data_YTF
#
_chem_comp.id YTF
_chem_comp.name 'ethyl (4~{S})-4,7-bis(azanyl)-7-oxidanylidene-heptanoate'
_chem_comp.type 'L-peptide COOH carboxy terminus'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C9 H18 N2 O3'
_chem_comp.mon_nstd_parent_comp_id GLN
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-02-21
_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 202.251
_chem_comp.one_letter_code Q
_chem_comp.three_letter_code YTF
_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 2B0F
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_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
YTF N N N 0 1 N N N Y Y N 302.708 -0.340 9.491 -1.008 1.723 -0.833 N YTF 1
YTF CA CA C 0 1 N N S Y N N 302.680 0.936 10.164 -0.979 0.626 0.143 CA YTF 2
YTF CB CB C 0 1 N N N N N N 303.479 1.977 9.371 -2.220 -0.251 -0.038 CB YTF 3
YTF CG CG C 0 1 N N N N N N 304.994 1.741 9.453 -3.471 0.561 0.303 CG YTF 4
YTF CD CD C 0 1 N N N N N N 305.815 2.730 8.638 -4.694 -0.303 0.125 CD YTF 5
YTF OE1 OE1 O 0 1 N N N N N N 305.313 3.353 7.708 -4.575 -1.454 -0.239 OE1 YTF 6
YTF NE2 NE2 N 0 1 N N N N N N 307.098 2.865 8.975 -5.918 0.204 0.370 NE2 YTF 7
YTF C CX5 C 0 1 N N N Y N Y 301.248 1.416 10.547 0.278 -0.219 -0.077 CX5 YTF 8
YTF CX6 CX6 C 0 1 N N N N N N 301.037 1.020 12.010 1.518 0.625 0.226 CX6 YTF 9
YTF CX7 CX7 C 0 1 N N N N N N 299.841 1.675 12.657 2.757 -0.207 0.009 CX7 YTF 10
YTF OX8 OX8 O 0 1 N N N N N N 299.133 2.444 12.011 2.657 -1.356 -0.349 OX8 YTF 11
YTF OX9 OX9 O 0 1 N N N N N N 299.622 1.398 13.861 3.970 0.330 0.216 OX9 YTF 12
YTF CJ1 CJ1 C 0 1 N N N N N N 298.460 1.980 14.686 5.118 -0.530 -0.012 CJ1 YTF 13
YTF CJ2 CJ2 C 0 1 N N N N N N 298.283 1.600 16.145 6.403 0.250 0.272 CJ2 YTF 14
YTF H2 H9 H 0 1 N Y N Y Y N 302.183 -1.008 10.019 -0.232 2.353 -0.693 H9 YTF 15
YTF H H H 0 1 N N N Y Y N 302.306 -0.245 8.580 -1.018 1.367 -1.778 H YTF 16
YTF HA HA H 0 1 N N N Y N N 303.215 0.807 11.117 -0.968 1.037 1.152 HA YTF 17
YTF HB2 HB2 H 0 1 N N N N N N 303.255 2.976 9.774 -2.277 -0.590 -1.072 HB2 YTF 18
YTF HB3 HB3 H 0 1 N N N N N N 303.171 1.930 8.316 -2.155 -1.114 0.625 HB3 YTF 19
YTF HG2 HG2 H 0 1 N N N N N N 305.207 0.727 9.085 -3.414 0.900 1.337 HG2 YTF 20
YTF HG3 HG3 H 0 1 N N N N N N 305.301 1.821 10.506 -3.536 1.423 -0.360 HG3 YTF 21
YTF HE22 HE22 H 0 0 N N N N N N 307.686 3.491 8.463 -6.013 1.125 0.660 HE22 YTF 22
YTF HE21 HE21 H 0 0 N N N N N N 307.472 2.340 9.740 -6.705 -0.351 0.255 HE21 YTF 23
YTF H11 H11 H 0 1 N Y N Y N Y 301.169 2.507 10.433 0.256 -1.083 0.587 H11 YTF 24
YTF H1 H1 H 0 1 N N N Y N Y 300.499 0.926 9.908 0.312 -0.557 -1.112 H1 YTF 25
YTF H31 H2 H 0 1 N N N Y N N 300.902 -0.071 12.057 1.541 1.489 -0.438 H2 YTF 26
YTF H3 H3 H 0 1 N N N N N N 301.936 1.303 12.578 1.484 0.963 1.261 H3 YTF 27
YTF H4 H4 H 0 1 N N N N N N 298.570 3.074 14.657 5.062 -1.393 0.651 H4 YTF 28
YTF H5 H5 H 0 1 N N N N N N 297.532 1.691 14.171 5.119 -0.867 -1.048 H5 YTF 29
YTF H7 H7 H 0 1 N N N N N N 297.403 2.117 16.555 6.402 0.588 1.309 H7 YTF 30
