data_GDM
#
_chem_comp.id GDM
_chem_comp.name GELDANAMYCIN
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C29 H40 N2 O9"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2011-06-04
_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 560.636
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GDM
_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 1YET
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
GDM O1 O1 O 0 1 N N N N N N 38.435 -50.989 68.147 1.705 0.636 -1.266 O1 GDM 1
GDM O2 O2 O 0 1 N N N N N N 37.589 -47.387 62.638 1.793 1.918 4.186 O2 GDM 2
GDM O3 O3 O 0 1 N N N N N N 37.968 -44.717 63.248 0.583 0.045 5.545 O3 GDM 3
GDM O4 O4 O 0 1 N N N N N N 38.937 -43.256 61.763 -0.223 -1.993 5.885 O4 GDM 4
GDM O5 O5 O 0 1 N N N N N N 44.943 -43.478 64.421 -4.511 -1.193 0.882 O5 GDM 5
GDM O6 O6 O 0 1 N N N N N N 45.405 -46.265 63.758 -1.518 0.718 0.011 O6 GDM 6
GDM O7 O7 O 0 1 N N N N N N 43.245 -44.819 68.520 -1.147 -0.165 -6.473 O7 GDM 7
GDM O8 O8 O 0 1 N N N N N N 40.642 -44.516 69.253 1.534 0.075 -7.103 O8 GDM 8
GDM O9 O9 O 0 1 N N N N N N 42.112 -49.448 68.120 0.294 -1.032 -2.127 O9 GDM 9
GDM N1 N1 N 0 1 N N N N N N 39.589 -49.161 68.817 2.972 -0.481 -2.662 N1 GDM 10
GDM N2 N2 N 0 1 N N N N N N 36.729 -43.186 62.247 0.278 -0.809 7.694 N2 GDM 11
GDM C1 C1 C 0 1 N N N N N N 39.217 -50.118 67.848 2.657 -0.107 -1.422 C1 GDM 12
GDM C2 C2 C 0 1 N N N N N N 39.878 -50.073 66.504 3.358 -0.522 -0.215 C2 GDM 13
GDM C3 C3 C 0 1 N N N N N N 39.713 -48.980 65.714 2.863 -0.088 0.967 C3 GDM 14
GDM C4 C4 C 0 1 N N N N N N 40.293 -48.799 64.387 3.461 -0.420 2.250 C4 GDM 15
GDM C5 C5 C 0 1 N N N N N N 39.856 -47.939 63.444 2.883 -0.052 3.397 C5 GDM 16
GDM C6 C6 C 0 1 N N S N N N 38.709 -46.995 63.529 1.591 0.717 3.433 C6 GDM 17
GDM C7 C7 C 0 1 N N S N N N 39.111 -45.501 63.147 0.495 -0.112 4.105 C7 GDM 18
GDM C8 C8 C 0 1 N N N N N N 40.274 -44.880 64.112 -0.865 0.346 3.633 C8 GDM 19
GDM C9 C9 C 0 1 N N N N N N 41.406 -44.432 63.592 -1.551 -0.419 2.826 C9 GDM 20
GDM C10 C10 C 0 1 N N S N N N 42.567 -43.787 64.288 -2.913 -0.062 2.300 C10 GDM 21
GDM C11 C11 C 0 1 N N R N N N 43.932 -44.337 63.843 -3.142 -0.791 0.968 C11 GDM 22
GDM C12 C12 C 0 1 N N S N N N 44.143 -45.789 64.274 -2.814 0.152 -0.191 C12 GDM 23
GDM C13 C13 C 0 1 N N N N N N 44.198 -45.976 65.787 -2.838 -0.635 -1.503 C13 GDM 24
GDM C14 C14 C 0 1 N N R N N N 44.363 -47.432 66.283 -2.217 0.183 -2.633 C14 GDM 25
GDM C15 C15 C 0 1 N N N N N N 44.162 -47.582 67.831 -1.927 -0.723 -3.835 C15 GDM 26
GDM C16 C16 C 0 1 N N N N N N 42.782 -47.190 68.272 -0.489 -0.547 -4.256 C16 GDM 27
