data_7V9
#
_chem_comp.id 7V9
_chem_comp.name "~{S}-[2-[3-[[(2~{S})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] pyridine-3-carbothioate"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C17 H26 N3 O8 P S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-01-19
_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 463.442
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 7V9
_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 5WPX
_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
7V9 O8 O1 O 0 1 N N N N N N -6.198 -3.608 8.059 0.873 -1.180 1.654 O8 7V9 1
7V9 P P1 P 0 1 N N N N N N -12.944 3.718 7.345 -6.713 2.477 0.251 P 7V9 2
7V9 C4 C1 C 0 1 N N N N N N -10.038 -0.347 9.087 -3.898 -2.081 0.412 C4 7V9 3
7V9 C2 C2 C 0 1 N N N N N N -10.412 2.062 9.634 -5.651 -1.115 -1.052 C2 7V9 4
7V9 O1P O2 O 0 1 N N N N N N -13.140 2.506 6.518 -5.365 3.067 0.906 O1P 7V9 5
7V9 O2P O3 O 0 1 N N N N N N -13.963 4.087 8.354 -7.357 3.576 -0.733 O2P 7V9 6
7V9 O3P O4 O 0 1 N N N N N N -11.525 3.577 8.097 -6.365 1.146 -0.585 O3P 7V9 7
7V9 C1 C3 C 0 1 N N N N N N -11.365 2.195 8.440 -5.877 -0.051 0.024 C1 7V9 8
7V9 CE1 C4 C 0 1 N N N N N N -10.833 3.039 10.734 -6.973 -1.408 -1.764 CE1 7V9 9
7V9 CE2 C5 C 0 1 N N N N N N -8.974 2.374 9.203 -4.627 -0.605 -2.067 CE2 7V9 10
7V9 C3 C6 C 0 1 N N S N N N -10.477 0.634 10.175 -5.128 -2.397 -0.399 C3 7V9 11
7V9 O3 O5 O 0 1 N N N N N N -9.607 0.515 11.294 -6.135 -2.941 0.455 O3 7V9 12
7V9 O4 O6 O 0 1 N N N N N N -10.826 -0.769 8.265 -3.954 -2.078 1.623 O4 7V9 13
7V9 N5 N1 N 0 1 N N N N N N -8.775 -0.668 9.041 -2.734 -1.803 -0.209 N5 7V9 14
7V9 C6 C7 C 0 1 N N N N N N -8.012 -0.518 7.769 -1.514 -1.602 0.577 C6 7V9 15
7V9 C7 C8 C 0 1 N N N N N N -6.682 -1.269 7.884 -0.345 -1.302 -0.363 C7 7V9 16
7V9 C8 C9 C 0 1 N N N N N N -6.886 -2.748 7.546 0.909 -1.095 0.445 C8 7V9 17
7V9 N9 N2 N 0 1 N N N N N N -7.731 -3.040 6.597 2.073 -0.817 -0.176 N9 7V9 18
7V9 C10 C10 C 0 1 N N N N N N -7.238 -3.321 5.220 3.293 -0.616 0.610 C10 7V9 19
7V9 C11 C11 C 0 1 N N N N N N -6.958 -4.819 5.074 4.462 -0.316 -0.331 C11 7V9 20
7V9 S12 S1 S 0 1 N N N N N N -5.474 -5.065 4.070 5.969 -0.068 0.641 S12 7V9 21
7V9 C13 C12 C 0 1 N N N N N N -6.304 -5.675 2.581 7.119 0.251 -0.656 C13 7V9 22
7V9 O13 O7 O 0 1 N N N N N N -6.976 -6.685 2.633 6.747 0.248 -1.813 O13 7V9 23
7V9 C14 C13 C 0 1 Y N N N N N -5.196 -5.613 1.727 8.536 0.522 -0.336 C14 7V9 24
7V9 C15 C14 C 0 1 Y N N N N N -4.005 -6.260 2.078 8.976 0.529 0.988 C15 7V9 25
7V9 N16 N3 N 0 1 Y N N N N N -2.900 -6.103 1.331 10.239 0.770 1.273 N16 7V9 26
