data_OV7
#
_chem_comp.id OV7
_chem_comp.name '(2R)-amino[(carboxymethyl)sulfanyl]acetic acid'
_chem_comp.type 'D-peptide linking'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C4 H7 N O4 S'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-07-08
_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 165.168
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code OV7
_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 6PO6
_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
OV7 N N N 0 1 N N N Y Y N 3.338 5.787 2.149 1.141 1.758 0.111 N OV7 1
OV7 CA CA C 0 1 N N R Y N N 2.606 5.137 1.203 1.373 0.474 -0.564 CA OV7 2
OV7 C CB1 C 0 1 N N N Y N Y 1.307 5.619 0.977 2.499 -0.258 0.120 CB1 OV7 3
OV7 SB2 SB2 S 0 1 N N N N N N 3.623 5.182 -0.375 -0.135 -0.531 -0.487 SB2 OV7 4
OV7 OXT OG1 O 0 1 N N N Y N Y 1.036 6.767 1.338 3.757 0.197 0.015 OG1 OV7 5
OV7 O OG2 O 0 1 N N N Y N Y 0.487 4.860 0.455 2.269 -1.254 0.764 OG2 OV7 6
OV7 CG3 CG3 C 0 1 N N N N N N 3.403 3.574 -0.836 -1.404 0.674 -0.007 CG3 OV7 7
OV7 CD CD C 0 1 N N N N N N 1.935 3.214 -1.358 -2.738 -0.018 0.100 CD OV7 8
OV7 OE1 OE1 O 0 1 N N N N N N 1.480 2.280 -0.774 -3.831 0.682 0.445 OE1 OV7 9
OV7 OE2 OE2 O 0 1 N N N N N N 1.497 3.708 -2.471 -2.825 -1.202 -0.124 OE2 OV7 10
OV7 H H1 H 0 1 N N N Y Y N 2.837 5.791 3.014 0.895 1.617 1.080 H1 OV7 11
OV7 H2 H2 H 0 1 N Y N Y Y N 4.213 5.319 2.273 1.946 2.361 0.027 H2 OV7 12
OV7 HA H4 H 0 1 N N N Y N N 2.550 4.067 1.453 1.637 0.654 -1.606 H4 OV7 13
OV7 HXT H5 H 0 1 N N N Y N Y 0.123 6.952 1.150 4.446 -0.305 0.471 H5 OV7 14
OV7 H6 H6 H 0 1 N N N N N N 3.621 2.937 0.034 -1.143 1.112 0.956 H6 OV7 15
OV7 H7 H7 H 0 1 N N N N N N 4.116 3.350 -1.643 -1.462 1.460 -0.760 H7 OV7 16
OV7 H8 H8 H 0 1 N N N N N N 0.732 1.941 -1.252 -4.664 0.195 0.502 H8 OV7 17
#
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
OV7 OE2 CD DOUB N N 1
OV7 CD CG3 SING N N 2
OV7 CD OE1 SING N N 3
OV7 CG3 SB2 SING N N 4
OV7 SB2 CA SING N N 5
OV7 O C DOUB N N 6
OV7 C CA SING N N 7
OV7 C OXT SING N N 8
OV7 CA N SING N N 9
OV7 N H SING N N 10
OV7 N H2 SING N N 11
OV7 CA HA SING N N 12
OV7 OXT HXT SING N N 13
OV7 CG3 H6 SING N N 14
OV7 CG3 H7 SING N N 15
OV7 OE1 H8 SING N N 16
#
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
OV7 SMILES ACDLabs 12.01 'NC(C(O)=O)SCC(O)=O'
OV7 InChI InChI 1.03 'InChI=1S/C4H7NO4S/c5-3(4(8)9)10-1-2(6)7/h3H,1,5H2,(H,6,7)(H,8,9)/t3-/m1/s1'
OV7 InChIKey InChI 1.03 FDUUQONQQWJTKJ-GSVOUGTGSA-N
OV7 SMILES_CANONICAL CACTVS 3.385 'N[C@H](SCC(O)=O)C(O)=O'
OV7 SMILES CACTVS 3.385 'N[CH](SCC(O)=O)C(O)=O'
OV7 SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.7 'C(C(=O)O)S[C@H](C(=O)O)N'
OV7 SMILES 'OpenEye OEToolkits' 2.0.7 'C(C(=O)O)SC(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
OV7 'SYSTEMATIC NAME' ACDLabs 12.01 '(2R)-amino[(carboxymethyl)sulfanyl]acetic acid'
OV7 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 2.0.7 '(2~{R})-2-azanyl-2-(2-hydroxy-2-oxoethylsulfanyl)ethanoic 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