GDM C17 C17 C 0 1 N N N N N N 42.359 -45.958 68.576 -0.175 -0.282 -5.541 C17 GDM 28
GDM C18 C18 C 0 1 N N N N N N 40.973 -45.667 68.987 1.249 -0.121 -5.937 C18 GDM 29
GDM C19 C19 C 0 1 N N N N N N 40.001 -46.762 69.066 2.305 -0.196 -4.927 C19 GDM 30
GDM C20 C20 C 0 1 N N N N N N 40.371 -48.009 68.782 1.994 -0.431 -3.639 C20 GDM 31
GDM C21 C21 C 0 1 N N N N N N 41.783 -48.291 68.373 0.577 -0.683 -3.256 C21 GDM 32
GDM C22 C22 C 0 1 N N N N N N 40.664 -51.289 66.124 4.576 -1.397 -0.285 C22 GDM 33
GDM C23 C23 C 0 1 N N N N N N 37.854 -48.536 61.758 2.211 2.922 3.259 C23 GDM 34
GDM C24 C24 C 0 1 N N N N N N 37.970 -43.672 62.356 0.197 -0.956 6.357 C24 GDM 35
GDM C25 C25 C 0 1 N N N N N N 39.940 -44.815 65.604 -1.404 1.671 4.106 C25 GDM 36
GDM C26 C26 C 0 1 N N N N N N 42.479 -42.276 63.978 -3.986 -0.517 3.296 C26 GDM 37
GDM C27 C27 C 0 1 N N N N N N 45.400 -46.454 62.308 -1.690 2.135 0.060 C27 GDM 38
GDM C28 C28 C 0 1 N N N N N N 43.452 -48.342 65.511 -3.196 1.280 -3.064 C28 GDM 39
GDM C29 C29 C 0 1 N N N N N N 44.622 -44.825 68.924 -1.151 1.199 -6.897 C29 GDM 40
GDM HO5 HO5 H 0 1 N N N N N N 45.786 -43.817 64.146 -4.677 -1.782 1.630 HO5 GDM 41
GDM HN1 HN1 H 0 1 N N N N N N 39.209 -49.341 69.746 3.876 -0.780 -2.892 HN1 GDM 42
GDM HN21 1HN2 H 0 0 N N N N N N 35.912 -43.537 62.747 0.000 -1.531 8.280 HN21 GDM 43
GDM HN22 2HN2 H 0 0 N N N N N N 36.730 -42.410 61.584 0.614 0.018 8.072 HN22 GDM 44
GDM H3 H3 H 0 1 N N N N N N 39.078 -48.202 66.171 1.976 0.540 0.928 H3 GDM 45
GDM H4 H4 H 0 1 N N N N N N 41.168 -49.383 64.056 4.393 -0.971 2.303 H4 GDM 46
GDM H5 H5 H 0 1 N N N N N N 40.481 -48.013 62.538 3.367 -0.318 4.330 H5 GDM 47
GDM H6 H6 H 0 1 N N N N N N 38.389 -47.041 64.596 1.276 0.980 2.428 H6 GDM 48
GDM H7 H7 H 0 1 N N N N N N 39.526 -45.508 62.112 0.629 -1.163 3.846 H7 GDM 49
GDM H9 H9 H 0 1 N N N N N N 41.380 -44.608 62.503 -1.110 -1.368 2.521 H9 GDM 50
GDM H10 H10 H 0 1 N N N N N N 42.502 -44.004 65.379 -2.998 1.008 2.135 H10 GDM 51
GDM H11 H11 H 0 1 N N N N N N 43.990 -44.339 62.729 -2.500 -1.668 0.921 H11 GDM 52
GDM H12 H12 H 0 1 N N N N N N 43.268 -46.352 63.874 -3.558 0.947 -0.225 H12 GDM 53
GDM H131 1H13 H 0 0 N N N N N N 45.001 -45.335 66.219 -2.274 -1.561 -1.376 H131 GDM 54
GDM H132 2H13 H 0 0 N N N N N N 43.299 -45.514 66.258 -3.870 -0.879 -1.760 H132 GDM 55
GDM H14 H14 H 0 1 N N N N N N 45.419 -47.732 66.091 -1.290 0.641 -2.295 H14 GDM 56
GDM H151 1H15 H 0 0 N N N N N N 44.413 -48.614 68.170 -2.103 -1.762 -3.555 H151 GDM 57
