data_STD
#
_chem_comp.id STD
_chem_comp.name STREPTOLYDIGIN
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAD
_chem_comp.formula "C32 H44 N2 O9"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "2-PYRROLIDINEACETAMIDE; PORTAMYCIN"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2005-08-01
_chem_comp.pdbx_modified_date 2021-03-13
_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 600.700
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code STD
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 2A6H
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
# #
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.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
STD C1 C1 C 0 1 N N N 142.093 116.230 64.085 -2.402 0.668 -1.257 C1 STD 1
STD C2 C2 C 0 1 N N N 140.843 115.687 64.473 -2.965 -0.397 -0.427 C2 STD 2
STD N1 N1 N 0 1 N N N 140.648 115.357 65.823 -4.293 -0.244 -0.299 N1 STD 3
STD C3 C3 C 0 1 N N N 142.870 116.091 65.260 -3.454 1.523 -1.661 C3 STD 4
STD C4 C4 C 0 1 N N S 139.334 115.083 66.482 -5.182 -1.125 0.462 C4 STD 5
STD O1 O1 O 0 1 N N N 144.040 116.438 65.428 -3.366 2.514 -2.358 O1 STD 6
STD O2 O2 O 0 1 N N N 139.926 115.507 63.691 -2.320 -1.296 0.078 O2 STD 7
STD C5 C5 C 0 1 N N N 142.613 116.799 62.881 -1.049 0.816 -1.597 C5 STD 8
STD C6 C6 C 0 1 N N N 141.921 116.911 61.716 -0.099 -0.111 -1.126 C6 STD 9
STD C7 C7 C 0 1 N N N 141.599 118.041 61.076 1.223 0.094 -1.358 C7 STD 10
STD C8 C8 C 0 1 N N N 140.935 118.111 59.911 2.169 -0.899 -0.996 C8 STD 11
STD C9 C9 C 0 1 N N N 141.686 118.547 58.822 3.470 -0.698 -1.225 C9 STD 12
STD C10 C10 C 0 1 N N R 141.305 118.758 57.370 4.489 -1.665 -0.680 C10 STD 13
STD C11 C11 C 0 1 N N N 139.451 117.692 59.814 1.706 -2.182 -0.355 C11 STD 14
STD O3 O3 O 0 1 N N N 143.912 117.273 62.890 -0.657 1.848 -2.374 O3 STD 15
STD O4 O4 O 0 1 N N N 139.529 114.138 67.610 -6.526 -0.664 0.339 O4 STD 16
STD C12 C12 C 0 1 N N N 138.661 116.441 66.991 -5.073 -2.551 -0.084 C12 STD 17
STD C13 C13 C 0 1 N N R 140.952 117.439 56.621 5.574 -0.893 0.073 C13 STD 18
STD C14 C14 C 0 1 N N N 142.460 119.582 56.680 5.124 -2.441 -1.836 C14 STD 19
STD C15 C15 C 0 1 N N N 137.639 116.322 67.635 -5.980 -3.472 0.740 C15 STD 20
STD C16 C16 C 0 1 N N S 142.103 116.634 55.719 4.953 -0.181 1.282 C16 STD 21
STD O5 O5 O 0 1 N N N 139.658 117.813 55.739 6.153 0.083 -0.792 O5 STD 22
STD C17 C17 C 0 1 N N R 141.556 115.960 54.760 6.077 0.611 1.969 C17 STD 23
STD C18 C18 C 0 1 N N N 142.848 115.968 56.478 4.388 -1.225 2.248 C18 STD 24
STD C19 C19 C 0 1 N N R 139.334 117.199 54.779 7.136 0.807 -0.082 C19 STD 25
STD C20 C20 C 0 1 N N S 142.009 115.353 66.370 -4.710 0.949 -1.045 C20 STD 26
STD C21 C21 C 0 1 N N S 142.624 113.829 66.703 -5.344 1.967 -0.095 C21 STD 27
STD C22 C22 C 0 1 N N N 142.924 112.913 65.395 -4.339 2.371 0.952 C22 STD 28
STD C23 C23 C 0 1 N N N 143.636 113.866 67.372 -5.779 3.202 -0.888 C23 STD 29
STD N2 N2 N 0 1 N N N 143.842 113.390 64.412 -4.678 3.266 1.902 N2 STD 30
