data_VHF
#
_chem_comp.id VHF
_chem_comp.name "(2~{S})-2-azanyl-5-oxidanylidene-5-phosphonooxy-pentanoic acid"
_chem_comp.type "L-peptide linking"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C5 H10 N O7 P"
_chem_comp.mon_nstd_parent_comp_id GLU
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-03-06
_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 227.109
_chem_comp.one_letter_code E
_chem_comp.three_letter_code VHF
_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 7OY3
_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
VHF PA PA P 0 1 N N N N N N 110.735 114.059 -3.318 3.211 -0.018 0.042 PA VHF 1
VHF OA1 OA1 O 0 1 N N N N N N 111.168 114.932 -4.462 3.172 -0.025 1.521 OA1 VHF 2
VHF OA2 OA2 O 0 1 N N N N N N 111.726 113.598 -2.275 4.482 0.835 -0.457 OA2 VHF 3
VHF OA3 OA3 O 0 1 N N N N N N 109.721 113.005 -3.725 3.332 -1.529 -0.500 OA3 VHF 4
VHF OE2 OE2 O 0 1 N N N N N N 109.728 115.272 -2.309 1.860 0.649 -0.527 OE2 VHF 5
VHF CD CD C 0 1 N N N N N N 108.508 115.588 -2.542 0.698 0.117 -0.117 CD VHF 6
VHF OE1 OE1 O 0 1 N N N N N N 107.943 115.277 -3.593 0.699 -0.820 0.646 OE1 VHF 7
VHF CG CG C 0 1 N N N N N N 107.729 116.311 -1.457 -0.607 0.689 -0.607 CG VHF 8
VHF CB CB C 0 1 N N N N N N 106.967 115.250 -0.631 -1.770 -0.094 0.007 CB VHF 9
VHF CA CA C 0 1 N N S Y N N 105.889 115.878 0.242 -3.095 0.487 -0.491 CA VHF 10
VHF C C C 0 1 N N N Y N Y 105.001 114.790 0.942 -4.235 -0.359 0.016 C VHF 11
VHF O O O 0 1 N N N Y N Y 105.131 113.601 0.579 -4.871 -0.001 0.979 O VHF 12
VHF OXT OXT O 0 1 N Y N Y N Y 104.187 115.205 1.810 -4.544 -1.508 -0.604 OXT VHF 13
VHF N N N 0 1 N N N Y Y N 106.528 116.735 1.244 -3.245 1.861 0.007 N VHF 14
VHF HA2 HA2 H 0 1 N N N N N N 112.587 113.944 -2.480 5.332 0.490 -0.151 HA2 VHF 15
VHF HA3 HA3 H 0 1 N N N N N N 109.535 113.086 -4.653 3.363 -1.600 -1.464 HA3 VHF 16
VHF HG2 HG2 H 0 1 N N N N N N 108.421 116.865 -0.806 -0.678 1.736 -0.313 HG2 VHF 17
VHF HG3 HG3 H 0 1 N N N N N N 107.015 117.012 -1.914 -0.652 0.613 -1.693 HG3 VHF 18
VHF HB2 HB2 H 0 1 N N N N N N 106.495 114.534 -1.320 -1.698 -1.141 -0.287 HB2 VHF 19
VHF HB3 HB3 H 0 1 N N N N N N 107.683 114.720 0.014 -1.725 -0.017 1.094 HB3 VHF 20
VHF HA HA H 0 1 N N N Y N N 105.235 116.490 -0.396 -3.102 0.492 -1.581 HA VHF 21
VHF HXT HXT H 0 1 N Y N Y N Y 103.684 114.474 2.149 -5.284 -2.016 -0.243 HXT VHF 22
VHF H2 H H 0 1 N Y N Y Y N 105.827 117.152 1.822 -4.082 2.289 -0.360 H VHF 23
VHF H H2 H 0 1 N N N Y Y N 107.143 116.185 1.809 -3.241 1.883 1.016 H2 VHF 24
#
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
VHF OA1 PA DOUB N N 1
VHF OA3 PA SING N N 2
VHF OE1 CD DOUB N N 3
VHF PA OE2 SING N N 4
VHF PA OA2 SING N N 5
VHF CD OE2 SING N N 6
VHF CD CG SING N N 7
VHF CG CB SING N N 8
VHF CB CA SING N N 9
VHF CA C SING N N 10
VHF CA N SING N N 11
VHF O C DOUB N N 12
VHF C OXT SING N N 13
VHF OA2 HA2 SING N N 14
VHF OA3 HA3 SING N N 15
VHF CG HG2 SING N N 16
VHF CG HG3 SING N N 17
VHF CB HB2 SING N N 18
VHF CB HB3 SING N N 19
VHF CA HA SING N N 20
VHF OXT HXT SING N N 21
VHF N H2 SING N N 22
VHF N H SING N N 23
#
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
VHF InChI InChI 1.06 "InChI=1S/C5H10NO7P/c6-3(5(8)9)1-2-4(7)13-14(10,11)12/h3H,1-2,6H2,(H,8,9)(H2,10,11,12)/t3-/m0/s1"
VHF InChIKey InChI 1.06 PJRXVIJAERNUIP-VKHMYHEASA-N
VHF SMILES_CANONICAL CACTVS 3.385 "N[C@@H](CCC(=O)O[P](O)(O)=O)C(O)=O"
VHF SMILES CACTVS 3.385 "N[CH](CCC(=O)O[P](O)(O)=O)C(O)=O"
VHF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C(CC(=O)OP(=O)(O)O)[C@@H](C(=O)O)N"
VHF SMILES "OpenEye OEToolkits" 2.0.7 "C(CC(=O)OP(=O)(O)O)C(C(=O)O)N"
#
_pdbx_chem_comp_identifier.comp_id VHF
_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-5-oxidanylidene-5-phosphonooxy-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
VHF "Create component" 2023-03-06 PDBE
VHF "Modify atom id" 2023-03-06 PDBE
VHF "Initial release" 2023-03-15 RCSB
VHF "Modify backbone" 2023-11-03 PDBE
VHF "Modify PCM" 2024-09-27 PDBE
#
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_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
1 VHF GLU Phosphorylation "Named protein modification" "Amino-acid side chain" "Any position" ? ? ? ?
2 VHF CYS None "Covalent chemical modification" "Amino-acid side chain" "Any position" CD SG ? ?
#