GDM H152 2H15 H 0 0 N N N N N N 44.939 -47.014 68.393 -2.591 -0.454 -4.657 H152 GDM 58
GDM H19 H19 H 0 1 N N N N N N 38.942 -46.642 69.352 3.339 -0.065 -5.215 H19 GDM 59
GDM H221 1H22 H 0 0 N N N N N N 41.155 -51.255 65.123 4.944 -1.588 0.722 H221 GDM 60
GDM H222 2H22 H 0 0 N N N N N N 41.420 -51.514 66.911 4.317 -2.342 -0.763 H222 GDM 61
GDM H223 3H22 H 0 0 N N N N N N 40.020 -52.196 66.200 5.350 -0.897 -0.866 H223 GDM 62
GDM H231 1H23 H 0 0 N N N N N N 37.012 -48.830 61.088 2.378 3.860 3.789 H231 GDM 63
GDM H232 2H23 H 0 0 N N N N N N 38.774 -48.352 61.156 3.136 2.608 2.776 H232 GDM 64
GDM H233 3H23 H 0 0 N N N N N N 38.185 -49.412 62.362 1.437 3.064 2.504 H233 GDM 65
GDM H251 1H25 H 0 0 N N N N N N 40.733 -44.391 66.262 -2.389 1.839 3.670 H251 GDM 66
GDM H252 2H25 H 0 0 N N N N N N 38.985 -44.259 65.754 -1.485 1.664 5.193 H252 GDM 67
GDM H253 3H25 H 0 0 N N N N N N 39.642 -45.825 65.970 -0.729 2.469 3.797 H253 GDM 68
GDM H261 1H26 H 0 0 N N N N N N 43.342 -41.796 64.495 -3.827 -0.020 4.253 H261 GDM 69
GDM H262 2H26 H 0 0 N N N N N N 42.437 -42.050 62.886 -4.972 -0.256 2.911 H262 GDM 70
GDM H263 3H26 H 0 0 N N N N N N 41.495 -41.825 64.249 -3.922 -1.596 3.431 H263 GDM 71
GDM H271 1H27 H 0 0 N N N N N N 46.374 -46.821 61.909 -0.741 2.608 0.311 H271 GDM 72
GDM H272 2H27 H 0 0 N N N N N N 44.566 -47.126 61.998 -2.029 2.494 -0.911 H272 GDM 73
GDM H273 3H27 H 0 0 N N N N N N 45.085 -45.519 61.787 -2.432 2.385 0.818 H273 GDM 74
GDM H281 1H28 H 0 0 N N N N N N 43.570 -49.391 65.868 -2.754 1.865 -3.870 H281 GDM 75
GDM H282 2H28 H 0 0 N N N N N N 42.390 -48.003 65.551 -4.123 0.823 -3.411 H282 GDM 76
GDM H283 3H28 H 0 0 N N N N N N 43.608 -48.254 64.410 -3.407 1.931 -2.216 H283 GDM 77
GDM H291 1H29 H 0 0 N N N N N N 45.306 -43.945 68.880 -1.887 1.331 -7.689 H291 GDM 78
GDM H292 2H29 H 0 0 N N N N N N 44.646 -45.198 69.974 -1.405 1.840 -6.053 H292 GDM 79
GDM H293 3H29 H 0 0 N N N N N N 45.119 -45.645 68.356 -0.162 1.465 -7.271 H293 GDM 80
#
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
GDM O1 C1 DOUB N N 1
GDM O2 C6 SING N N 2
GDM O2 C23 SING N N 3
GDM O3 C7 SING N N 4
GDM O3 C24 SING N N 5
GDM O4 C24 DOUB N N 6
GDM O5 C11 SING N N 7
GDM O5 HO5 SING N N 8
GDM O6 C12 SING N N 9
GDM O6 C27 SING N N 10
GDM O7 C17 SING N N 11
GDM O7 C29 SING N N 12
GDM O8 C18 DOUB N N 13
GDM O9 C21 DOUB N N 14
GDM N1 C1 SING N N 15
GDM N1 C20 SING N N 16
GDM N1 HN1 SING N N 17
GDM N2 C24 SING N N 18
GDM N2 HN21 SING N N 19
GDM N2 HN22 SING N N 20
GDM C1 C2 SING N N 21
GDM C2 C3 DOUB N E 22
GDM C2 C22 SING N N 23
GDM C3 C4 SING N N 24
GDM C3 H3 SING N N 25