STD O6 O6 O 0 1 N N N 142.329 111.863 65.262 -3.225 1.892 0.941 O6 STD 31
STD C24 C24 C 0 1 N N N 145.189 112.870 64.300 -3.700 3.659 2.920 C24 STD 32
STD C25 C25 C 0 1 N N S 138.340 113.943 68.508 -7.329 -1.432 1.233 C25 STD 33
STD C26 C26 C 0 1 N N S 137.737 115.377 68.950 -7.396 -2.883 0.751 C26 STD 34
STD O7 O7 O 0 1 N N N 138.586 116.068 69.933 -7.941 -2.926 -0.569 O7 STD 35
STD C27 C27 C 0 1 N N N 138.791 113.059 69.719 -8.742 -0.846 1.278 C27 STD 36
STD O8 O8 O 0 1 N N N 140.585 116.828 53.976 6.619 1.529 1.026 O8 STD 37
STD C28 C28 C 0 1 N N R 138.517 115.847 55.146 8.295 -0.071 0.376 C28 STD 38
STD C29 C29 C 0 1 N N N 138.527 118.147 53.854 7.718 1.838 -1.051 C29 STD 39
STD C30 C30 C 0 1 N N N 140.723 114.592 55.114 7.122 -0.348 2.467 C30 STD 40
STD C31 C31 C 0 1 N N N 137.278 115.950 56.013 9.031 -0.877 -0.693 C31 STD 41
STD C32 C32 C 0 1 N N N 139.334 114.573 55.284 8.149 -0.684 1.729 C32 STD 42
STD O9 O9 O 0 1 N N N 137.143 115.623 54.527 9.607 0.271 -0.065 O9 STD 43
STD H4 H4 H 0 1 N N N 138.645 114.620 65.737 -4.890 -1.116 1.512 H4 STD 44
STD H6 H6 H 0 1 N N N 141.582 115.978 61.234 -0.423 -0.985 -0.580 H6 STD 45
STD H7 H7 H 0 1 N N N 141.905 118.990 61.546 1.555 1.013 -1.818 H7 STD 46
STD H9 H9 H 0 1 N N N 142.718 118.752 59.152 3.791 0.158 -1.800 H9 STD 47
STD H10 H10 H 0 1 N N N 140.355 119.340 57.320 4.001 -2.363 0.001 H10 STD 48
STD H111 1H11 H 0 0 N N N 138.899 117.750 58.846 2.568 -2.817 -0.150 H111 STD 49
STD H112 2H11 H 0 0 N N N 139.359 116.651 60.202 1.191 -1.956 0.579 H112 STD 50
STD H113 3H11 H 0 0 N N N 138.877 118.271 60.574 1.024 -2.700 -1.029 H113 STD 51
STD HO3 HO3 H 0 1 N N N 144.257 117.651 62.089 0.309 1.811 -2.422 HO3 STD 52
STD H121 1H12 H 0 0 N N N 139.404 117.037 67.569 -5.388 -2.568 -1.127 H121 STD 53
STD H122 2H12 H 0 0 N N N 138.485 117.122 66.126 -4.041 -2.893 -0.007 H122 STD 54
STD H13 H13 H 0 1 N N N 140.806 116.664 57.409 6.345 -1.584 0.412 H13 STD 55
STD H141 1H14 H 0 0 N N N 142.179 119.737 55.612 5.798 -3.200 -1.437 H141 STD 56
STD H142 2H14 H 0 0 N N N 142.685 120.536 57.210 4.342 -2.922 -2.424 H142 STD 57
STD H143 3H14 H 0 0 N N N 143.461 119.105 56.799 5.685 -1.754 -2.470 H143 STD 58
STD H151 1H15 H 0 0 N N N 137.250 117.327 67.918 -6.000 -4.464 0.290 H151 STD 59
STD H152 2H15 H 0 0 N N N 136.813 115.968 66.974 -5.604 -3.538 1.761 H152 STD 60
STD H16 H16 H 0 1 N N N 142.767 117.364 55.201 4.161 0.498 0.968 H16 STD 61
STD H17 H17 H 0 1 N N N 142.466 115.635 54.204 5.658 1.161 2.811 H17 STD 62
STD H181 1H18 H 0 0 N N N 143.616 115.430 55.875 4.084 -0.736 3.173 H181 STD 63
STD H182 2H18 H 0 0 N N N 143.305 116.598 57.275 3.525 -1.711 1.793 H182 STD 64
STD H183 3H18 H 0 0 N N N 142.268 115.275 57.132 5.153 -1.971 2.464 H183 STD 65
STD H20 H20 H 0 1 N N N 142.030 115.855 67.365 -5.419 0.673 -1.826 H20 STD 66
STD H21 H21 H 0 1 N N N 141.796 113.351 67.277 -6.213 1.522 0.388 H21 STD 67
STD H231 1H23 H 0 0 N N N 144.044 112.852 67.593 -6.327 3.879 -0.234 H231 STD 68
