 CK1 C 3.000 2.788 13
ZS8 OXT O 14.049 1.141 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
ZS8 CK1 CI1 SINGLE NONE 1
ZS8 CI1 CT1 TRIPLE NONE 2
ZS8 CT1 CE1 SINGLE NONE 3
ZS8 CE1 CZ1 SINGLE NONE 4
ZS8 CZ1 CD1 SINGLE NONE 5
ZS8 CD1 CG1 SINGLE NONE 6
ZS8 CG1 CB1 SINGLE NONE 7
ZS8 CB1 CA SINGLE NONE 8
ZS8 CA C SINGLE NONE 9
ZS8 CA N SINGLE NONE 10
ZS8 CA CB2 SINGLE BEGINDASH 11
ZS8 C O DOUBLE NONE 12
ZS8 C OXT SINGLE NONE 13
#
_pdbe_chem_comp_substructure.comp_id ZS8
_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
ZS8 O F1 1
ZS8 C F1 1
ZS8 CA F1 1
ZS8 N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id ZS8
_pdbe_chem_comp_rdkit_properties.exactmw 197.142
_pdbe_chem_comp_rdkit_properties.amw 197.278
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 33
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.727
_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 112.581
_pdbe_chem_comp_rdkit_properties.tpsa 63.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.762
_pdbe_chem_comp_rdkit_properties.CrippenMR 56.763
_pdbe_chem_comp_rdkit_properties.chi0v 6.764
_pdbe_chem_comp_rdkit_properties.chi1v 3.132
_pdbe_chem_comp_rdkit_properties.chi2v 0.851
_pdbe_chem_comp_rdkit_properties.chi3v 0.851
_pdbe_chem_comp_rdkit_properties.chi4v 0.298
_pdbe_chem_comp_rdkit_properties.chi0n 25.764
_pdbe_chem_comp_rdkit_properties.chi1n 12.435
_pdbe_chem_comp_rdkit_properties.chi2n 0.851
_pdbe_chem_comp_rdkit_properties.chi3n 0.851
_pdbe_chem_comp_rdkit_properties.chi4n 0.298
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.010
_pdbe_chem_comp_rdkit_properties.kappa1 1.944
_pdbe_chem_comp_rdkit_properties.kappa2 6.445
_pdbe_chem_comp_rdkit_properties.kappa3 5.604
_pdbe_chem_comp_rdkit_properties.Phi 0.895
#
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
ZS8 UniChem ZINC ZINC000584905720
ZS8 UniChem PubChem 137350215
#
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
ZS8 N -1.839 0.508 -3.001 ETKDGv3 1
ZS8 CA -2.335 1.095 -1.744 ETKDGv3 2
ZS8 C -1.666 2.428 -1.460 ETKDGv3 3
ZS8 O -1.075 3.060 -2.377 ETKDGv3 4
ZS8 CB2 -3.850 1.340 -1.878 ETKDGv3 5
ZS8 CB1 -2.100 0.095 -0.577 ETKDGv3 6
ZS8 CG1 -0.619 -0.242 -0.322 ETKDGv3 7
ZS8 CD1 -0.466 -1.116 0.933 ETKDGv3 8
ZS8 CZ1 0.978 -1.595 1.149 ETKDGv3 9
ZS8 CE1 1.918 -0.462 1.579 ETKDGv3 10
ZS8 CT1 3.247 -0.994 1.897 ETKDGv3 11
ZS8 CI1 4.340 -1.432 2.157 ETKDGv3 12
ZS8 CK1 5.665 -1.964 2.474 ETKDGv3 13
ZS8 H -0.793 0.501 -3.003 ETKDGv3 14
ZS8 H2 -2.128 1.108 -3.809 ETKDGv3 15
ZS8 H7 -4.059 2.070 -2.690 ETKDGv3 16
ZS8 H8 -4.271 1.743 -0.932 ETKDGv3 17
ZS8 H9 -4.376 0.391 -2.122 ETKDGv3 18
ZS8 H10 -2.642 -0.852 -0.797 ETKDGv3 19
ZS8 H11 -2.540 0.512 0.357 ETKDGv3 20
ZS8 H12 -0.042 0.696 -0.188 ETKDGv3 21
ZS8 H13 -0.208 -0.793 -1.194 ETKDGv3 22
ZS8 H14 -1.112 -2.014 0.826 ETKDGv3 23
ZS8 H15 -0.814 -0.556 1.829 ETKDGv3 24
ZS8 H16 1.360 -2.073 0.219 ETKDGv3 25
ZS8 H17 0.965 -2.372 1.945 ETKDGv3 26
ZS8 H18 2.028 0.282 0.763 ETKDGv3 27
ZS8 H19 1.515 0.048 2.480 ETKDGv3 28
ZS8 H20 5.638 -2.459 3.466 ETKDGv3 29
ZS8 H21 5.962 -2.702 1.700 ETKDGv3 30
ZS8 H22 6.401 -1.134 2.494 ETKDGv3 31
ZS8 OXT -1.754 2.993 -0.189 ETKDGv3 32
ZS8 HXT -1.329 3.890 0.012 ETKDGv3 33
#