GDM C4 C5 DOUB N Z 26
GDM C4 H4 SING N N 27
GDM C5 C6 SING N N 28
GDM C5 H5 SING N N 29
GDM C6 C7 SING N N 30
GDM C6 H6 SING N N 31
GDM C7 C8 SING N N 32
GDM C7 H7 SING N N 33
GDM C8 C9 DOUB N E 34
GDM C8 C25 SING N N 35
GDM C9 C10 SING N N 36
GDM C9 H9 SING N N 37
GDM C10 C11 SING N N 38
GDM C10 C26 SING N N 39
GDM C10 H10 SING N N 40
GDM C11 C12 SING N N 41
GDM C11 H11 SING N N 42
GDM C12 C13 SING N N 43
GDM C12 H12 SING N N 44
GDM C13 C14 SING N N 45
GDM C13 H131 SING N N 46
GDM C13 H132 SING N N 47
GDM C14 C15 SING N N 48
GDM C14 C28 SING N N 49
GDM C14 H14 SING N N 50
GDM C15 C16 SING N N 51
GDM C15 H151 SING N N 52
GDM C15 H152 SING N N 53
GDM C16 C17 DOUB N N 54
GDM C16 C21 SING N N 55
GDM C17 C18 SING N N 56
GDM C18 C19 SING N N 57
GDM C19 C20 DOUB N N 58
GDM C19 H19 SING N N 59
GDM C20 C21 SING N N 60
GDM C22 H221 SING N N 61
GDM C22 H222 SING N N 62
GDM C22 H223 SING N N 63
GDM C23 H231 SING N N 64
GDM C23 H232 SING N N 65
GDM C23 H233 SING N N 66
GDM C25 H251 SING N N 67
GDM C25 H252 SING N N 68
GDM C25 H253 SING N N 69
GDM C26 H261 SING N N 70
GDM C26 H262 SING N N 71
GDM C26 H263 SING N N 72
GDM C27 H271 SING N N 73
GDM C27 H272 SING N N 74
GDM C27 H273 SING N N 75
GDM C28 H281 SING N N 76
GDM C28 H282 SING N N 77
GDM C28 H283 SING N N 78
GDM C29 H291 SING N N 79
GDM C29 H292 SING N N 80
GDM C29 H293 SING N N 81
#
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
GDM SMILES ACDLabs 10.04 O=C1C(OC)=C2C(=O)C(=C1)NC(=O)C(=CC=CC(OC)C(OC(=O)N)C(=CC(C)C(O)C(OC)CC(C)C2)C)C
GDM SMILES_CANONICAL CACTVS 3.341 CO[C@H]1C[C@H](C)CC2=C(OC)C(=O)C=C(NC(=O)\C(=C\C=C/[C@H](OC)[C@@H](OC(N)=O)\C(=C\[C@H](C)[C@H]1O)C)C)C2=O
GDM SMILES CACTVS 3.341 CO[CH]1C[CH](C)CC2=C(OC)C(=O)C=C(NC(=O)C(=CC=C[CH](OC)[CH](OC(N)=O)C(=C[CH](C)[CH]1O)C)C)C2=O
GDM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[C@H]1C[C@@H]([C@@H]([C@H](\C=C(\[C@@H]([C@H](\C=C/C=C(/C(=O)NC2=CC(=O)C(=C(C1)C2=O)OC)\C)OC)OC(=O)N)/C)C)O)OC
GDM SMILES "OpenEye OEToolkits" 1.5.0 CC1CC(C(C(C=C(C(C(C=CC=C(C(=O)NC2=CC(=O)C(=C(C1)C2=O)OC)C)OC)OC(=O)N)C)C)O)OC
GDM InChI InChI 1.03 InChI=1S/C29H40N2O9/c1-15-11-19-25(34)20(14-21(32)27(19)39-7)31-28(35)16(2)9-8-10-22(37-5)26(40-29(30)36)18(4)13-17(3)24(33)23(12-15)38-6/h8-10,13-15,17,22-24,26,33H,11-12H2,1-7H3,(H2,30,36)(H,31,35)/b10-8-,16-9+,18-13+/t15-,17+,22+,23+,24-,26+/m1/s1
GDM InChIKey InChI 1.03 QTQAWLPCGQOSGP-KSRBKZBZSA-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
GDM "SYSTEMATIC NAME" ACDLabs 10.04 "(4E,6Z,8S,9S,10E,12S,13R,14S,16R)-13-hydroxy-8,14,19-trimethoxy-4,10,12,16-tetramethyl-3,20,22-trioxo-2-azabicyclo[16.3.1]docosa-1(21),4,6,10,18-pentaen-9-yl carbamate"
