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.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
STD C1 C1 C 0 1 N N N 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 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 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 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 N N N 139.334 115.083 66.482 -5.182 -1.125 0.462 C4 STD 5
STD O1 O1 O 0 1 N N N 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 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 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 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 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 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 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 N N N 141.305 118.758 57.370 4.489 -1.665 -0.680 C10 STD 13
STD C11 C11 C 0 1 N N N 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 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 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 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 N N N 140.952 117.439 56.621 5.574 -0.893 0.073 C13 STD 18
STD C14 C14 C 0 1 N N N 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 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 N N N 142.103 116.634 55.719 4.953 -0.181 1.282 C16 STD 21
STD O5 O5 O 0 1 N N N 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 N N N 141.556 115.960 54.760 6.077 0.611 1.969 C17 STD 23
STD C18 C18 C 0 1 N N N 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 N N N 139.334 117.199 54.779 7.136 0.807 -0.082 C19 STD 25
STD C20 C20 C 0 1 N N S N N N 142.009 115.353 66.370 -4.710 0.949 -1.045 C20 STD 26
STD C21 C21 C 0 1 N N S N N N 142.624 113.829 66.703 -5.344 1.967 -0.095 C21 STD 27
STD C22 C22 C 0 1 N N N 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 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 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 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 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 N N N 138.340 113.943 68.508 -7.329 -1.432 1.233 C25 STD 33
STD C26 C26 C 0 1 N N S N N N 137.737 115.377 68.950 -7.396 -2.883 0.751 C26 STD 34
STD O7 O7 O 0 1 N N N 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 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 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 N N N 138.517 115.847 55.146 8.295 -0.071 0.376 C28 STD 38
STD C29 C29 C 0 1 N N N 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 ? ?
#
_pdbe_chem_comp_drugbank_details.comp_id STD
_pdbe_chem_comp_drugbank_details.drugbank_id DB04785
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Streptolydigin
_pdbe_chem_comp_drugbank_details.description
'Streptolydigin is an antibiotic isolated from culture filtrates of Streptomyces lydicus. It is active against gram-postive bacteria except micrococci.'
_pdbe_chem_comp_drugbank_details.cas_number 7229-50-7
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
STD 2-PYRROLIDINEACETAMIDE wwPDB ?
STD PORTAMYCIN wwPDB ?
STD 'Afragilimycin A' DrugBank ?
STD Portamycin DrugBank ?
STD Portamycin DrugBank 'International brand'
#
_pdbe_chem_comp_drugbank_classification.comp_id STD
