data_V6W
#
_chem_comp.id V6W
_chem_comp.name NE-Acetyl-L-tryptophan
_chem_comp.type 'L-peptide linking'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C13 H14 N2 O4'
_chem_comp.mon_nstd_parent_comp_id TRP
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-04-20
_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 262.261
_chem_comp.one_letter_code W
_chem_comp.three_letter_code V6W
_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 7OAZ
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
_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_n_terminal_atom_flag
_chem_comp_atom.pdbx_backbone_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
V6W C C1 C 0 1 N N N N Y Y -2.319 -13.477 16.351 -4.249 -0.857 -0.020 C V6W 1
V6W CA C2 C 0 1 N N S N Y N -3.371 -13.107 15.290 -2.866 -0.430 -0.440 CA V6W 2
V6W CB C3 C 0 1 N N N N N N -4.711 -13.757 15.782 -1.896 -0.621 0.727 CB V6W 3
V6W CG C4 C 0 1 Y N N N N N -5.244 -12.996 17.014 -0.494 -0.312 0.271 CG V6W 4
V6W CD1 C5 C 0 1 Y N N N N N -5.092 -13.311 18.359 0.417 -1.196 -0.166 CD1 V6W 5
V6W C24 C6 C 0 1 N N N N N N -5.691 -12.336 20.578 2.787 -1.194 -1.006 C24 V6W 6
V6W CE2 C7 C 0 1 Y N N N N N -6.229 -11.413 18.288 1.437 0.804 -0.269 CE2 V6W 7
V6W O O1 O 0 1 N N N N Y Y -1.976 -14.602 16.488 -5.065 -0.027 0.305 O V6W 8
V6W NE1 N1 N 0 1 Y N N N N N -5.700 -12.368 19.089 1.577 -0.547 -0.493 NE1 V6W 9
V6W C25 C8 C 0 1 N N N N N N -6.761 -13.113 21.261 3.728 -1.478 0.136 C25 V6W 10
V6W O26 O2 O 0 1 N N N N N N -7.660 -13.662 20.604 3.420 -1.171 1.263 O26 V6W 11
V6W O27 O3 O 0 1 N N N N N N -6.690 -13.168 22.512 4.909 -2.071 -0.099 O27 V6W 12
V6W CD2 C9 C 0 1 Y N N N N N -5.976 -11.773 16.967 0.132 1.012 0.214 CD2 V6W 13
V6W CE3 C10 C 0 1 Y N N N N N -6.403 -10.949 15.927 -0.298 2.303 0.526 CE3 V6W 14
V6W CZ3 C11 C 0 1 Y N N N N N -7.125 -9.780 16.242 0.551 3.360 0.357 CZ3 V6W 15
V6W CH2 C12 C 0 1 Y N N N N N -7.393 -9.440 17.554 1.839 3.161 -0.122 CH2 V6W 16
V6W CZ2 C13 C 0 1 Y N N N N N -6.955 -10.240 18.594 2.283 1.895 -0.436 CZ2 V6W 17
V6W N N2 N 0 1 N N N Y Y N -3.039 -13.686 14.012 -2.889 0.985 -0.832 N V6W 18
V6W HA H2 H 0 1 N N N N Y N -3.484 -12.015 15.227 -2.541 -1.036 -1.286 HA V6W 19
V6W HB2 H3 H 0 1 N N N N N N -5.457 -13.711 14.974 -2.170 0.051 1.541 HB2 V6W 20
V6W HB3 H4 H 0 1 N N N N N N -4.529 -14.807 16.053 -1.946 -1.653 1.076 HB3 V6W 21
V6W HD1 H5 H 0 1 N N N N N N -4.571 -14.172 18.750 0.258 -2.261 -0.248 HD1 V6W 22
V6W H6 H6 H 0 1 N N N N N N -4.722 -12.732 20.916 2.518 -2.130 -1.497 H6 V6W 23
V6W H7 H7 H 0 1 N N N N N N -5.788 -11.286 20.891 3.275 -0.535 -1.724 H7 V6W 24