GDM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(3R,5S,6R,7S,8E,10S,11S,12Z,14E)-6-hydroxy-5,11,21-trimethoxy-3,7,9,15-tetramethyl-16,20,22-trioxo-17-azabicyclo[16.3.1]docosa-1(21),8,12,14,18-pentaen-10-yl] carbamate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
GDM 'Create component' 1999-07-08 EBI
GDM 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id GDM
_pdbe_chem_comp_drugbank_details.drugbank_id DB02424
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Geldanamycin
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 30562-34-6
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id GDM
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02424
_pdbe_chem_comp_drugbank_classification.parent Macrolactams
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class Macrolactams
_pdbe_chem_comp_drugbank_classification.superclass 'Phenylpropanoids and polyketides'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as macrolactams. These are cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring.  They are nitrogen analogues (the a nitrogen atom replacing the o atom of the cyclic carboxylic acid group ) of the naturally occurring macrolides.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
GDM DB02424 'Heat shock protein HSP 90-alpha' Humans P07900 yes 1
GDM DB02424 Endoplasmin Humans P14625 unknown 2
GDM DB02424 'Heat shock protein HSP 90-beta' Humans P08238 unknown 3
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 '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
GDM O1 O -6.064 0.244 1
GDM O2 O -1.021 4.232 2
GDM O3 O 1.765 5.727 3
GDM O4 O -0.780 5.896 4
GDM O5 O 5.598 -1.073 5
GDM O6 O 2.934 -2.493 6
GDM O7 O 0.174 -5.128 7
GDM O8 O -2.296 -6.785 8
GDM O9 O -2.386 -1.354 9
GDM N1 N -5.067 -2.299 10
GDM N2 N 0.654 8.059 11
GDM C1 C -4.820 -0.565 12
GDM C2 C -3.196 0.326 13
GDM C3 C -1.817 -0.473 14
GDM C4 C -1.078 0.313 15
GDM C5 C 0.171 1.761 16
GDM C6 C 0.199 3.416 17
GDM C7 C 1.675 4.203 18
GDM C8 C 3.014 3.434 19
GDM C9 C 3.034 1.955 20
GDM C10 C 4.343 1.203 21
GDM C11 C 4.317 -0.290 22
GDM C12 C 2.986 -0.994 23
GDM C13 C 1.706 -0.145 24
GDM C14 C 0.283 -0.736 25
GDM C15 C 0.069 -2.189 26
GDM C16 C -1.335 -2.943 27
GDM C17 C -1.222 -4.432 28
GDM C18 C -2.455 -5.283 29
GDM C19 C -3.810 -4.636 30
GDM C20 C -3.926 -3.138 31
GDM C21 C -2.683 -2.297 32
GDM C22 C -3.174 1.826 33
GDM C23 C -2.325 3.588 34
GDM C24 C 0.549 6.555 35
GDM C25 C 4.333 4.201 36
GDM C26 C 5.657 1.943 37
