data_6VC
#
_chem_comp.id 6VC
_chem_comp.name "~{N}-[(2~{S})-1-[[(2~{S},3~{R},4~{S})-2,6-dimethyl-1,2,3-tris(oxidanyl)heptan-4-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]-6-methyl-heptanamide"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C20 H40 N2 O6"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "Dihydroeponemycin bound form"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2016-07-05
_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 404.541
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 6VC
_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 5LF1
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
_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
6VC C5 C1 C 0 1 N N N N N N 61.750 203.795 43.659 -3.626 -0.026 -0.408 C5 6VC 1
6VC C6 C2 C 0 1 N N N N N N 62.823 203.204 42.797 -4.873 -0.091 0.477 C6 6VC 2
6VC C8 C3 C 0 1 N N N N N N 61.869 205.303 43.613 -2.396 -0.195 0.445 C8 6VC 3
6VC O2 O1 O 0 1 N N N N N N 61.515 205.854 42.545 -2.505 -0.352 1.642 O2 6VC 4
6VC N2 N1 N 0 1 N N N N N N 62.246 205.938 44.743 -1.174 -0.172 -0.124 N2 6VC 5
6VC C9 C4 C 0 1 N N S N N N 62.366 207.390 44.854 0.023 -0.336 0.706 C9 6VC 6
6VC C10 C5 C 0 1 N N N N N N 61.617 208.049 46.024 0.305 -1.827 0.904 C10 6VC 7
6VC O3 O2 O 0 1 N N N N N N 60.390 207.320 46.022 0.632 -2.421 -0.353 O3 6VC 8
6VC C12 C6 C 0 1 N N N N N N 63.777 207.857 45.018 1.200 0.311 0.023 C12 6VC 9
6VC O4 O3 O 0 1 N N N N N N 64.610 207.088 45.477 1.054 0.856 -1.051 O4 6VC 10
6VC N3 N2 N 0 1 N N N N N N 63.959 209.132 44.672 2.415 0.285 0.605 N3 6VC 11
6VC C13 C7 C 0 1 N N S N N N 65.233 209.792 44.722 3.559 0.914 -0.059 C13 6VC 12
6VC C21 C8 C 0 1 N N R N N N 65.130 210.996 45.663 4.854 0.254 0.421 C211 6VC 13
6VC C22 C9 C 0 1 N N S N N N 64.724 210.685 47.148 4.846 -1.226 0.032 C22 6VC 14
6VC C23 C10 C 0 1 N N N N N N 64.920 211.943 48.082 6.194 -1.855 0.391 C23 6VC 15
6VC O6 O4 O 0 1 N N N N N N 63.327 210.353 47.225 3.803 -1.899 0.741 O6 6VC 16
6VC C24 C11 C 0 1 N N N N N N 65.450 209.464 47.755 4.607 -1.357 -1.473 C24 6VC 17
6VC O5 O5 O 0 1 N N N N N N 64.145 211.861 45.077 4.951 0.373 1.841 O5 6VC 18
6VC C14 C12 C 0 1 N N N N N N 65.672 210.184 43.292 3.591 2.405 0.282 C14 6VC 19
6VC C15 C13 C 0 1 N N N N N N 65.771 209.000 42.324 2.355 3.089 -0.306 C15 6VC 20
6VC C16 C14 C 0 1 N N N N N N 66.072 209.530 40.919 2.321 4.552 0.139 C16 6VC 21
6VC C20 C15 C 0 1 N N N N N N 66.836 208.025 42.763 2.414 3.022 -1.834 C20 6VC 22
6VC C1 C16 C 0 1 N N N N N N 64.089 203.103 43.641 -6.123 0.080 -0.389 C1 6VC 23
6VC C2 C17 C 0 1 N N N N N N 64.804 201.773 43.445 -7.369 0.015 0.495 C2 6VC 24
6VC C3 C18 C 0 1 N N N N N N 65.937 201.701 42.417 -8.619 0.187 -0.370 C3 6VC 25
6VC C4 C19 C 0 1 N N N N N N 66.225 203.076 41.762 -8.741 -0.999 -1.330 C4 6VC 26
6VC C7 C20 C 0 1 N N N N N N 65.635 200.657 41.327 -9.857 0.247 0.527 C7 6VC 27
6VC O8 O6 O 0 1 N N N N N N 64.917 209.151 49.058 4.599 -2.739 -1.836 O8 6VC 28
6VC H1 H1 H 0 1 N N N N N N 60.762 203.490 43.283 -3.666 -0.823 -1.151 H1 6VC 29
6VC H2 H2 H 0 1 N N N N N N 61.872 203.445 44.695 -3.589 0.939 -0.913 H2 6VC 30