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04785
_pdbe_chem_comp_drugbank_classification.parent 'Beta amino acids and derivatives'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Carboxylic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as beta amino acids and derivatives. These are amino acids having a (-NH2) group attached to the beta carbon atom.'
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
STD C1 C 0.044 -3.141 1
STD C2 C -1.459 -3.136 2
STD N1 N -1.926 -4.561 3
STD C3 C 0.500 -4.569 4
STD C4 C -3.351 -5.021 5
STD O1 O 1.927 -5.038 6
STD O2 O -2.335 -1.919 7
STD C5 C 0.930 -1.927 8
STD C6 C 0.326 -0.547 9
STD C7 C 1.220 0.670 10
STD C8 C 0.619 2.057 11
STD C9 C 1.526 3.288 12
STD C10 C 0.926 4.692 13
STD C11 C -0.875 2.221 14
STD O3 O 2.420 -2.091 15
STD O4 O -4.465 -4.018 16
STD C12 C -3.670 -6.487 17
STD C13 C 1.843 5.943 18
STD C14 C -0.567 4.855 19
STD C15 C -5.097 -6.951 20
STD C16 C 3.396 5.840 21
STD O5 O 1.283 7.397 22
STD C17 C 4.077 7.169 23
STD C18 C 4.136 4.535 24
STD C19 C 2.356 8.443 25
STD C20 C -0.716 -5.448 26
STD C21 C -0.720 -6.947 27
STD C22 C 0.578 -7.700 28
STD C23 C -2.021 -7.693 29
STD N2 N 0.575 -9.200 30
STD O6 O 1.879 -6.953 31
STD C24 C 1.872 -9.953 32
STD C25 C -5.894 -4.475 33
STD C26 C -6.207 -5.943 34
STD O7 O -7.636 -6.403 35
STD C27 C -7.006 -3.470 36
STD O8 O 3.365 8.005 37
STD C28 C 2.809 9.761 38
STD C29 C 1.082 9.246 39
STD C30 C 5.212 7.976 40
STD C31 C 1.549 10.573 41
STD C32 C 4.607 9.668 42
STD O9 O 2.888 11.254 43
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
STD C1 C2 SINGLE ENDUPRIGHT 1
STD C1 C3 SINGLE ENDDOWNRIGHT 2
STD C1 C5 DOUBLE NONE 3
STD C2 N1 SINGLE NONE 4
STD C2 O2 DOUBLE NONE 5
STD C4 N1 SINGLE BEGINDASH 6
STD C20 N1 SINGLE BEGINDASH 7
STD C3 O1 DOUBLE NONE 8
STD C3 C20 SINGLE NONE 9
STD C4 O4 SINGLE NONE 10
STD C4 C12 SINGLE NONE 11
STD C5 C6 SINGLE ENDUPRIGHT 12
STD C5 O3 SINGLE ENDDOWNRIGHT 13
STD C6 C7 DOUBLE NONE 14
STD C7 C8 SINGLE ENDUPRIGHT 15
STD C8 C9 DOUBLE NONE 16
STD C8 C11 SINGLE ENDUPRIGHT 17
STD C9 C10 SINGLE ENDUPRIGHT 18
STD C10 C13 SINGLE NONE 19
STD C10 C14 SINGLE BEGINWEDGE 20
STD O4 C25 SINGLE NONE 21
STD C12 C15 SINGLE NONE 22
STD C13 C16 SINGLE NONE 23
STD C13 O5 SINGLE BEGINWEDGE 24
STD C15 C26 SINGLE NONE 25
STD C16 C17 SINGLE NONE 26
STD C16 C18 SINGLE BEGINDASH 27
STD O5 C19 SINGLE NONE 28
STD C17 O8 SINGLE NONE 29
STD C17 C30 SINGLE NONE 30
STD C19 O8 SINGLE NONE 31
STD C19 C28 SINGLE NONE 32
STD C19 C29 SINGLE BEGINWEDGE 33
STD C20 C21 SINGLE NONE 34
STD C21 C22 SINGLE NONE 35
STD C21 C23 SINGLE BEGINWEDGE 36
STD C22 N2 SINGLE NONE 37
STD C22 O6 DOUBLE NONE 38
STD N2 C24 SINGLE NONE 39
STD C25 C26 SINGLE NONE 40
STD C25 C27 SINGLE BEGINDASH 41
STD C26 O7 SINGLE BEGINDASH 42
STD C28 C31 SINGLE BEGINDASH 43
STD C28 C32 SINGLE NONE 44
STD C28 O9 SINGLE NONE 45
STD C30 C32 DOUBLE NONE 46
STD C31 O9 SINGLE NONE 47
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
STD MurckoScaffold S1 scaffold 'O=C1CN([C@@H]2CCCCO2)C(=O)/C1=C\C=C\C=C\C[C@@H]1C[C@H]2C=C[C@@]3(CO3)C(O1)O2' InChI=1S/C23H27NO6/c25-19-14-24(20-9-5-6-12-27-20)21(26)18(19)8-4-2-1-3-7-16-13-17-10-11-23(15-28-23)22(29-16)30-17/h1-4,8,10-11,16-17,20,22H,5-7,9,12-15H2/b3-1+,4-2+,18-8-/t16-,17-,20+,22?,23-/m1/s1 OYKAMOXBUNAEEY-JRGFIOETSA-N