GDM C27 C 4.219 -3.283 38
GDM C28 C 1.503 -1.678 39
GDM C29 C 0.269 -6.670 40
#
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
GDM O1 C1 DOUBLE NONE 1
GDM C6 O2 SINGLE BEGINDASH 2
GDM O2 C23 SINGLE NONE 3
GDM C7 O3 SINGLE BEGINWEDGE 4
GDM O3 C24 SINGLE NONE 5
GDM O4 C24 DOUBLE NONE 6
GDM C11 O5 SINGLE BEGINWEDGE 7
GDM C12 O6 SINGLE BEGINWEDGE 8
GDM O6 C27 SINGLE NONE 9
GDM O7 C17 SINGLE NONE 10
GDM O7 C29 SINGLE NONE 11
GDM O8 C18 DOUBLE NONE 12
GDM O9 C21 DOUBLE NONE 13
GDM N1 C1 SINGLE NONE 14
GDM N1 C20 SINGLE NONE 15
GDM N2 C24 SINGLE NONE 16
GDM C1 C2 SINGLE ENDUPRIGHT 17
GDM C2 C3 DOUBLE NONE 18
GDM C2 C22 SINGLE ENDUPRIGHT 19
GDM C3 C4 SINGLE ENDUPRIGHT 20
GDM C4 C5 DOUBLE NONE 21
GDM C5 C6 SINGLE ENDDOWNRIGHT 22
GDM C6 C7 SINGLE NONE 23
GDM C7 C8 SINGLE ENDUPRIGHT 24
GDM C8 C9 DOUBLE NONE 25
GDM C8 C25 SINGLE ENDUPRIGHT 26
GDM C9 C10 SINGLE ENDUPRIGHT 27
GDM C10 C11 SINGLE NONE 28
GDM C10 C26 SINGLE BEGINDASH 29
GDM C11 C12 SINGLE NONE 30
GDM C12 C13 SINGLE NONE 31
GDM C13 C14 SINGLE NONE 32
GDM C14 C15 SINGLE NONE 33
GDM C14 C28 SINGLE BEGINWEDGE 34
GDM C15 C16 SINGLE NONE 35
GDM C16 C17 DOUBLE NONE 36
GDM C16 C21 SINGLE NONE 37
GDM C17 C18 SINGLE NONE 38
GDM C18 C19 SINGLE NONE 39
GDM C19 C20 DOUBLE NONE 40
GDM C20 C21 SINGLE NONE 41
#
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
GDM MurckoScaffold S1 scaffold O=C1C=C2CCCCCC/C=C/CC/C=C\C=C\C(=O)NC(=C1)C2=O InChI=1S/C21H25NO3/c23-18-15-17-13-11-9-7-5-3-1-2-4-6-8-10-12-14-20(24)22-19(16-18)21(17)25/h1-2,8,10,12,14-16H,3-7,9,11,13H2,(H,22,24)/b2-1+,10-8-,14-12+ WVVWBFUIUJXRSP-PTEYMDDJSA-N
GDM amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
GDM 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
GDM O1 S1 1
GDM O8 S1 1
GDM O9 S1 1
GDM N1 S1 1
GDM C1 S1 1
GDM C2 S1 1
GDM C3 S1 1
GDM C4 S1 1
GDM C5 S1 1
GDM C6 S1 1
GDM C7 S1 1
GDM C8 S1 1
GDM C9 S1 1
GDM C10 S1 1
GDM C11 S1 1
GDM C12 S1 1
GDM C13 S1 1
GDM C14 S1 1
GDM C15 S1 1
GDM C16 S1 1
GDM C17 S1 1
GDM C18 S1 1
GDM C19 S1 1
GDM C20 S1 1
GDM C21 S1 1
GDM N1 F1 1
GDM C1 F1 1
GDM O1 F1 1
GDM C2 F1 1
GDM O9 F2 1
GDM C21 F2 1
GDM C20 F2 1
GDM N1 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id GDM
_pdbe_chem_comp_rdkit_properties.exactmw 560.273
_pdbe_chem_comp_rdkit_properties.amw 560.644
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 11
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 12
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 9
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 40
_pdbe_chem_comp_rdkit_properties.NumAtoms 80
