data_VLT
#
_chem_comp.id VLT
_chem_comp.name '(2E,4S)-4-amino-5-(4-hydroxyphenyl)pent-2-enoic acid'
_chem_comp.type peptide-like
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C11 H13 N O3'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2010-09-24
_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 207.226
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VLT
_chem_comp.pdbx_model_coordinates_details 'not provided'
_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 1TMB
_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
VLT N N N 0 1 N N N Y Y N 16.098 -15.522 16.138 -0.644 1.262 -0.618 N VLT 1
VLT CA CA C 0 1 N N S Y N N 15.503 -16.844 16.396 -0.748 -0.193 -0.437 CA VLT 2
VLT C2 C2 C 0 1 N N N Y N N 15.559 -16.774 17.919 -2.186 -0.565 -0.182 C2 VLT 3
VLT C3 C3 C 0 1 N N N N N N 16.364 -17.938 15.691 0.109 -0.621 0.756 C3 VLT 4
VLT C4 C4 C 0 1 Y N N N N N 16.309 -17.538 14.202 1.562 -0.360 0.450 C4 VLT 5
VLT C5 C5 C 0 1 Y N N N N N 15.050 -17.678 13.579 2.128 0.859 0.775 C5 VLT 6
VLT C6 C6 C 0 1 Y N N N N N 17.368 -17.004 13.476 2.327 -1.342 -0.151 C6 VLT 7
VLT C7 C7 C 0 1 Y N N N N N 14.842 -17.313 12.253 3.459 1.100 0.496 C7 VLT 8
VLT C8 C8 C 0 1 Y N N N N N 17.166 -16.611 12.151 3.659 -1.106 -0.433 C8 VLT 9
VLT C9 C9 C 0 1 Y N N N N N 15.921 -16.772 11.554 4.228 0.118 -0.112 C9 VLT 10
VLT O1 O1 O 0 1 N N N N N N 15.716 -16.395 10.237 5.537 0.354 -0.389 O1 VLT 11
VLT C10 C10 C 0 1 N N N Y N N 15.559 -17.829 18.680 -3.136 0.364 -0.249 C10 VLT 12
VLT C C C 0 1 N N N Y N Y 15.581 -17.734 20.147 -4.538 0.000 0.000 C VLT 13
VLT O O O 0 1 N N N Y N Y 15.552 -18.855 20.642 -4.830 -1.149 0.267 O VLT 14
VLT OXT OXT O 0 1 N Y N Y N Y 15.609 -16.680 20.913 -5.501 0.942 -0.068 OXT VLT 15
VLT H H H 0 1 N N N Y Y N 16.152 -15.367 15.152 -1.150 1.561 -1.438 H VLT 16
VLT HA H1 H 0 1 N N N Y N N 14.499 -17.089 16.020 -0.396 -0.697 -1.337 H1 VLT 17
VLT H3 H3 H 0 1 N N N Y N N 15.601 -15.802 18.388 -2.445 -1.587 0.056 H3 VLT 18
VLT H4 H4 H 0 1 N N N N N N 17.397 -17.943 16.069 -0.184 -0.051 1.637 H4 VLT 19
VLT H5 H5 H 0 1 N N N N N N 15.949 -18.944 15.854 -0.037 -1.684 0.945 H5 VLT 20
VLT H6 H6 H 0 1 N N N N N N 14.225 -18.080 14.148 1.528 1.622 1.249 H6 VLT 21
VLT H7 H7 H 0 1 N N N N N N 18.340 -16.894 13.934 1.884 -2.295 -0.401 H7 VLT 22
VLT H8 H8 H 0 1 N N N N N N 13.879 -17.444 11.781 3.900 2.052 0.750 H8 VLT 23
VLT H9 H9 H 0 1 N N N N N N 17.981 -16.180 11.588 4.257 -1.873 -0.901 H9 VLT 24
VLT H10 H10 H 0 1 N N N N N N 16.523 -16.045 9.878 6.141 0.106 0.325 H10 VLT 25
VLT H11 H11 H 0 1 N N N Y N N 15.542 -18.806 18.220 -2.877 1.385 -0.486 H11 VLT 26
VLT HXT HXT H 0 1 N Y N Y N Y 15.602 -16.950 21.824 -6.408 0.655 0.103 HXT VLT 27
VLT H2 H2 H 0 1 N Y N Y Y N 15.529 -14.813 16.556 -0.964 1.752 0.204 H2 VLT 28
