data_V5N
#
_chem_comp.id V5N
_chem_comp.name "(2S,3S)-2-azanyl-3-(1H-imidazol-5-yl)-3-oxidanyl-propanoic acid"
_chem_comp.type "L-peptide linking"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C6 H9 N3 O3"
_chem_comp.mon_nstd_parent_comp_id HIS
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-04-19
_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 171.154
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code V5N
_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 7O81
_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_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
V5N N N1 N 0 1 N N N Y Y N 287.691 303.036 291.357 -0.685 -1.174 1.192 N V5N 1
V5N CA C1 C 0 1 N N S Y N N 287.548 303.175 289.901 -1.004 0.143 0.627 CA V5N 2
V5N C C2 C 0 1 N N N Y N Y 286.422 304.172 289.630 -2.459 0.183 0.235 C V5N 3
V5N O O1 O 0 1 N N N Y N Y 285.415 304.142 290.367 -3.066 -0.847 0.063 O V5N 4
V5N CB C3 C 0 1 N N S N N N 287.240 301.839 289.215 -0.136 0.392 -0.609 CB V5N 5
V5N CG C4 C 0 1 Y N N N N N 288.365 300.830 289.454 1.317 0.231 -0.243 CG V5N 6
V5N CD2 C5 C 0 1 Y N N N N N 288.591 300.195 290.596 2.013 -0.921 -0.207 CD2 V5N 7
V5N ND1 N2 N 0 1 Y N N N N N 289.251 300.456 288.540 2.184 1.229 0.112 ND1 V5N 8
V5N CE1 C6 C 0 1 Y N N N N N 290.050 299.572 289.130 3.379 0.651 0.357 CE1 V5N 9
V5N NE2 N3 N 0 1 Y N N N N N 289.646 299.412 290.390 3.270 -0.635 0.164 NE2 V5N 10
V5N O2 O2 O 0 1 N N N N N N 286.011 301.308 289.717 -0.478 -0.549 -1.628 O2 V5N 11
V5N H H1 H 0 1 N N N Y Y N 287.891 303.929 291.760 -0.859 -1.908 0.521 H1 V5N 12
V5N H2 H2 H 0 1 N Y N Y Y N 286.840 302.679 291.743 0.268 -1.205 1.522 H2 V5N 13
V5N HA H4 H 0 1 N N N Y N N 288.481 303.577 289.480 -0.807 0.915 1.371 H4 V5N 14
V5N HB2 H6 H 0 1 N N N N N N 287.155 302.016 288.133 -0.309 1.404 -0.976 H6 V5N 15
V5N HD2 H7 H 0 1 N N N N N N 288.029 300.294 291.513 1.627 -1.903 -0.437 H7 V5N 16
V5N HD1 H8 H 0 1 N N N N N N 289.307 300.776 287.594 1.978 2.175 0.178 H8 V5N 17
V5N HE1 H9 H 0 1 N N N N N N 290.885 299.069 288.666 4.278 1.168 0.660 H9 V5N 18
V5N H11 H11 H 0 1 N N N N N N 285.476 302.015 290.059 -0.349 -1.472 -1.370 H11 V5N 19
V5N OXT O3 O 0 1 N Y N Y N Y 286.573 305.028 288.626 -3.080 1.362 0.078 O1 V5N 20
V5N HXT H3 H 0 1 N Y N Y N Y 285.809 305.590 288.571 -4.013 1.337 -0.174 H3 V5N 21
#
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
V5N ND1 CE1 SING Y N 1
V5N ND1 CG SING Y N 2
V5N CE1 NE2 DOUB Y N 3
V5N CB CG SING N N 4
V5N CB O2 SING N N 5
V5N CB CA SING N N 6
V5N CG CD2 DOUB Y N 7
V5N C CA SING N N 8
V5N C O DOUB N N 9
V5N CA N SING N N 10
V5N NE2 CD2 SING Y N 11
V5N N H SING N N 12
V5N N H2 SING N N 13
V5N CA HA SING N N 14
V5N CB HB2 SING N N 15
V5N CD2 HD2 SING N N 16
V5N ND1 HD1 SING N N 17
V5N CE1 HE1 SING N N 18
V5N O2 H11 SING N N 19
V5N C OXT SING N N 20
V5N 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
V5N InChI InChI 1.03 "InChI=1S/C6H9N3O3/c7-4(6(11)12)5(10)3-1-8-2-9-3/h1-2,4-5,10H,7H2,(H,8,9)(H,11,12)/t4-,5+/m0/s1"
V5N InChIKey InChI 1.03 KQMBIBBJWXGSEI-CRCLSJGQSA-N
V5N SMILES_CANONICAL CACTVS 3.385 "N[C@@H]([C@H](O)c1[nH]cnc1)C(O)=O"
V5N SMILES CACTVS 3.385 "N[CH]([CH](O)c1[nH]cnc1)C(O)=O"
V5N SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1c([nH]cn1)[C@H]([C@@H](C(=O)O)N)O"
V5N SMILES "OpenEye OEToolkits" 2.0.7 "c1c([nH]cn1)C(C(C(=O)O)N)O"
#
_pdbx_chem_comp_identifier.comp_id V5N
_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},3~{S})-2-azanyl-3-(1~{H}-imidazol-5-yl)-3-oxidanyl-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
V5N "Create component" 2021-04-19 PDBE
V5N "Initial release" 2021-06-02 RCSB
V5N "Modify parent residue" 2021-07-10 PDBE
V5N "Modify linking type" 2021-07-10 PDBE
V5N "Modify leaving atom flag" 2021-07-11 PDBE
V5N "Modify backbone" 2023-11-03 PDBE
V5N "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id V5N
_pdbx_chem_comp_pcm.modified_residue_id HIS
_pdbx_chem_comp_pcm.type Hydroxylation
_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 PTM-0477
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#