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 11
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.517
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 2
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 6
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 290.742
_pdbe_chem_comp_rdkit_properties.tpsa 163.480
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.408
_pdbe_chem_comp_rdkit_properties.CrippenMR 146.548
_pdbe_chem_comp_rdkit_properties.chi0v 19.069
_pdbe_chem_comp_rdkit_properties.chi1v 9.574
_pdbe_chem_comp_rdkit_properties.chi2v 3.999
_pdbe_chem_comp_rdkit_properties.chi3v 3.999
_pdbe_chem_comp_rdkit_properties.chi4v 2.385
_pdbe_chem_comp_rdkit_properties.chi0n 59.069
_pdbe_chem_comp_rdkit_properties.chi1n 29.324
_pdbe_chem_comp_rdkit_properties.chi2n 3.999
_pdbe_chem_comp_rdkit_properties.chi3n 3.999
_pdbe_chem_comp_rdkit_properties.chi4n 2.385
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.540
_pdbe_chem_comp_rdkit_properties.kappa1 7.641
_pdbe_chem_comp_rdkit_properties.kappa2 14.734
_pdbe_chem_comp_rdkit_properties.kappa3 8.232
_pdbe_chem_comp_rdkit_properties.Phi 2.814
#
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
GDM UniChem ChEMBL CHEMBL278315
GDM UniChem DrugBank DB02424
GDM UniChem 'Guide to Pharmacology' 9829
GDM UniChem 'KEGG LIGAND' C11222
GDM UniChem ChEBI 5292
GDM UniChem ZINC ZINC000100064834
GDM UniChem eMolecules 1934769
GDM UniChem eMolecules 30154536
GDM UniChem eMolecules 36500472
GDM UniChem atlas geldanamycin
GDM UniChem fdasrs Z3K3VJ16KU
GDM UniChem LINCS LSM-42789
GDM UniChem BindingDb 50008059
GDM UniChem 'EPA CompTox Dashboard' DTXSID7042691
GDM UniChem ChemicalBook CB8462842
GDM UniChem ClinicalTrials GELDANAMYCIN
GDM UniChem 'Probes And Drugs' PD021225
GDM UniChem CCDC GUTVOJ
GDM UniChem SureChEMBL SCHEMBL4154
GDM UniChem 'PubChem TPHARMA' 14886316
GDM UniChem 'PubChem TPHARMA' 15061987
GDM UniChem PubChem 5288382
GDM UniChem NMRShiftDB 70058292
GDM UniChem Nikkaji J21.396I
#
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
GDM O1 1.284 5.332 -0.229 ETKDGv3 1
GDM O2 -2.998 1.717 -1.392 ETKDGv3 2
GDM O3 -3.775 -0.765 -1.687 ETKDGv3 3
GDM O4 -5.340 -2.401 -1.205 ETKDGv3 4
GDM O5 1.220 -3.905 1.105 ETKDGv3 5
GDM O6 1.928 -1.139 1.354 ETKDGv3 6
GDM O7 4.883 -0.775 -0.354 ETKDGv3 7
GDM O8 5.581 0.852 1.952 ETKDGv3 8
GDM O9 1.700 2.638 -1.226 ETKDGv3 9
GDM N1 1.921 3.818 1.425 ETKDGv3 10
GDM N2 -4.851 -2.061 -3.451 ETKDGv3 11
GDM C1 0.931 4.517 0.665 ETKDGv3 12
GDM C2 -0.497 4.321 0.969 ETKDGv3 13
GDM C3 -0.989 3.071 0.989 ETKDGv3 14