STD H232 2H23 H 0 0 N N N 144.408 114.512 66.892 -4.898 3.709 -1.282 H232 STD 69
STD H233 3H23 H 0 0 N N N 143.473 114.444 68.311 -6.421 2.895 -1.714 H233 STD 70
STD HN2 HN2 H 0 1 N N N 143.527 114.120 63.773 -5.568 3.649 1.911 HN2 STD 71
STD H241 1H24 H 0 0 N N N 145.906 113.242 63.532 -3.391 2.779 3.485 H241 STD 72
STD H242 2H24 H 0 0 N N N 145.676 112.973 65.297 -2.831 4.104 2.436 H242 STD 73
STD H243 3H24 H 0 0 N N N 145.117 111.763 64.187 -4.152 4.385 3.596 H243 STD 74
STD H25 H25 H 0 1 N N N 137.512 113.413 67.981 -6.892 -1.402 2.231 H25 STD 75
STD H26 H26 H 0 1 N N N 136.740 115.191 69.415 -8.027 -3.463 1.425 H26 STD 76
STD HO7 HO7 H 0 1 N N N 138.643 115.514 70.703 -7.959 -3.856 -0.834 HO7 STD 77
STD H271 1H27 H 0 0 N N N 137.908 112.914 70.385 -9.356 -1.429 1.965 H271 STD 78
STD H272 2H27 H 0 0 N N N 139.255 112.096 69.401 -8.695 0.187 1.622 H272 STD 79
STD H273 3H27 H 0 0 N N N 139.673 113.479 70.255 -9.180 -0.878 0.281 H273 STD 80
STD H291 1H29 H 0 0 N N N 138.222 117.569 52.950 6.924 2.501 -1.395 H291 STD 81
STD H292 2H29 H 0 0 N N N 137.663 118.623 54.373 8.485 2.422 -0.543 H292 STD 82
STD H293 3H29 H 0 0 N N N 139.082 119.080 53.602 8.158 1.325 -1.906 H293 STD 83
STD H30 H30 H 0 1 N N N 141.140 113.580 55.252 7.023 -0.769 3.457 H30 STD 84
STD H311 1H31 H 0 0 N N N 136.936 115.469 56.959 9.418 -1.857 -0.414 H311 STD 85
STD H312 2H31 H 0 0 N N N 136.852 116.726 56.690 8.696 -0.776 -1.726 H312 STD 86
STD H32 H32 H 0 1 N N N 138.898 113.587 55.518 8.880 -1.389 2.096 H32 STD 87
# #
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
STD C1 C2 SING N N 1
STD C1 C3 SING N N 2
STD C1 C5 DOUB N E 3
STD C2 N1 SING N N 4
STD C2 O2 DOUB N N 5
STD N1 C4 SING N N 6
STD N1 C20 SING N N 7
STD C3 O1 DOUB N N 8
STD C3 C20 SING N N 9
STD C4 O4 SING N N 10
STD C4 C12 SING N N 11
STD C4 H4 SING N N 12
STD C5 C6 SING N N 13
STD C5 O3 SING N N 14
STD C6 C7 DOUB N E 15
STD C6 H6 SING N N 16
STD C7 C8 SING N N 17
STD C7 H7 SING N N 18
STD C8 C9 DOUB N E 19
STD C8 C11 SING N N 20
STD C9 C10 SING N N 21
STD C9 H9 SING N N 22
STD C10 C13 SING N N 23
STD C10 C14 SING N N 24
STD C10 H10 SING N N 25
STD C11 H111 SING N N 26
STD C11 H112 SING N N 27
STD C11 H113 SING N N 28
STD O3 HO3 SING N N 29
STD O4 C25 SING N N 30
STD C12 C15 SING N N 31
STD C12 H121 SING N N 32
STD C12 H122 SING N N 33
STD C13 C16 SING N N 34
STD C13 O5 SING N N 35
STD C13 H13 SING N N 36
STD C14 H141 SING N N 37
STD C14 H142 SING N N 38
STD C14 H143 SING N N 39
STD C15 C26 SING N N 40
STD C15 H151 SING N N 41
STD C15 H152 SING N N 42
STD C16 C17 SING N N 43
STD C16 C18 SING N N 44
STD C16 H16 SING N N 45
STD O5 C19 SING N N 46
STD C17 O8 SING N N 47
STD C17 C30 SING N N 48
STD C17 H17 SING N N 49
STD C18 H181 SING N N 50
STD C18 H182 SING N N 51
STD C18 H183 SING N N 52
STD C19 O8 SING N N 53
STD C19 C28 SING N N 54
STD C19 C29 SING N N 55
STD C20 C21 SING N N 56
STD C20 H20 SING N N 57
STD C21 C22 SING N N 58