V6W H8 H8 H 0 1 N N N N N N -7.415 -13.682 22.848 5.479 -2.232 0.666 H8 V6W 25
V6W HE3 H9 H 0 1 N N N N N N -6.185 -11.201 14.900 -1.298 2.465 0.899 HE3 V6W 26
V6W HZ3 H10 H 0 1 N N N N N N -7.474 -9.140 15.445 0.218 4.358 0.598 HZ3 V6W 27
V6W HH2 H11 H 0 1 N N N N N N -7.950 -8.540 17.770 2.498 4.006 -0.250 HH2 V6W 28
V6W HZ2 H12 H 0 1 N N N N N N -7.164 -9.973 19.620 3.283 1.752 -0.818 HZ2 V6W 29
V6W H H13 H 0 1 N N N Y Y N -2.186 -13.287 13.676 -3.187 1.568 -0.064 H V6W 30
V6W H2 H14 H 0 1 N Y N Y Y N -2.927 -14.675 14.113 -1.988 1.279 -1.179 H2 V6W 31
V6W OXT OXT O 0 1 N Y N N Y Y -1.805 -12.473 17.194 -4.576 -2.158 -0.011 OXT V6W 32
V6W HXT HXT H 0 1 N Y N N Y Y -1.199 -12.860 17.815 -5.476 -2.383 0.262 H1 V6W 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
V6W N CA SING N N 1
V6W CA CB SING N N 2
V6W CA C SING N N 3
V6W CB CG SING N N 4
V6W CE3 CZ3 DOUB Y N 5
V6W CE3 CD2 SING Y N 6
V6W CZ3 CH2 SING Y N 7
V6W C O DOUB N N 8
V6W CD2 CG SING Y N 9
V6W CD2 CE2 DOUB Y N 10
V6W CG CD1 DOUB Y N 11
V6W CH2 CZ2 DOUB Y N 12
V6W CE2 CZ2 SING Y N 13
V6W CE2 NE1 SING Y N 14
V6W CD1 NE1 SING Y N 15
V6W NE1 C24 SING N N 16
V6W C24 C25 SING N N 17
V6W O26 C25 DOUB N N 18
V6W C25 O27 SING N N 19
V6W CA HA SING N N 20
V6W CB HB2 SING N N 21
V6W CB HB3 SING N N 22
V6W CD1 HD1 SING N N 23
V6W C24 H6 SING N N 24
V6W C24 H7 SING N N 25
V6W O27 H8 SING N N 26
V6W CE3 HE3 SING N N 27
V6W CZ3 HZ3 SING N N 28
V6W CH2 HH2 SING N N 29
V6W CZ2 HZ2 SING N N 30
V6W N H SING N N 31
V6W N H2 SING N N 32
V6W OXT C SING N N 33
V6W OXT HXT SING N N 34
#
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
V6W InChI InChI 1.06 'InChI=1S/C13H14N2O4/c14-10(13(18)19)5-8-6-15(7-12(16)17)11-4-2-1-3-9(8)11/h1-4,6,10H,5,7,14H2,(H,16,17)(H,18,19)/t10-/m0/s1'
V6W InChIKey InChI 1.06 NUIINCMATQEUSS-JTQLQIEISA-N
V6W SMILES_CANONICAL CACTVS 3.385 'N[C@@H](Cc1cn(CC(O)=O)c2ccccc12)C(O)=O'
V6W SMILES CACTVS 3.385 'N[CH](Cc1cn(CC(O)=O)c2ccccc12)C(O)=O'
V6W SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.7 'c1ccc2c(c1)c(cn2CC(=O)O)C[C@@H](C(=O)O)N'
V6W SMILES 'OpenEye OEToolkits' 2.0.7 'c1ccc2c(c1)c(cn2CC(=O)O)CC(C(=O)O)N'
#
_pdbx_chem_comp_identifier.comp_id V6W
_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 '(2~{S})-2-azanyl-3-[1-(2-hydroxy-2-oxoethyl)indol-3-yl]propanoic 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
V6W 'Create component' 2021-04-20 PDBE
V6W 'Modify leaving atom flag' 2022-08-08 PDBE
V6W 'Initial release' 2023-08-16 RCSB
V6W 'Modify backbone' 2023-11-03 PDBE
V6W 'Other modification' 2024-06-28 PDBE
