data_19W
#
_chem_comp.id 19W
_chem_comp.name 5-(aminooxy)-L-norvaline
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C5 H12 N2 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2012-11-12
_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 148.160
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 19W
_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 4HU6
_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
19W N N N 0 1 N N N Y Y N -19.461 -2.919 29.604 -1.427 1.794 -0.206 N 19W 1
19W CA CA C 0 1 N N S Y N N -18.653 -1.825 29.064 -1.395 0.352 -0.485 CA 19W 2
19W C C C 0 1 N N N Y N Y -18.246 -2.126 27.616 -2.660 -0.286 0.029 C 19W 3
19W O O O 0 1 N N N Y N Y -18.394 -1.218 26.774 -3.324 0.277 0.867 O 19W 4
19W CB CB C 0 1 N N N N N N -17.416 -1.790 29.930 -0.187 -0.276 0.213 CB 19W 5
19W CG CG C 0 1 N N N N N N -16.423 -0.768 29.417 1.101 0.282 -0.397 CG 19W 6
19W CD CD C 0 1 N N N N N N -15.214 -0.774 30.353 2.309 -0.346 0.301 CD 19W 7
19W OE OE O 0 1 N N N N N N -15.611 -0.388 31.679 3.511 0.175 -0.268 OE 19W 8
19W NZ NZ N 0 1 N N N N N N -16.063 -1.316 32.778 4.734 -0.363 0.330 NZ 19W 9
19W H H1 H 0 1 N N N Y Y N -19.719 -2.710 30.547 -1.498 1.969 0.785 H1 19W 10
19W H2 H2 H 0 1 N Y N Y Y N -20.286 -3.029 29.050 -0.619 2.256 -0.598 H2 19W 11
19W HA H4 H 0 1 N N N Y N N -19.191 -0.867 29.118 -1.318 0.191 -1.560 H4 19W 12
19W H6 H6 H 0 1 N N N N N N -17.704 -1.527 30.958 -0.218 -0.039 1.276 H6 19W 13
19W H7 H7 H 0 1 N N N N N N -16.945 -2.784 29.924 -0.213 -1.358 0.080 H7 19W 14
19W H8 H8 H 0 1 N N N N N N -16.107 -1.033 28.397 1.132 0.045 -1.460 H8 19W 15
19W H9 H9 H 0 1 N N N N N N -16.885 0.230 29.410 1.126 1.363 -0.264 H9 19W 16
19W H10 H10 H 0 1 N N N N N N -14.783 -1.785 30.383 2.278 -0.110 1.365 H10 19W 17
19W H11 H11 H 0 1 N N N N N N -14.461 -0.065 29.978 2.283 -1.428 0.169 H11 19W 18
19W H12 H12 H 0 1 N N N N N N -16.279 -0.784 33.597 4.749 -1.370 0.278 H12 19W 19
19W H13 H13 H 0 1 N N N N N N -16.877 -1.814 32.480 5.554 0.035 -0.104 H13 19W 20
19W OXT OXT O 0 1 N Y N Y N Y ? ? ? -3.050 -1.480 -0.445 OXT 19W 21
19W HXT HXT H 0 1 N Y N Y N Y ? ? ? -3.868 -1.850 -0.085 HXT 19W 22
#
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
19W O C DOUB N N 1
19W C CA SING N N 2
19W CA N SING N N 3
19W CA CB SING N N 4
19W CG CB SING N N 5
19W CG CD SING N N 6
19W CD OE SING N N 7
19W OE NZ SING N N 8
19W N H SING N N 9
19W N H2 SING N N 10
19W CA HA SING N N 11
19W CB H6 SING N N 12
19W CB H7 SING N N 13
19W CG H8 SING N N 14
19W CG H9 SING N N 15
19W CD H10 SING N N 16
19W CD H11 SING N N 17
19W NZ H12 SING N N 18
19W NZ H13 SING N N 19
19W C OXT SING N N 20
19W OXT HXT SING N N 21
#
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
19W SMILES ACDLabs 12.01 O=C(O)C(N)CCCON
19W InChI InChI 1.03 InChI=1S/C5H12N2O3/c6-4(5(8)9)2-1-3-10-7/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1
19W InChIKey InChI 1.03 GFOZTGXHZSBIOB-BYPYZUCNSA-N
19W SMILES_CANONICAL CACTVS 3.385 NOCCC[C@H](N)C(O)=O
19W SMILES CACTVS 3.385 NOCCC[CH](N)C(O)=O
19W SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C(C[C@@H](C(=O)O)N)CON
19W SMILES "OpenEye OEToolkits" 1.7.6 C(CC(C(=O)O)N)CON
#
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