6VC H3 H3 H 0 1 N N N N N N 63.003 203.851 41.926 -4.910 -1.056 0.981 H3 6VC 31
6VC H4 H4 H 0 1 N N N N N N 62.520 202.204 42.454 -4.833 0.706 1.219 H4 6VC 32
6VC H5 H5 H 0 1 N N N N N N 62.455 205.384 45.549 -1.087 -0.046 -1.082 H5 6VC 33
6VC H6 H6 H 0 1 N N N N N N 61.974 207.835 43.928 -0.139 0.136 1.675 H6 6VC 34
6VC H7 H7 H 0 1 N N N N N N 62.160 207.920 46.972 1.141 -1.949 1.593 H7 6VC 35
6VC H8 H8 H 0 1 N N N N N N 61.448 209.120 45.841 -0.580 -2.312 1.317 H8 6VC 36
6VC H9 H9 H 0 1 N N N N N N 59.828 207.642 46.717 0.823 -3.368 -0.303 H9 6VC 37
6VC H10 H10 H 0 1 N N N N N N 63.166 209.656 44.361 2.532 -0.151 1.464 H10 6VC 38
6VC H11 H11 H 0 1 N N N N N N 65.986 209.102 45.130 3.467 0.790 -1.138 H11 6VC 39
6VC H12 H12 H 0 1 N N N N N N 66.105 211.506 45.680 5.707 0.747 -0.045 H12 6VC 40
6VC H13 H13 H 0 1 N N N N N N 64.626 211.686 49.110 6.398 -1.696 1.450 H13 6VC 41
6VC H14 H14 H 0 1 N N N N N N 65.977 212.249 48.068 6.163 -2.924 0.183 H14 6VC 42
6VC H15 H15 H 0 1 N N N N N N 64.294 212.771 47.718 6.981 -1.391 -0.204 H15 6VC 43
6VC H16 H16 H 0 1 N N N N N N 63.094 210.167 48.127 2.912 -1.659 0.451 H16 6VC 44
6VC H17 H17 H 0 1 N N N N N N 65.315 208.597 47.092 3.646 -0.909 -1.729 H17 6VC 45
6VC H18 H18 H 0 1 N N N N N N 66.522 209.691 47.848 5.402 -0.844 -2.014 H18 6VC 46
6VC H19 H19 H 0 1 N N N N N N 64.036 212.632 45.621 4.223 -0.044 2.322 H19 6VC 47
6VC H20 H20 H 0 1 N N N N N N 66.660 210.665 43.353 3.594 2.530 1.365 H20 6VC 48
6VC H21 H21 H 0 1 N N N N N N 64.940 210.900 42.889 4.490 2.855 -0.138 H21 6VC 49
6VC H22 H22 H 0 1 N N N N N N 64.801 208.482 42.303 1.457 2.581 0.045 H22 6VC 50
6VC H23 H23 H 0 1 N N N N N N 65.286 210.238 40.617 1.441 5.039 -0.280 H23 6VC 51
6VC H24 H24 H 0 1 N N N N N N 67.045 210.042 40.921 2.279 4.600 1.227 H24 6VC 52
6VC H25 H25 H 0 1 N N N N N N 66.101 208.690 40.209 3.219 5.060 -0.212 H25 6VC 53
6VC H26 H26 H 0 1 N N N N N N 66.602 207.656 43.773 2.438 1.980 -2.151 H26 6VC 54
6VC H27 H27 H 0 1 N N N N N N 66.869 207.178 42.062 1.534 3.509 -2.253 H27 6VC 55
6VC H28 H28 H 0 1 N N N N N N 67.813 208.530 42.774 3.312 3.530 -2.185 H28 6VC 56
6VC H29 H29 H 0 1 N N N N N N 64.771 203.918 43.356 -6.085 1.046 -0.894 H29 6VC 57
6VC H30 H30 H 0 1 N N N N N N 63.817 203.206 44.702 -6.162 -0.716 -1.132 H30 6VC 58
6VC H31 H31 H 0 1 N N N N N N 64.044 201.036 43.144 -7.406 -0.950 1.000 H31 6VC 59
6VC H32 H32 H 0 1 N N N N N N 65.229 201.485 44.418 -7.330 0.812 1.238 H32 6VC 60
6VC H33 H33 H 0 1 N N N N N N 66.850 201.384 42.942 -8.540 1.111 -0.943 H33 6VC 61
6VC H34 H34 H 0 1 N N N N N N 66.440 203.818 42.545 -9.632 -0.876 -1.947 H34 6VC 62
6VC H35 H35 H 0 1 N N N N N N 67.093 202.988 41.092 -7.859 -1.041 -1.969 H35 6VC 63
6VC H36 H36 H 0 1 N N N N N N 65.346 203.398 41.184 -8.820 -1.923 -0.757 H36 6VC 64
6VC H37 H37 H 0 1 N N N N N N 65.431 199.684 41.797 -9.769 1.092 1.210 H37 6VC 65
6VC H38 H38 H 0 1 N N N N N N 64.756 200.975 40.748 -10.747 0.369 -0.090 H38 6VC 66
6VC H39 H39 H 0 1 N N N N N N 66.502 200.566 40.656 -9.936 -0.677 1.099 H39 6VC 67
6VC H40 H40 H 0 1 N N N N N N 65.374 208.399 49.415 4.452 -2.898 -2.779 H40 6VC 68
#
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