7V9 C17 C15 C 0 1 Y N N N N N -2.903 -5.329 0.235 11.132 1.013 0.332 C17 7V9 27
7V9 C18 C16 C 0 1 Y N N N N N -4.068 -4.660 -0.162 10.775 1.025 -1.005 C18 7V9 28
7V9 C19 C17 C 0 1 Y N N N N N -5.213 -4.762 0.625 9.462 0.771 -1.357 C19 7V9 29
7V9 H1 H1 H 0 1 N N N N N N -12.854 2.679 5.629 -4.686 3.305 0.260 H1 7V9 30
7V9 H2 H2 H 0 1 N N N N N N -14.384 4.899 8.097 -7.592 4.406 -0.295 H2 7V9 31
7V9 H3 H3 H 0 1 N N N N N N -10.949 1.651 7.579 -6.607 -0.414 0.748 2H1 7V9 32
7V9 H4 H4 H 0 1 N N N N N N -12.344 1.769 8.705 -4.935 0.158 0.532 1H1 7V9 33
7V9 H5 H5 H 0 1 N N N N N N -10.150 2.944 11.591 -7.299 -0.520 -2.305 2HE1 7V9 34
7V9 H6 H6 H 0 1 N N N N N N -10.793 4.067 10.346 -6.833 -2.230 -2.467 3HE1 7V9 35
7V9 H7 H7 H 0 1 N N N N N N -11.859 2.808 11.056 -7.729 -1.684 -1.028 1HE1 7V9 36
7V9 H8 H8 H 0 1 N N N N N N -8.302 2.275 10.068 -3.728 -0.277 -1.544 1HE2 7V9 37
7V9 H9 H9 H 0 1 N N N N N N -8.666 1.669 8.417 -4.371 -1.407 -2.760 2HE2 7V9 38
7V9 H10 H10 H 0 1 N N N N N N -8.923 3.402 8.815 -5.050 0.233 -2.621 3HE2 7V9 39
7V9 H11 H11 H 0 1 N N N N N N -11.513 0.407 10.466 -4.877 -3.122 -1.173 3H 7V9 40
7V9 H12 H12 H 0 1 N N N N N N -9.877 1.123 11.972 -6.408 -2.349 1.169 3HO 7V9 41
7V9 H13 H13 H 0 1 N N N N N N -8.318 -1.015 9.860 -2.705 -1.735 -1.176 5H 7V9 42
7V9 H14 H14 H 0 1 N N N N N N -8.599 -0.935 6.937 -1.656 -0.764 1.260 2H6 7V9 43
7V9 H15 H15 H 0 1 N N N N N N -7.817 0.548 7.581 -1.298 -2.504 1.149 1H6 7V9 44
7V9 H16 H16 H 0 1 N N N N N N -5.955 -0.832 7.184 -0.204 -2.140 -1.046 1H7 7V9 45
7V9 H17 H17 H 0 1 N N N N N N -6.301 -1.179 8.912 -0.562 -0.400 -0.936 2H7 7V9 46
7V9 H18 H18 H 0 1 N N N N N N -8.711 -3.075 6.794 2.102 -0.749 -1.143 9H 7V9 47
7V9 H19 H19 H 0 1 N N N N N N -8.001 -3.018 4.488 3.151 0.222 1.293 2H10 7V9 48
7V9 H20 H20 H 0 1 N N N N N N -6.312 -2.756 5.040 3.509 -1.518 1.182 1H10 7V9 49
7V9 H21 H21 H 0 1 N N N N N N -6.804 -5.261 6.069 4.603 -1.153 -1.013 1H11 7V9 50
7V9 H22 H22 H 0 1 N N N N N N -7.815 -5.306 4.585 4.245 0.587 -0.902 2H11 7V9 51
7V9 H25 H25 H 0 1 N N N N N N -3.975 -6.889 2.955 8.275 0.335 1.786 5H1 7V9 52
7V9 H26 H26 H 0 1 N N N N N N -1.999 -5.221 -0.346 12.158 1.205 0.610 7H1 7V9 53
7V9 H27 H27 H 0 1 N N N N N N -4.078 -4.072 -1.068 11.515 1.225 -1.765 8H1 7V9 54
7V9 H28 H28 H 0 1 N N N N N N -6.098 -4.191 0.385 9.157 0.770 -2.393 9H1 7V9 55
7V9 O1 O8 O 0 1 N Y N N N N -12.635 4.054 6.581 -7.679 2.148 1.323 O1 7V9 56
#
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
7V9 O8 C8 DOUB N N 1
7V9 P O1P SING N N 2
7V9 P O2P SING N N 3
7V9 P O3P SING N N 4
7V9 C4 C3 SING N N 5
7V9 C4 O4 DOUB N N 6
7V9 C4 N5 SING N N 7