YTF H8 H8 H 0 1 N N N N N N 298.140 0.512 16.226 7.265 -0.395 0.101 H8 YTF 31
YTF H6 H6 H 0 1 N N N N N N 299.178 1.895 16.712 6.458 1.113 -0.391 H6 YTF 32
#
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
YTF OE1 CD DOUB N N 1
YTF CD NE2 SING N N 2
YTF CD CG SING N N 3
YTF CB CG SING N N 4
YTF CB CA SING N N 5
YTF N CA SING N N 6
YTF CA C SING N N 7
YTF C CX6 SING N N 8
YTF CX6 CX7 SING N N 9
YTF OX8 CX7 DOUB N N 10
YTF CX7 OX9 SING N N 11
YTF OX9 CJ1 SING N N 12
YTF CJ1 CJ2 SING N N 13
YTF N H2 SING N N 14
YTF N H SING N N 15
YTF CA HA SING N N 16
YTF CB HB2 SING N N 17
YTF CB HB3 SING N N 18
YTF CG HG2 SING N N 19
YTF CG HG3 SING N N 20
YTF NE2 HE22 SING N N 21
YTF NE2 HE21 SING N N 22
YTF C H11 SING N N 23
YTF C H1 SING N N 24
YTF CX6 H31 SING N N 25
YTF CX6 H3 SING N N 26
YTF CJ1 H4 SING N N 27
YTF CJ1 H5 SING N N 28
YTF CJ2 H7 SING N N 29
YTF CJ2 H8 SING N N 30
YTF CJ2 H6 SING N N 31
#
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
YTF InChI InChI 1.06 'InChI=1S/C9H18N2O3/c1-2-14-9(13)6-4-7(10)3-5-8(11)12/h7H,2-6,10H2,1H3,(H2,11,12)/t7-/m0/s1'
YTF InChIKey InChI 1.06 ZEVHIIRETBYBHR-ZETCQYMHSA-N
YTF SMILES_CANONICAL CACTVS 3.385 'CCOC(=O)CC[C@@H](N)CCC(N)=O'
YTF SMILES CACTVS 3.385 'CCOC(=O)CC[CH](N)CCC(N)=O'
YTF SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.7 'CCOC(=O)CC[C@H](CCC(=O)N)N'
YTF SMILES 'OpenEye OEToolkits' 2.0.7 'CCOC(=O)CCC(CCC(=O)N)N'
#
_pdbx_chem_comp_identifier.comp_id YTF
_pdbx_chem_comp_identifier.type 'SYSTEMATIC NAME'
_pdbx_chem_comp_identifier.program 'OpenEye OEToolkits'
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier 'ethyl (4~{S})-4,7-bis(azanyl)-7-oxidanylidene-heptanoate'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
YTF 'Create component' 2023-02-21 RCSB
YTF 'Initial release' 2023-03-01 RCSB
YTF 'Modify backbone' 2023-11-03 PDBE
YTF 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id YTF
_pdbx_chem_comp_pcm.modified_residue_id GLN
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Non-standard residue'
_pdbx_chem_comp_pcm.position 'Amino-acid backbone'
_pdbx_chem_comp_pcm.polypeptide_position C-terminal
_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 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
YTF N N 3.805 2.340 1
YTF CA C 5.104 1.590 2
YTF CB C 5.104 0.090 3
YTF CG C 6.404 -0.660 4
YTF CD C 6.404 -2.160 5
YTF OE1 O 5.104 -2.910 6
YTF NE2 N 7.702 -2.910 7
YTF C C 6.404 2.340 8
YTF CX6 C 7.702 1.590 9
YTF CX7 C 9.002 2.340 10
YTF OX8 O 9.002 3.840 11
YTF OX9 O 10.301 1.590 12
YTF CJ1 C 11.600 2.340 13
YTF CJ2 C 12.899 1.590 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
YTF OE1 CD DOUBLE NONE 1
YTF CD NE2 SINGLE NONE 2
YTF CD CG SINGLE NONE 3
YTF CB CG SINGLE NONE 4
YTF CB CA SINGLE NONE 5
YTF CA N SINGLE BEGINDASH 6
YTF CA C SINGLE NONE 7
YTF C CX6 SINGLE NONE 8
YTF CX6 CX7 SINGLE NONE 9
YTF OX8 CX7 DOUBLE NONE 10
YTF CX7 OX9 SINGLE NONE 11
YTF OX9 CJ1 SINGLE NONE 12