STD amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
STD peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
STD C1 S1 1
STD C2 S1 1
STD N1 S1 1
STD C3 S1 1
STD C4 S1 1
STD O1 S1 1
STD O2 S1 1
STD C5 S1 1
STD C6 S1 1
STD C7 S1 1
STD C8 S1 1
STD C9 S1 1
STD C10 S1 1
STD O4 S1 1
STD C12 S1 1
STD C13 S1 1
STD C15 S1 1
STD C16 S1 1
STD O5 S1 1
STD C17 S1 1
STD C19 S1 1
STD C20 S1 1
STD C25 S1 1
STD C26 S1 1
STD O8 S1 1
STD C28 S1 1
STD C30 S1 1
STD C31 S1 1
STD C32 S1 1
STD O9 S1 1
STD N1 F1 1
STD C2 F1 1
STD O2 F1 1
STD C1 F1 1
STD N2 F1 2
STD C22 F1 2
STD O6 F1 2
STD C21 F1 2
STD O1 F2 1
STD C3 F2 1
STD C20 F2 1
STD N1 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id STD
_pdbe_chem_comp_rdkit_properties.exactmw 600.305
_pdbe_chem_comp_rdkit_properties.amw 600.709
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 11
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 16
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 9
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 43
_pdbe_chem_comp_rdkit_properties.NumAtoms 87
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 11
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.656
_pdbe_chem_comp_rdkit_properties.NumRings 5
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 5
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 4
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 5
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 4
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 5
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 1
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 2
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 11
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 314.152
_pdbe_chem_comp_rdkit_properties.tpsa 147.160
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.460
_pdbe_chem_comp_rdkit_properties.CrippenMR 155.301
_pdbe_chem_comp_rdkit_properties.chi0v 20.569
_pdbe_chem_comp_rdkit_properties.chi1v 11.022
_pdbe_chem_comp_rdkit_properties.chi2v 5.599
_pdbe_chem_comp_rdkit_properties.chi3v 5.599
_pdbe_chem_comp_rdkit_properties.chi4v 3.524
_pdbe_chem_comp_rdkit_properties.chi0n 64.569
_pdbe_chem_comp_rdkit_properties.chi1n 32.785
_pdbe_chem_comp_rdkit_properties.chi2n 5.599
_pdbe_chem_comp_rdkit_properties.chi3n 5.599
_pdbe_chem_comp_rdkit_properties.chi4n 3.524
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.830
_pdbe_chem_comp_rdkit_properties.kappa1 7.928
_pdbe_chem_comp_rdkit_properties.kappa2 11.590
_pdbe_chem_comp_rdkit_properties.kappa3 5.503
_pdbe_chem_comp_rdkit_properties.Phi 2.137
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
STD UniChem ChEMBL CHEMBL1236068
STD UniChem DrugBank DB04785
STD UniChem PDBe STD
STD UniChem ChEBI 45773
STD UniChem ZINC ZINC000169363256
STD UniChem MetaboLights MTBLC45773
STD UniChem MedChemExpress HY-122337
STD UniChem 'Probes And Drugs' PD016292
STD UniChem Nikkaji J37.255B
STD UniChem PubChem 54708748
STD UniChem NMRShiftDB 70092883
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
STD C1 -2.132 -1.573 0.427 ETKDGv3 1
STD C2 -2.694 -0.362 1.017 ETKDGv3 2
STD N1 -4.056 -0.543 1.410 ETKDGv3 3