#
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
VLT N CA SING N N 1
VLT N H SING N N 2
VLT CA C2 SING N N 3
VLT CA C3 SING N N 4
VLT CA HA SING N N 5
VLT C2 C10 DOUB N N 6
VLT C2 H3 SING N E 7
VLT C3 C4 SING N N 8
VLT C3 H4 SING N N 9
VLT C3 H5 SING N N 10
VLT C4 C5 DOUB Y N 11
VLT C4 C6 SING Y N 12
VLT C5 C7 SING Y N 13
VLT C5 H6 SING N N 14
VLT C6 C8 DOUB Y N 15
VLT C6 H7 SING N N 16
VLT C7 C9 DOUB Y N 17
VLT C7 H8 SING N N 18
VLT C8 C9 SING Y N 19
VLT C8 H9 SING N N 20
VLT C9 O1 SING N N 21
VLT O1 H10 SING N N 22
VLT C10 C SING N N 23
VLT C10 H11 SING N N 24
VLT C O DOUB N N 25
VLT C OXT SING N N 26
VLT OXT HXT SING N N 27
VLT N H2 SING N N 28
#
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
VLT SMILES ACDLabs 12.01 'O=C(O)\C=C\C(N)Cc1ccc(O)cc1'
VLT SMILES_CANONICAL CACTVS 3.370 'N[C@@H](Cc1ccc(O)cc1)\C=C\C(O)=O'
VLT SMILES CACTVS 3.370 'N[CH](Cc1ccc(O)cc1)C=CC(O)=O'
VLT SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.0 'c1cc(ccc1C[C@@H](/C=C/C(=O)O)N)O'
VLT SMILES 'OpenEye OEToolkits' 1.7.0 'c1cc(ccc1CC(C=CC(=O)O)N)O'
VLT InChI InChI 1.03 'InChI=1S/C11H13NO3/c12-9(3-6-11(14)15)7-8-1-4-10(13)5-2-8/h1-6,9,13H,7,12H2,(H,14,15)/b6-3+/t9-/m1/s1'
VLT InChIKey InChI 1.03 ZAFPASBXHDOXMD-BSPAPZMXSA-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
VLT 'SYSTEMATIC NAME' ACDLabs 12.01 '(2E,4S)-4-amino-5-(4-hydroxyphenyl)pent-2-enoic acid'
VLT 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.7.0 '(E,4S)-4-azanyl-5-(4-hydroxyphenyl)pent-2-enoic 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
VLT 'Create component' 2010-09-24 RCSB
VLT 'Modify aromatic_flag' 2011-06-04 RCSB
VLT 'Modify descriptor' 2011-06-04 RCSB
VLT 'Modify backbone' 2023-11-03 PDBE
VLT 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id VLT
_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 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
VLT N N 6.897 0.142 1
VLT CA C 5.598 0.892 2
VLT C2 C 5.598 2.393 3
VLT C3 C 4.299 0.142 4
VLT C4 C 4.299 -1.357 5
VLT C5 C 5.598 -2.107 6
VLT C6 C 3.000 -2.107 7
VLT C7 C 5.598 -3.607 8
VLT C8 C 3.000 -3.607 9
VLT C9 C 4.299 -4.357 10
VLT O1 O 4.299 -5.857 11
VLT C10 C 6.897 3.143 12
VLT C C 6.897 4.643 13
VLT O O 8.196 5.393 14
VLT OXT O 5.598 5.393 15
#
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
VLT CA N SINGLE BEGINWEDGE 1
VLT CA C2 SINGLE ENDUPRIGHT 2
VLT CA C3 SINGLE NONE 3
VLT C2 C10 DOUBLE NONE 4
VLT C3 C4 SINGLE NONE 5
VLT C4 C5 DOUBLE NONE 6
VLT C4 C6 SINGLE NONE 7
VLT C5 C7 SINGLE NONE 8
VLT C6 C8 DOUBLE NONE 9
VLT C7 C9 DOUBLE NONE 10
VLT C8 C9 SINGLE NONE 11
VLT C9 O1 SINGLE NONE 12
VLT C10 C SINGLE ENDUPRIGHT 13
VLT C O DOUBLE NONE 14
VLT C OXT SINGLE NONE 15
