data_RIO
#
_chem_comp.id RIO
_chem_comp.name RIBOSTAMYCIN
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C17 H34 N4 O10"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
;5-AMINO-2-AMINOMETHYL-6-[4,6-DIAMINO-2-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-3-HYDROXY-CYCLOHEXYLOXY
]-TETRAHYDRO-PYRAN-3,4-DIOL; (1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl
2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside
;
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2002-07-08
_chem_comp.pdbx_modified_date 2020-06-17
_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 454.473
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code RIO
_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 1M4G
_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
RIO O1 O1 O 0 1 N N N N N N 24.194 29.545 11.223 -2.539 2.965 -2.713 O1 RIO 1
RIO C1 C1 C 0 1 N N N N N N 23.639 29.733 9.924 -3.088 3.041 -1.396 C1 RIO 2
RIO C2 C2 C 0 1 N N R N N N 22.270 30.359 10.078 -3.564 1.653 -0.962 C2 RIO 3
RIO O2 O2 O 0 1 N N N N N N 21.509 29.585 11.021 -2.437 0.773 -0.817 O2 RIO 4
RIO C3 C3 C 0 1 N N S N N N 20.725 30.474 11.854 -2.741 -0.126 0.271 C3 RIO 5
RIO O3 O3 O 0 1 N N N N N N 21.403 30.562 13.096 -1.543 -0.688 0.810 O3 RIO 6
RIO C4 C4 C 0 1 N N R N N N 21.114 29.584 14.101 -0.851 -1.556 -0.090 C4 RIO 7
RIO C5 C5 C 0 1 N N S N N N 21.571 28.179 13.689 -1.357 -2.988 0.093 C5 RIO 8
RIO O4 O4 O 0 1 N N N N N N 22.987 28.206 13.417 -2.759 -3.037 -0.181 O4 RIO 9
RIO C6 C6 C 0 1 N N R N N N 21.303 27.081 14.764 -0.617 -3.917 -0.871 C6 RIO 10
RIO N1 N1 N 0 1 N N N N N N 21.626 25.763 14.126 -1.102 -5.293 -0.696 N1 RIO 11
RIO C7 C7 C 0 1 N N N N N N 19.823 27.049 15.165 0.884 -3.865 -0.578 C7 RIO 12
RIO C8 C8 C 0 1 N N S N N N 19.357 28.493 15.631 1.390 -2.433 -0.761 C8 RIO 13
RIO N2 N2 N 0 1 N N N N N N 17.884 28.464 15.950 2.831 -2.382 -0.479 N2 RIO 14
RIO C9 C9 C 0 1 N N R N N N 19.619 29.587 14.567 0.650 -1.503 0.203 C9 RIO 15
RIO O5 O5 O 0 1 N N N N N N 19.242 30.771 15.224 1.122 -0.166 0.032 O5 RIO 16
RIO C10 C10 C 0 1 N N R N N N 19.276 32.054 14.610 1.709 0.398 1.207 C10 RIO 17
RIO O6 O6 O 0 1 N N N N N N 18.499 32.005 13.376 3.099 0.066 1.251 O6 RIO 18
RIO C11 C11 C 0 1 N N R N N N 17.073 31.761 13.441 3.844 0.523 0.121 C11 RIO 19
RIO C12 C12 C 0 1 N N N N N N 16.509 32.091 12.051 5.304 0.088 0.263 C12 RIO 20
RIO N3 N3 N 0 1 N N N N N N 17.198 31.238 11.064 5.388 -1.376 0.189 N3 RIO 21
RIO C13 C13 C 0 1 N N S N N N 16.388 32.628 14.526 3.771 2.051 0.047 C13 RIO 22