6VC C16 C15 SING N N 1
6VC C7 C3 SING N N 2
6VC C4 C3 SING N N 3
6VC C15 C20 SING N N 4
6VC C15 C14 SING N N 5
6VC C3 C2 SING N N 6
6VC O2 C8 DOUB N N 7
6VC C6 C1 SING N N 8
6VC C6 C5 SING N N 9
6VC C14 C13 SING N N 10
6VC C2 C1 SING N N 11
6VC C8 C5 SING N N 12
6VC C8 N2 SING N N 13
6VC N3 C13 SING N N 14
6VC N3 C12 SING N N 15
6VC C13 C21 SING N N 16
6VC N2 C9 SING N N 17
6VC C9 C12 SING N N 18
6VC C9 C10 SING N N 19
6VC C12 O4 DOUB N N 20
6VC O5 C21 SING N N 21
6VC C21 C22 SING N N 22
6VC O3 C10 SING N N 23
6VC C22 O6 SING N N 24
6VC C22 C24 SING N N 25
6VC C22 C23 SING N N 26
6VC C24 O8 SING N N 27
6VC C5 H1 SING N N 28
6VC C5 H2 SING N N 29
6VC C6 H3 SING N N 30
6VC C6 H4 SING N N 31
6VC N2 H5 SING N N 32
6VC C9 H6 SING N N 33
6VC C10 H7 SING N N 34
6VC C10 H8 SING N N 35
6VC O3 H9 SING N N 36
6VC N3 H10 SING N N 37
6VC C13 H11 SING N N 38
6VC C21 H12 SING N N 39
6VC C23 H13 SING N N 40
6VC C23 H14 SING N N 41
6VC C23 H15 SING N N 42
6VC O6 H16 SING N N 43
6VC C24 H17 SING N N 44
6VC C24 H18 SING N N 45
6VC O5 H19 SING N N 46
6VC C14 H20 SING N N 47
6VC C14 H21 SING N N 48
6VC C15 H22 SING N N 49
6VC C16 H23 SING N N 50
6VC C16 H24 SING N N 51
6VC C16 H25 SING N N 52
6VC C20 H26 SING N N 53
6VC C20 H27 SING N N 54
6VC C20 H28 SING N N 55
6VC C1 H29 SING N N 56
6VC C1 H30 SING N N 57
6VC C2 H31 SING N N 58
6VC C2 H32 SING N N 59
6VC C3 H33 SING N N 60
6VC C4 H34 SING N N 61
6VC C4 H35 SING N N 62
6VC C4 H36 SING N N 63
6VC C7 H37 SING N N 64
6VC C7 H38 SING N N 65
6VC C7 H39 SING N N 66
6VC O8 H40 SING N N 67
#
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
6VC InChI InChI 1.03 "InChI=1S/C20H40N2O6/c1-13(2)8-6-7-9-17(25)21-16(11-23)19(27)22-15(10-14(3)4)18(26)20(5,28)12-24/h13-16,18,23-24,26,28H,6-12H2,1-5H3,(H,21,25)(H,22,27)/t15-,16-,18+,20-/m0/s1"
6VC InChIKey InChI 1.03 FMSNRWQINDLCNQ-YTXYEVPYSA-N
6VC SMILES_CANONICAL CACTVS 3.385 "CC(C)CCCCC(=O)N[C@@H](CO)C(=O)N[C@@H](CC(C)C)[C@@H](O)[C@@](C)(O)CO"
6VC SMILES CACTVS 3.385 "CC(C)CCCCC(=O)N[CH](CO)C(=O)N[CH](CC(C)C)[CH](O)[C](C)(O)CO"
6VC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.5 "CC(C)CCCCC(=O)N[C@@H](CO)C(=O)N[C@@H](CC(C)C)[C@H]([C@](C)(CO)O)O"
6VC SMILES "OpenEye OEToolkits" 2.0.5 "CC(C)CCCCC(=O)NC(CO)C(=O)NC(CC(C)C)C(C(C)(CO)O)O"
#
_pdbx_chem_comp_identifier.comp_id 6VC
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.5
_pdbx_chem_comp_identifier.identifier "~{N}-[(2~{S})-1-[[(2~{S},3~{R},4~{S})-2,6-dimethyl-1,2,3-tris(oxidanyl)heptan-4-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]-6-methyl-heptanamide"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
6VC "Create component" 2016-07-05 EBI
6VC "Initial release" 2016-08-17 RCSB
6VC "Modify synonyms" 2021-03-01 PDBE
6VC "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 6VC
_pdbx_chem_comp_synonyms.name "Dihydroeponemycin bound form"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id 6VC
_pdbx_chem_comp_pcm.modified_residue_id THR
_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 C21
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom OG1
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#