V6W 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id V6W
_pdbx_chem_comp_pcm.modified_residue_id TRP
_pdbx_chem_comp_pcm.type Carboxymethylation
_pdbx_chem_comp_pcm.category 'Named protein modification'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_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
V6W C C 9.953 1.576 1
V6W CA C 8.951 2.692 2
V6W CB C 7.483 2.383 3
V6W CG C 7.018 0.957 4
V6W CD1 C 7.893 -0.250 5
V6W C24 C 7.483 -2.883 6
V6W CE2 C 5.598 -1.000 7
V6W O O 11.421 1.885 8
V6W NE1 N 7.018 -1.457 9
V6W C25 C 8.951 -3.192 10
V6W O26 O 9.417 -4.618 11
V6W O27 O 9.953 -2.076 12
V6W CD2 C 5.598 0.500 13
V6W CE3 C 4.299 1.250 14
V6W CZ3 C 3.000 0.500 15
V6W CH2 C 3.000 -1.000 16
V6W CZ2 C 4.299 -1.750 17
V6W N N 9.417 4.118 18
V6W OXT O 9.487 0.150 19
#
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
V6W CA N SINGLE BEGINDASH 1
V6W CA CB SINGLE NONE 2
V6W CA C SINGLE NONE 3
V6W CB CG SINGLE NONE 4
V6W CE3 CZ3 SINGLE NONE 5
V6W CE3 CD2 DOUBLE NONE 6
V6W CZ3 CH2 DOUBLE NONE 7
V6W C O DOUBLE NONE 8
V6W CD2 CG SINGLE NONE 9
V6W CD2 CE2 SINGLE NONE 10
V6W CG CD1 DOUBLE NONE 11
V6W CH2 CZ2 SINGLE NONE 12
V6W CE2 CZ2 DOUBLE NONE 13
V6W CE2 NE1 SINGLE NONE 14
V6W CD1 NE1 SINGLE NONE 15
V6W NE1 C24 SINGLE NONE 16
V6W C24 C25 SINGLE NONE 17
V6W O26 C25 DOUBLE NONE 18
V6W C25 O27 SINGLE NONE 19
V6W OXT C SINGLE NONE 20
#
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
V6W MurckoScaffold S1 scaffold 'c1ccc2[nH]ccc2c1' InChI=1S/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9H SIKJAQJRHWYJAI-UHFFFAOYSA-N
V6W indole F1 fragment 'c1ccc2[nH]ccc2c1' InChI=1S/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9H SIKJAQJRHWYJAI-UHFFFAOYSA-N
V6W peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
V6W phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
V6W pyrrole F4 fragment 'c1cc[nH]c1' InChI=1S/C4H5N/c1-2-4-5-3-1/h1-5H KAESVJOAVNADME-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
V6W CG S1 1
V6W CD1 S1 1
V6W CE2 S1 1
V6W NE1 S1 1
V6W CD2 S1 1
V6W CE3 S1 1
V6W CZ3 S1 1
V6W CH2 S1 1
V6W CZ2 S1 1
V6W CE2 F1 1
V6W CD2 F1 1
V6W CG F1 1
V6W CD1 F1 1
V6W NE1 F1 1
V6W CE3 F1 1
V6W CZ3 F1 1
V6W CH2 F1 1
V6W CZ2 F1 1
V6W O F2 1
V6W C F2 1
V6W CA F2 1
V6W N F2 1
V6W O26 F2 2
V6W C25 F2 2
V6W C24 F2 2
V6W NE1 F2 2
V6W CE2 F3 1
V6W CD2 F3 1
V6W CE3 F3 1
V6W CZ3 F3 1
V6W CH2 F3 1
V6W CZ2 F3 1
V6W CD1 F4 1
V6W CG F4 1
V6W CD2 F4 1
V6W CE2 F4 1
V6W NE1 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id V6W
_pdbe_chem_comp_rdkit_properties.exactmw 262.095
_pdbe_chem_comp_rdkit_properties.amw 262.265