STD C21 C23 SING N N 59
STD C21 H21 SING N N 60
STD C22 N2 SING N N 61
STD C22 O6 DOUB N N 62
STD C23 H231 SING N N 63
STD C23 H232 SING N N 64
STD C23 H233 SING N N 65
STD N2 C24 SING N N 66
STD N2 HN2 SING N N 67
STD C24 H241 SING N N 68
STD C24 H242 SING N N 69
STD C24 H243 SING N N 70
STD C25 C26 SING N N 71
STD C25 C27 SING N N 72
STD C25 H25 SING N N 73
STD C26 O7 SING N N 74
STD C26 H26 SING N N 75
STD O7 HO7 SING N N 76
STD C27 H271 SING N N 77
STD C27 H272 SING N N 78
STD C27 H273 SING N N 79
STD C28 C31 SING N N 80
STD C28 C32 SING N N 81
STD C28 O9 SING N N 82
STD C29 H291 SING N N 83
STD C29 H292 SING N N 84
STD C29 H293 SING N N 85
STD C30 C32 DOUB N N 86
STD C30 H30 SING N N 87
STD C31 O9 SING N N 88
STD C31 H311 SING N N 89
STD C31 H312 SING N N 90
STD C32 H32 SING N N 91
# #
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
STD SMILES ACDLabs 10.04 "O=C(NC)C(C)C2C(=O)/C(C(=O)N2C1OC(C)C(O)CC1)=C(\O)/C=C/C(=C/C(C5OC4(OC(C=CC34OC3)C5C)C)C)C"
STD SMILES_CANONICAL CACTVS 3.341 "CNC(=O)[C@@H](C)[C@@H]1N([C@@H]2CC[C@H](O)[C@H](C)O2)C(=O)\C(=C(O)/C=C/C(C)=C/[C@@H](C)[C@H]3O[C@@]4(C)O[C@H](C=C[C@@]45CO5)[C@@H]3C)C1=O"
STD SMILES CACTVS 3.341 "CNC(=O)[CH](C)[CH]1N([CH]2CC[CH](O)[CH](C)O2)C(=O)C(=C(O)C=CC(C)=C[CH](C)[CH]3O[C]4(C)O[CH](C=C[C]45CO5)[CH]3C)C1=O"
STD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@H]1[C@H]2C=C[C@@]3(CO3)[C@](O2)(O[C@@H]1[C@H](C)\C=C(/C)\C=C\C(=C/4\C(=O)[C@@H](N(C4=O)[C@@H]5CC[C@@H]([C@@H](O5)C)O)[C@H](C)C(=O)NC)\O)C"
STD SMILES "OpenEye OEToolkits" 1.5.0 "CC1C2C=CC3(CO3)C(O2)(OC1C(C)C=C(C)C=CC(=C4C(=O)C(N(C4=O)C5CCC(C(O5)C)O)C(C)C(=O)NC)O)C"
STD InChI InChI 1.03 "InChI=1S/C32H44N2O9/c1-16(14-17(2)28-18(3)23-12-13-32(15-40-32)31(6,42-23)43-28)8-9-22(36)25-27(37)26(19(4)29(38)33-7)34(30(25)39)24-11-10-21(35)20(5)41-24/h8-9,12-14,17-21,23-24,26,28,35-36H,10-11,15H2,1-7H3,(H,33,38)/b9-8+,16-14+,25-22+/t17-,18+,19+,20+,21+,23-,24+,26+,28-,31-,32-/m1/s1"
STD InChIKey InChI 1.03 KVTPRMVXYZKLIG-NCAOFHFGSA-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
STD "SYSTEMATIC NAME" ACDLabs 10.04 "(2S)-2-{(2S,4E)-4-{(2E,4E,6R)-6-[(1R,2R,5R,6S,7R)-1,6-dimethylspiro[8,9-dioxabicyclo[3.3.1]non-3-ene-2,2'-oxiran]-7-yl]-1-hydroxy-4-methylhepta-2,4-dien-1-ylidene}-1-[(2S,5S,6S)-5-hydroxy-6-methyltetrahydro-2H-pyran-2-yl]-3,5-dioxopyrrolidin-2-yl}-N-methylpropanamide"
STD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-[(2S,4E)-4-[(2E,4E,6R)-6-[(1R,4R,5R,7R,8S)-5,8-dimethylspiro[6,9-dioxabicyclo[3.3.1]non-2-ene-4,2'-oxirane]-7-yl]-1-hydroxy-4-methyl-hepta-2,4-dienylidene]-1-[(2S,5S,6S)-5-hydroxy-6-methyl-oxan-2-yl]-3,5-dioxo-pyrrolidin-2-yl]-N-methyl-propanamide"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
STD "Create component" 2005-08-01 RCSB
STD "Modify descriptor" 2011-06-04 RCSB
STD "Modify synonyms" 2020-05-27 PDBE
STD "Modify synonyms" 2021-03-13 RCSB
# #
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 STD 2-PYRROLIDINEACETAMIDE ? ?
2 STD PORTAMYCIN ? ?
##