#
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
VLT MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
VLT phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-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
VLT C4 S1 1
VLT C5 S1 1
VLT C6 S1 1
VLT C7 S1 1
VLT C8 S1 1
VLT C9 S1 1
VLT C4 F1 1
VLT C5 F1 1
VLT C7 F1 1
VLT C9 F1 1
VLT C8 F1 1
VLT C6 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id VLT
_pdbe_chem_comp_rdkit_properties.exactmw 207.090
_pdbe_chem_comp_rdkit_properties.amw 207.229
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.182
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_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 106.210
_pdbe_chem_comp_rdkit_properties.tpsa 83.550
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.386
_pdbe_chem_comp_rdkit_properties.CrippenMR 55.686
_pdbe_chem_comp_rdkit_properties.chi0v 7.172
_pdbe_chem_comp_rdkit_properties.chi1v 3.586
_pdbe_chem_comp_rdkit_properties.chi2v 1.128
_pdbe_chem_comp_rdkit_properties.chi3v 1.128
_pdbe_chem_comp_rdkit_properties.chi4v 0.623
_pdbe_chem_comp_rdkit_properties.chi0n 20.172
_pdbe_chem_comp_rdkit_properties.chi1n 9.797
_pdbe_chem_comp_rdkit_properties.chi2n 1.128
_pdbe_chem_comp_rdkit_properties.chi3n 1.128
_pdbe_chem_comp_rdkit_properties.chi4n 0.623
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.810
_pdbe_chem_comp_rdkit_properties.kappa1 2.857
_pdbe_chem_comp_rdkit_properties.kappa2 5.165
_pdbe_chem_comp_rdkit_properties.kappa3 4.284
_pdbe_chem_comp_rdkit_properties.Phi 0.984
#
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
VLT UniChem ZINC ZINC000098209529
VLT UniChem PubChem 137350124
#
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
VLT N -0.674 0.285 1.556 ETKDGv3 1
VLT CA -0.980 0.208 0.124 ETKDGv3 2
VLT C2 -2.435 -0.138 -0.095 ETKDGv3 3
VLT C3 -0.070 -0.831 -0.555 ETKDGv3 4
VLT C4 1.383 -0.444 -0.449 ETKDGv3 5
VLT C5 1.927 0.425 -1.320 ETKDGv3 6
VLT C6 2.215 -0.980 0.658 ETKDGv3 7
VLT C7 3.345 0.823 -1.190 ETKDGv3 8
VLT C8 3.497 -0.615 0.776 ETKDGv3 9
VLT C9 4.094 0.331 -0.195 ETKDGv3 10
VLT O1 5.428 0.712 -0.079 ETKDGv3 11
VLT C10 -3.405 0.740 0.177 ETKDGv3 12
VLT C -4.826 0.427 -0.037 ETKDGv3 13
VLT O -5.698 1.295 0.233 ETKDGv3 14
VLT OXT -5.217 -0.814 -0.532 ETKDGv3 15
VLT H -1.202 1.084 1.976 ETKDGv3 16
VLT HA -0.780 1.199 -0.343 ETKDGv3 17
VLT H3 -2.688 -1.112 -0.499 ETKDGv3 18
VLT H4 -0.347 -0.925 -1.628 ETKDGv3 19
VLT H5 -0.226 -1.830 -0.091 ETKDGv3 20
VLT H6 1.335 0.844 -2.125 ETKDGv3 21
VLT H7 1.785 -1.668 1.375 ETKDGv3 22
VLT H8 3.772 1.517 -1.903 ETKDGv3 23
VLT H9 4.098 -1.010 1.586 ETKDGv3 24
VLT H10 6.013 0.353 0.666 ETKDGv3 25
VLT H11 -3.148 1.720 0.564 ETKDGv3 26
VLT HXT -6.196 -1.030 -0.679 ETKDGv3 27
VLT H2 -0.999 -0.591 2.028 ETKDGv3 28
#