19W "SYSTEMATIC NAME" ACDLabs 12.01 5-(aminooxy)-L-norvaline
19W "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2S)-2-azanyl-5-azanyloxy-pentanoic 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
19W 'Create component' 2012-11-12 RCSB
19W 'Other modification' 2013-08-14 RCSB
19W 'Initial release' 2013-08-21 RCSB
19W '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
19W N N 5.104 2.857 1
19W CA C 6.404 2.107 2
19W C C 7.702 2.857 3
19W O O 9.002 2.107 4
19W CB C 6.404 0.608 5
19W CG C 5.104 -0.142 6
19W CD C 5.104 -1.643 7
19W OE O 3.805 -2.393 8
19W NZ N 3.805 -3.893 9
19W OXT O 7.702 4.357 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
19W O C DOUBLE NONE 1
19W C CA SINGLE NONE 2
19W CA N SINGLE BEGINDASH 3
19W CA CB SINGLE NONE 4
19W CG CB SINGLE NONE 5
19W CG CD SINGLE NONE 6
19W CD OE SINGLE NONE 7
19W OE NZ SINGLE NONE 8
19W C OXT SINGLE NONE 9
#
_pdbe_chem_comp_substructure.comp_id 19W
_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
19W O F1 1
19W C F1 1
19W CA F1 1
19W N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 19W
_pdbe_chem_comp_rdkit_properties.exactmw 148.085
_pdbe_chem_comp_rdkit_properties.amw 148.162
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.800
_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 76.081
_pdbe_chem_comp_rdkit_properties.tpsa 98.570
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.931
_pdbe_chem_comp_rdkit_properties.CrippenMR 34.985
_pdbe_chem_comp_rdkit_properties.chi0v 4.619
_pdbe_chem_comp_rdkit_properties.chi1v 2.019
_pdbe_chem_comp_rdkit_properties.chi2v 0.471
_pdbe_chem_comp_rdkit_properties.chi3v 0.471
_pdbe_chem_comp_rdkit_properties.chi4v 0.159
_pdbe_chem_comp_rdkit_properties.chi0n 16.619
_pdbe_chem_comp_rdkit_properties.chi1n 7.716
_pdbe_chem_comp_rdkit_properties.chi2n 0.471
_pdbe_chem_comp_rdkit_properties.chi3n 0.471
_pdbe_chem_comp_rdkit_properties.chi4n 0.159
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.650
_pdbe_chem_comp_rdkit_properties.kappa1 1.574
_pdbe_chem_comp_rdkit_properties.kappa2 5.160
_pdbe_chem_comp_rdkit_properties.kappa3 4.251
_pdbe_chem_comp_rdkit_properties.Phi 0.812
#
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
19W UniChem PDBe 19W
19W UniChem ZINC ZINC000058534155
19W UniChem SureChEMBL SCHEMBL2263651
19W UniChem Nikkaji J792.839D
19W UniChem PubChem 15217865
#
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
19W N 1.722 0.079 -1.497 ETKDGv3 1
19W CA 1.139 0.499 -0.220 ETKDGv3 2
19W C 2.191 1.121 0.662 ETKDGv3 3
19W O 2.050 2.303 1.074 ETKDGv3 4
19W CB 0.483 -0.695 0.501 ETKDGv3 5
19W CG -0.617 -1.393 -0.322 ETKDGv3 6
19W CD -1.854 -0.522 -0.569 ETKDGv3 7
19W OE -2.397 -0.097 0.657 ETKDGv3 8
19W NZ -3.469 0.676 0.347 ETKDGv3 9
19W H 2.504 -0.594 -1.321 ETKDGv3 10
19W H2 2.129 0.917 -1.973 ETKDGv3 11
19W HA 0.362 1.267 -0.422 ETKDGv3 12
19W H6 1.264 -1.451 0.738 ETKDGv3 13
19W H7 0.057 -0.355 1.471 ETKDGv3 14
19W H8 -0.937 -2.306 0.226 ETKDGv3 15
19W H9 -0.205 -1.729 -1.298 ETKDGv3 16
19W H10 -2.601 -1.136 -1.123 ETKDGv3 17
19W H11 -1.580 0.348 -1.206 ETKDGv3 18
19W H12 -3.297 1.614 0.774 ETKDGv3 19
19W H13 -4.290 0.267 0.848 ETKDGv3 20
19W OXT 3.317 0.390 1.030 ETKDGv3 21
19W HXT 4.029 0.796 1.624 ETKDGv3 22
#