GDM C4 -2.355 2.744 1.442 ETKDGv3 15
GDM C5 -3.072 1.714 0.972 ETKDGv3 16
GDM C6 -2.703 0.913 -0.259 ETKDGv3 17
GDM C7 -3.520 -0.411 -0.323 ETKDGv3 18
GDM C8 -2.776 -1.532 0.402 ETKDGv3 19
GDM C9 -1.886 -2.296 -0.287 ETKDGv3 20
GDM C10 -0.976 -3.398 0.244 ETKDGv3 21
GDM C11 0.257 -2.881 1.046 ETKDGv3 22
GDM C12 0.905 -1.580 0.473 ETKDGv3 23
GDM C13 1.534 -1.804 -0.932 ETKDGv3 24
GDM C14 1.455 -0.554 -1.865 ETKDGv3 25
GDM C15 2.822 0.151 -2.035 ETKDGv3 26
GDM C16 3.247 0.890 -0.782 ETKDGv3 27
GDM C17 4.237 0.422 0.009 ETKDGv3 28
GDM C18 4.595 1.181 1.242 ETKDGv3 29
GDM C19 3.779 2.331 1.661 ETKDGv3 30
GDM C20 2.783 2.792 0.895 ETKDGv3 31
GDM C21 2.530 2.142 -0.418 ETKDGv3 32
GDM C22 -1.356 5.521 1.262 ETKDGv3 33
GDM C23 -1.935 1.688 -2.321 ETKDGv3 34
GDM C24 -4.679 -1.763 -2.069 ETKDGv3 35
GDM C25 -3.021 -1.697 1.881 ETKDGv3 36
GDM C26 -1.736 -4.497 1.004 ETKDGv3 37
GDM C27 1.424 -0.231 2.311 ETKDGv3 38
GDM C28 0.915 -0.952 -3.248 ETKDGv3 39
GDM C29 5.838 -1.476 0.433 ETKDGv3 40
GDM HO5 1.799 -3.717 1.889 ETKDGv3 41
GDM HN1 1.908 3.973 2.459 ETKDGv3 42
GDM HN21 -4.304 -1.540 -4.172 ETKDGv3 43
GDM HN22 -5.520 -2.804 -3.755 ETKDGv3 44
GDM H3 -0.343 2.256 0.692 ETKDGv3 45
GDM H4 -2.791 3.344 2.231 ETKDGv3 46
GDM H5 -4.039 1.545 1.430 ETKDGv3 47
GDM H6 -1.623 0.648 -0.186 ETKDGv3 48
GDM H7 -4.512 -0.259 0.159 ETKDGv3 49
GDM H9 -1.760 -2.095 -1.348 ETKDGv3 50
GDM H10 -0.585 -3.912 -0.660 ETKDGv3 51
GDM H11 -0.091 -2.664 2.078 ETKDGv3 52
GDM H12 0.099 -0.820 0.380 ETKDGv3 53
GDM H131 1.040 -2.658 -1.432 ETKDGv3 54
GDM H132 2.587 -2.140 -0.814 ETKDGv3 55
GDM H14 0.728 0.184 -1.463 ETKDGv3 56
GDM H151 3.586 -0.583 -2.373 ETKDGv3 57
GDM H152 2.755 0.898 -2.856 ETKDGv3 58
GDM H19 3.979 2.787 2.623 ETKDGv3 59
GDM H221 -0.818 6.464 1.024 ETKDGv3 60
GDM H222 -2.282 5.488 0.650 ETKDGv3 61
GDM H223 -1.624 5.537 2.340 ETKDGv3 62
GDM H231 -1.696 0.647 -2.632 ETKDGv3 63
GDM H232 -2.240 2.250 -3.227 ETKDGv3 64
GDM H233 -1.033 2.184 -1.902 ETKDGv3 65
GDM H251 -2.070 -1.659 2.445 ETKDGv3 66
GDM H252 -3.662 -0.880 2.270 ETKDGv3 67
GDM H253 -3.557 -2.648 2.073 ETKDGv3 68
GDM H261 -1.134 -5.431 1.010 ETKDGv3 69
GDM H262 -2.706 -4.717 0.509 ETKDGv3 70
GDM H263 -1.914 -4.216 2.061 ETKDGv3 71
GDM H271 2.245 0.042 3.005 ETKDGv3 72
GDM H272 1.070 0.701 1.824 ETKDGv3 73
GDM H273 0.608 -0.678 2.917 ETKDGv3 74
GDM H281 1.600 -1.674 -3.742 ETKDGv3 75
GDM H282 -0.089 -1.417 -3.150 ETKDGv3 76
GDM H283 0.809 -0.055 -3.896 ETKDGv3 77
GDM H291 6.092 -2.429 -0.076 ETKDGv3 78
GDM H292 5.414 -1.714 1.431 ETKDGv3 79
GDM H293 6.768 -0.878 0.531 ETKDGv3 80
#