7V9 C2 C1 SING N N 8
7V9 C2 CE1 SING N N 9
7V9 C2 CE2 SING N N 10
7V9 C2 C3 SING N N 11
7V9 O3P C1 SING N N 12
7V9 C3 O3 SING N N 13
7V9 N5 C6 SING N N 14
7V9 C6 C7 SING N N 15
7V9 C7 C8 SING N N 16
7V9 C8 N9 SING N N 17
7V9 N9 C10 SING N N 18
7V9 C10 C11 SING N N 19
7V9 C11 S12 SING N N 20
7V9 S12 C13 SING N N 21
7V9 C13 O13 DOUB N N 22
7V9 C13 C14 SING N N 23
7V9 C14 C15 DOUB Y N 24
7V9 C14 C19 SING Y N 25
7V9 C15 N16 SING Y N 26
7V9 N16 C17 DOUB Y N 27
7V9 C17 C18 SING Y N 28
7V9 C18 C19 DOUB Y N 29
7V9 O1P H1 SING N N 30
7V9 O2P H2 SING N N 31
7V9 C1 H3 SING N N 32
7V9 C1 H4 SING N N 33
7V9 CE1 H5 SING N N 34
7V9 CE1 H6 SING N N 35
7V9 CE1 H7 SING N N 36
7V9 CE2 H8 SING N N 37
7V9 CE2 H9 SING N N 38
7V9 CE2 H10 SING N N 39
7V9 C3 H11 SING N N 40
7V9 O3 H12 SING N N 41
7V9 N5 H13 SING N N 42
7V9 C6 H14 SING N N 43
7V9 C6 H15 SING N N 44
7V9 C7 H16 SING N N 45
7V9 C7 H17 SING N N 46
7V9 N9 H18 SING N N 47
7V9 C10 H19 SING N N 48
7V9 C10 H20 SING N N 49
7V9 C11 H21 SING N N 50
7V9 C11 H22 SING N N 51
7V9 C15 H25 SING N N 52
7V9 C17 H26 SING N N 53
7V9 C18 H27 SING N N 54
7V9 C19 H28 SING N N 55
7V9 P O1 DOUB N N 56
#
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
7V9 InChI InChI 1.03 "InChI=1S/C17H26N3O8PS/c1-17(2,11-28-29(25,26)27)14(22)15(23)20-7-5-13(21)19-8-9-30-16(24)12-4-3-6-18-10-12/h3-4,6,10,14,22H,5,7-9,11H2,1-2H3,(H,19,21)(H,20,23)(H2,25,26,27)/t14-/m1/s1"
7V9 InChIKey InChI 1.03 WOIGSQAUIGDQKV-CQSZACIVSA-N
7V9 SMILES_CANONICAL CACTVS 3.385 "CC(C)(CO[P](O)(O)=O)[C@H](O)C(=O)NCCC(=O)NCCSC(=O)c1cccnc1"
7V9 SMILES CACTVS 3.385 "CC(C)(CO[P](O)(O)=O)[CH](O)C(=O)NCCC(=O)NCCSC(=O)c1cccnc1"
7V9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC(C)(COP(=O)(O)O)[C@@H](C(=O)NCCC(=O)NCCSC(=O)c1cccnc1)O"
7V9 SMILES "OpenEye OEToolkits" 2.0.6 "CC(C)(COP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(=O)c1cccnc1)O"
#
_pdbx_chem_comp_identifier.comp_id 7V9
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.6
_pdbx_chem_comp_identifier.identifier "~{S}-[2-[3-[[(2~{S})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] pyridine-3-carbothioate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
7V9 "Create component" 2017-01-19 RCSB
7V9 "Initial release" 2018-02-07 RCSB
7V9 "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id 7V9
_pdbx_chem_comp_pcm.modified_residue_id SER
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category "Covalent chemical 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 P
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom OG
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#