YTF CJ1 CJ2 SINGLE NONE 13
#
_pdbe_chem_comp_substructure.comp_id YTF
_pdbe_chem_comp_substructure.substructure_name amide
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles CC(N)=O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4)
_pdbe_chem_comp_substructure.substructure_inchikeys DLFVBJFMPXGRIB-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
YTF NE2 F1 1
YTF CD F1 1
YTF OE1 F1 1
YTF CG F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id YTF
_pdbe_chem_comp_rdkit_properties.exactmw 202.132
_pdbe_chem_comp_rdkit_properties.amw 202.254
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 32
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.778
_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 109.297
_pdbe_chem_comp_rdkit_properties.tpsa 95.410
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.077
_pdbe_chem_comp_rdkit_properties.CrippenMR 52.271
_pdbe_chem_comp_rdkit_properties.chi0v 6.619
_pdbe_chem_comp_rdkit_properties.chi1v 3.014
_pdbe_chem_comp_rdkit_properties.chi2v 0.715
_pdbe_chem_comp_rdkit_properties.chi3v 0.715
_pdbe_chem_comp_rdkit_properties.chi4v 0.326
_pdbe_chem_comp_rdkit_properties.chi0n 24.619
_pdbe_chem_comp_rdkit_properties.chi1n 11.803
_pdbe_chem_comp_rdkit_properties.chi2n 0.715
_pdbe_chem_comp_rdkit_properties.chi3n 0.715
_pdbe_chem_comp_rdkit_properties.chi4n 0.326
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.100
_pdbe_chem_comp_rdkit_properties.kappa1 2.043
_pdbe_chem_comp_rdkit_properties.kappa2 7.318
_pdbe_chem_comp_rdkit_properties.kappa3 7.544
_pdbe_chem_comp_rdkit_properties.Phi 1.068
#
_pdbe_chem_comp_external_mappings.comp_id YTF
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 166625106
#
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
YTF N -1.009 -2.488 -1.087 ETKDGv3 1
YTF CA -0.750 -1.047 -1.138 ETKDGv3 2
YTF CB -2.083 -0.264 -1.039 ETKDGv3 3
YTF CG -2.818 -0.462 0.295 ETKDGv3 4
YTF CD -4.152 0.221 0.261 ETKDGv3 5
YTF OE1 -5.185 -0.435 -0.036 ETKDGv3 6
YTF NE2 -4.252 1.621 0.522 ETKDGv3 7
YTF C 0.281 -0.667 -0.048 ETKDGv3 8
YTF CX6 0.663 0.819 -0.069 ETKDGv3 9
YTF CX7 1.798 1.077 0.869 ETKDGv3 10
YTF OX8 1.561 1.382 2.070 ETKDGv3 11
YTF OX9 3.113 0.935 0.412 ETKDGv3 12
YTF CJ1 4.256 1.065 1.255 ETKDGv3 13
YTF CJ2 4.427 -0.178 2.121 ETKDGv3 14
YTF H2 -1.638 -2.741 -1.884 ETKDGv3 15
YTF H -0.111 -2.995 -1.264 ETKDGv3 16
YTF HA -0.298 -0.807 -2.128 ETKDGv3 17
YTF HB2 -2.745 -0.598 -1.868 ETKDGv3 18
YTF HB3 -1.897 0.818 -1.207 ETKDGv3 19
YTF HG2 -2.965 -1.545 0.495 ETKDGv3 20
YTF HG3 -2.225 -0.034 1.130 ETKDGv3 21
YTF HE22 -3.401 2.183 0.747 ETKDGv3 22
YTF HE21 -5.180 2.099 0.485 ETKDGv3 23
YTF H11 1.203 -1.267 -0.221 ETKDGv3 24
YTF H1 -0.100 -0.945 0.959 ETKDGv3 25
YTF H31 0.967 1.118 -1.095 ETKDGv3 26
YTF H3 -0.203 1.445 0.237 ETKDGv3 27
YTF H4 4.166 1.971 1.893 ETKDGv3 28
YTF H5 5.156 1.181 0.616 ETKDGv3 29
YTF H7 3.561 -0.297 2.804 ETKDGv3 30
YTF H8 5.352 -0.084 2.729 ETKDGv3 31
YTF H6 4.509 -1.079 1.477 ETKDGv3 32
#