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_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 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 33
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.231
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 128.567
_pdbe_chem_comp_rdkit_properties.tpsa 105.550
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.197
_pdbe_chem_comp_rdkit_properties.CrippenMR 66.417
_pdbe_chem_comp_rdkit_properties.chi0v 9.027
_pdbe_chem_comp_rdkit_properties.chi1v 4.711
_pdbe_chem_comp_rdkit_properties.chi2v 2.005
_pdbe_chem_comp_rdkit_properties.chi3v 2.005
_pdbe_chem_comp_rdkit_properties.chi4v 1.313
_pdbe_chem_comp_rdkit_properties.chi0n 23.027
_pdbe_chem_comp_rdkit_properties.chi1n 11.422
_pdbe_chem_comp_rdkit_properties.chi2n 2.005
_pdbe_chem_comp_rdkit_properties.chi3n 2.005
_pdbe_chem_comp_rdkit_properties.chi4n 1.313
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.340
_pdbe_chem_comp_rdkit_properties.kappa1 4.076
_pdbe_chem_comp_rdkit_properties.kappa2 5.111
_pdbe_chem_comp_rdkit_properties.kappa3 2.739
_pdbe_chem_comp_rdkit_properties.Phi 1.097
#
_pdbe_chem_comp_external_mappings.comp_id V6W
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 140828719
#
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
V6W C 3.635 -1.822 -0.280 ETKDGv3 1
V6W CA 2.207 -1.360 -0.156 ETKDGv3 2
V6W CB 2.082 0.109 -0.595 ETKDGv3 3
V6W CG 0.649 0.557 -0.601 ETKDGv3 4
V6W CD1 -0.231 0.314 -1.583 ETKDGv3 5
V6W C24 -2.776 0.362 -1.939 ETKDGv3 6
V6W CE2 -1.442 1.288 0.065 ETKDGv3 7
V6W O 3.923 -2.782 -1.044 ETKDGv3 8
V6W NE1 -1.552 0.772 -1.257 ETKDGv3 9
V6W C25 -3.242 -0.955 -1.408 ETKDGv3 10
V6W O26 -4.111 -0.998 -0.496 ETKDGv3 11
V6W O27 -2.679 -2.133 -1.888 ETKDGv3 12
V6W CD2 -0.075 1.182 0.504 ETKDGv3 13
V6W CE3 0.312 1.565 1.724 ETKDGv3 14
V6W CZ3 -0.727 2.127 2.629 ETKDGv3 15
V6W CH2 -2.011 2.225 2.219 ETKDGv3 16
V6W CZ2 -2.404 1.774 0.857 ETKDGv3 17
V6W N 1.728 -1.531 1.218 ETKDGv3 18
V6W HA 1.573 -1.980 -0.829 ETKDGv3 19
V6W HB2 2.673 0.765 0.081 ETKDGv3 20
V6W HB3 2.498 0.227 -1.620 ETKDGv3 21
V6W HD1 0.009 -0.211 -2.499 ETKDGv3 22
V6W H6 -3.563 1.133 -1.801 ETKDGv3 23
V6W H7 -2.581 0.271 -3.029 ETKDGv3 24
V6W H8 -2.969 -3.033 -1.525 ETKDGv3 25
V6W HE3 1.338 1.464 2.050 ETKDGv3 26
V6W HZ3 -0.450 2.454 3.623 ETKDGv3 27
V6W HH2 -2.762 2.630 2.885 ETKDGv3 28
V6W HZ2 -3.432 1.838 0.527 ETKDGv3 29
V6W H 2.359 -1.016 1.876 ETKDGv3 30
V6W H2 1.778 -2.546 1.466 ETKDGv3 31
V6W OXT 4.640 -1.193 0.450 ETKDGv3 32
V6W HXT 5.603 -1.495 0.375 ETKDGv3 33
#