STD C3 -3.243 -2.525 0.484 ETKDGv3 4
STD C4 -4.845 0.512 2.072 ETKDGv3 5
STD O1 -3.131 -3.767 0.301 ETKDGv3 6
STD O2 -2.098 0.745 1.108 ETKDGv3 7
STD C5 -0.890 -1.773 -0.074 ETKDGv3 8
STD C6 0.198 -0.789 0.128 ETKDGv3 9
STD C7 1.268 -0.753 -0.677 ETKDGv3 10
STD C8 2.386 0.212 -0.501 ETKDGv3 11
STD C9 3.030 0.619 -1.619 ETKDGv3 12
STD C10 4.181 1.607 -1.759 ETKDGv3 13
STD C11 2.697 0.735 0.881 ETKDGv3 14
STD O3 -0.582 -2.927 -0.802 ETKDGv3 15
STD O4 -5.772 1.059 1.155 ETKDGv3 16
STD C12 -5.568 -0.014 3.334 ETKDGv3 17
STD C13 5.585 0.965 -1.576 ETKDGv3 18
STD C14 4.013 2.900 -0.945 ETKDGv3 19
STD C15 -6.799 0.845 3.672 ETKDGv3 20
STD C16 5.834 -0.240 -2.527 ETKDGv3 21
STD O5 5.753 0.583 -0.219 ETKDGv3 22
STD C17 7.146 -0.944 -2.121 ETKDGv3 23
STD C18 5.842 0.157 -4.014 ETKDGv3 24
STD C19 6.997 -0.061 0.036 ETKDGv3 25
STD C20 -4.517 -1.876 0.970 ETKDGv3 26
STD C21 -5.612 -1.772 -0.145 ETKDGv3 27
STD C22 -5.502 -2.866 -1.187 ETKDGv3 28
STD C23 -7.030 -1.794 0.451 ETKDGv3 29
STD N2 -4.846 -2.603 -2.435 ETKDGv3 30
STD O6 -5.934 -4.025 -0.934 ETKDGv3 31
STD C24 -4.655 -3.646 -3.435 ETKDGv3 32
STD C25 -6.331 2.281 1.629 ETKDGv3 33
STD C26 -6.619 2.279 3.170 ETKDGv3 34
STD O7 -7.753 3.039 3.503 ETKDGv3 35
STD C27 -7.592 2.554 0.801 ETKDGv3 36
STD O8 7.111 -1.250 -0.739 ETKDGv3 37
STD C28 8.206 0.885 -0.263 ETKDGv3 38
STD C29 6.977 -0.500 1.507 ETKDGv3 39
STD C30 8.396 -0.148 -2.461 ETKDGv3 40
STD C31 8.282 2.210 0.395 ETKDGv3 41
STD C32 8.900 0.723 -1.581 ETKDGv3 42
STD O9 9.090 1.126 0.807 ETKDGv3 43
STD H4 -4.142 1.312 2.405 ETKDGv3 44
STD H6 0.133 -0.094 0.952 ETKDGv3 45
STD H7 1.301 -1.414 -1.536 ETKDGv3 46
STD H9 2.688 0.212 -2.566 ETKDGv3 47
STD H10 4.134 1.955 -2.814 ETKDGv3 48
STD H111 3.781 0.800 1.067 ETKDGv3 49
STD H112 2.314 0.045 1.661 ETKDGv3 50
STD H113 2.224 1.728 1.025 ETKDGv3 51
STD HO3 -1.275 -3.578 -1.145 ETKDGv3 52
STD H121 -5.908 -1.061 3.213 ETKDGv3 53
STD H122 -4.856 0.005 4.187 ETKDGv3 54
STD H13 6.317 1.766 -1.823 ETKDGv3 55
STD H141 2.959 3.248 -0.981 ETKDGv3 56
STD H142 4.328 2.776 0.109 ETKDGv3 57
STD H143 4.651 3.699 -1.380 ETKDGv3 58
STD H151 -7.702 0.404 3.195 ETKDGv3 59
STD H152 -6.962 0.845 4.772 ETKDGv3 60
STD H16 5.020 -0.984 -2.382 ETKDGv3 61
STD H17 7.206 -1.905 -2.677 ETKDGv3 62
STD H181 4.818 0.413 -4.354 ETKDGv3 63
STD H182 6.510 1.027 -4.190 ETKDGv3 64
STD H183 6.192 -0.694 -4.637 ETKDGv3 65
STD H20 -4.880 -2.469 1.836 ETKDGv3 66
STD H21 -5.490 -0.801 -0.671 ETKDGv3 67
STD H231 -7.198 -0.943 1.134 ETKDGv3 68
STD H232 -7.786 -1.722 -0.360 ETKDGv3 69
STD H233 -7.205 -2.733 1.019 ETKDGv3 70
STD HN2 -4.469 -1.648 -2.629 ETKDGv3 71
STD H241 -5.640 -4.034 -3.767 ETKDGv3 72
STD H242 -4.116 -3.232 -4.313 ETKDGv3 73
STD H243 -4.054 -4.475 -3.003 ETKDGv3 74
STD H25 -5.614 3.104 1.409 ETKDGv3 75
STD H26 -5.733 2.704 3.699 ETKDGv3 76
STD HO7 -7.487 3.992 3.432 ETKDGv3 77
STD H271 -7.983 3.574 1.004 ETKDGv3 78
STD H272 -7.352 2.491 -0.281 ETKDGv3 79
STD H273 -8.376 1.803 1.034 ETKDGv3 80
STD H291 6.127 -1.194 1.680 ETKDGv3 81
STD H292 7.917 -1.032 1.768 ETKDGv3 82
STD H293 6.849 0.372 2.182 ETKDGv3 83
STD H30 8.881 -0.288 -3.422 ETKDGv3 84
STD H311 7.507 2.448 1.152 ETKDGv3 85
STD H312 8.889 2.994 -0.106 ETKDGv3 86
STD H32 9.788 1.300 -1.825 ETKDGv3 87
#