OV7 'Create component' 2019-07-08 RCSB
OV7 'Initial release' 2019-08-07 RCSB
OV7 'Modify backbone' 2023-11-03 PDBE
OV7 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id OV7
_pdbx_chem_comp_pcm.modified_residue_id GLU
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Non-standard residue'
_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
OV7 N N 4.299 2.340 1
OV7 CA C 5.598 1.590 2
OV7 C C 6.897 2.340 3
OV7 SB2 S 5.598 0.090 4
OV7 OXT O 6.897 3.840 5
OV7 O O 8.196 1.590 6
OV7 CG3 C 4.299 -0.660 7
OV7 CD C 4.299 -2.160 8
OV7 OE1 O 5.598 -2.910 9
OV7 OE2 O 3.000 -2.910 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
OV7 OE2 CD DOUBLE NONE 1
OV7 CD CG3 SINGLE NONE 2
OV7 CD OE1 SINGLE NONE 3
OV7 CG3 SB2 SINGLE NONE 4
OV7 SB2 CA SINGLE NONE 5
OV7 O C DOUBLE NONE 6
OV7 C CA SINGLE NONE 7
OV7 C OXT SINGLE NONE 8
OV7 CA N SINGLE BEGINWEDGE 9
#
_pdbe_chem_comp_substructure.comp_id OV7
_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
OV7 O F1 1
OV7 C F1 1
OV7 CA F1 1
OV7 N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id OV7
_pdbe_chem_comp_rdkit_properties.exactmw 165.010
_pdbe_chem_comp_rdkit_properties.amw 165.170
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 17
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_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 71.333
_pdbe_chem_comp_rdkit_properties.tpsa 100.620
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.826
_pdbe_chem_comp_rdkit_properties.CrippenMR 35.705
_pdbe_chem_comp_rdkit_properties.chi0v 5.305
_pdbe_chem_comp_rdkit_properties.chi1v 2.765
_pdbe_chem_comp_rdkit_properties.chi2v 1.034
_pdbe_chem_comp_rdkit_properties.chi3v 1.034
_pdbe_chem_comp_rdkit_properties.chi4v 0.395
_pdbe_chem_comp_rdkit_properties.chi0n 11.488
_pdbe_chem_comp_rdkit_properties.chi1n 5.159
_pdbe_chem_comp_rdkit_properties.chi2n 0.406
_pdbe_chem_comp_rdkit_properties.chi3n 0.406
_pdbe_chem_comp_rdkit_properties.chi4n 0.132
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.750
_pdbe_chem_comp_rdkit_properties.kappa1 2.707
_pdbe_chem_comp_rdkit_properties.kappa2 4.127
_pdbe_chem_comp_rdkit_properties.kappa3 4.161
_pdbe_chem_comp_rdkit_properties.Phi 1.117
#
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
OV7 UniChem SureChEMBL SCHEMBL23931412
OV7 UniChem PubChem 93495705
#
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
OV7 N -0.265 -1.248 -0.494 ETKDGv3 1
OV7 CA -0.873 0.043 -0.176 ETKDGv3 2
OV7 C -2.364 -0.086 -0.045 ETKDGv3 3
OV7 SB2 -0.181 0.697 1.390 ETKDGv3 4
OV7 OXT -3.197 0.630 -0.899 ETKDGv3 5
OV7 O -2.863 -0.840 0.833 ETKDGv3 6
OV7 CG3 1.431 1.238 0.718 ETKDGv3 7
OV7 CD 2.347 0.073 0.532 ETKDGv3 8
OV7 OE1 2.704 -0.332 -0.751 ETKDGv3 9
OV7 OE2 2.789 -0.548 1.535 ETKDGv3 10
OV7 H -0.678 -1.604 -1.387 ETKDGv3 11
OV7 H2 -0.496 -1.937 0.259 ETKDGv3 12
OV7 HA -0.655 0.758 -0.999 ETKDGv3 13
OV7 HXT -4.205 0.555 -0.825 ETKDGv3 14
OV7 H6 1.296 1.783 -0.240 ETKDGv3 15
OV7 H7 1.891 1.942 1.442 ETKDGv3 16
OV7 H8 3.319 -1.124 -0.893 ETKDGv3 17
#