RIO O7 O7 O 0 1 N N N N N N 15.072 32.122 14.687 4.468 2.507 -1.114 O7 RIO 23
RIO C14 C14 C 0 1 N N R N N N 17.180 32.539 15.849 2.303 2.481 -0.034 C14 RIO 24
RIO O8 O8 O 0 1 N N N N N N 16.552 33.398 16.846 2.222 3.907 -0.029 O8 RIO 25
RIO C15 C15 C 0 1 N N R N N N 18.631 33.011 15.610 1.551 1.920 1.177 C15 RIO 26
RIO N4 N4 N 0 1 N N N N N N 19.377 32.950 16.913 0.126 2.263 1.071 N4 RIO 27
RIO C16 C16 C 0 1 N N R N N N 20.846 31.839 11.190 -3.433 0.789 1.313 C16 RIO 28
RIO O9 O9 O 0 1 N N N N N N 19.857 31.990 10.220 -4.290 0.030 2.168 O9 RIO 29
RIO C17 C17 C 0 1 N N S N N N 22.237 31.788 10.569 -4.254 1.743 0.413 C17 RIO 30
RIO O10 O10 O 0 1 N N N N N N 22.233 32.707 9.446 -5.610 1.301 0.321 O10 RIO 31
RIO HO1 HO1 H 0 1 N N N N N N 25.141 29.503 11.160 -2.216 3.811 -3.054 HO1 RIO 32
RIO H1 H1 H 0 1 N N N N N N 24.288 30.395 9.332 -2.324 3.396 -0.704 H1 RIO 33
RIO H1A H1A H 0 1 N N N N N N 23.557 28.767 9.404 -3.931 3.732 -1.393 H1A RIO 34
RIO H2 H2 H 0 1 N N N N N N 21.859 30.367 9.058 -4.256 1.251 -1.701 H2 RIO 35
RIO H3 H3 H 0 1 N N N N N N 19.683 30.147 11.982 -3.418 -0.914 -0.061 H3 RIO 36
RIO H4 H4 H 0 1 N N N N N N 21.707 29.885 14.978 -1.033 -1.234 -1.116 H4 RIO 37
RIO H5 H5 H 0 1 N N N N N N 20.980 27.912 12.801 -1.176 -3.309 1.118 H5 RIO 38
RIO HO4 HO4 H 0 1 N N N N N N 23.129 28.212 12.478 -3.148 -3.917 -0.085 HO4 RIO 39
RIO H6 H6 H 0 1 N N N N N N 21.909 27.286 15.659 -0.798 -3.596 -1.897 H6 RIO 40
RIO HN1 HN1 H 0 1 N N N N N N 21.698 25.880 13.136 -0.628 -5.926 -1.321 HN1 RIO 41
RIO HN1A HN1A H 0 0 N N N N N N 22.495 25.423 14.485 -1.004 -5.591 0.263 HN1A RIO 42
RIO H7 H7 H 0 1 N N N N N N 19.219 26.733 14.302 1.066 -4.186 0.448 H7 RIO 43
RIO H7A H7A H 0 1 N N N N N N 19.688 26.340 15.995 1.412 -4.527 -1.265 H7A RIO 44
RIO H8 H8 H 0 1 N N N N N N 19.952 28.750 16.520 1.209 -2.112 -1.787 H8 RIO 45
RIO HN2 HN2 H 0 1 N N N N N N 17.757 28.458 16.942 3.353 -2.897 -1.173 HN2 RIO 46
RIO HN2A HN2A H 0 0 N N N N N N 17.443 29.274 15.563 3.154 -1.429 -0.417 HN2A RIO 47
RIO H9 H9 H 0 1 N N N N N N 19.056 29.441 13.634 0.831 -1.824 1.229 H9 RIO 48
RIO H10 H10 H 0 1 N N N N N N 20.297 32.376 14.359 1.212 -0.002 2.090 H10 RIO 49
RIO H11 H11 H 0 1 N N N N N N 16.879 30.714 13.718 3.424 0.095 -0.789 H11 RIO 50
RIO H12 H12 H 0 1 N N N N N N 15.427 31.893 12.028 5.894 0.527 -0.542 H12 RIO 51
RIO H12A H12A H 0 0 N N N N N N 16.672 33.153 11.816 5.692 0.427 1.224 H12A RIO 52
RIO HN3 HN3 H 0 1 N N N N N N 17.354 31.758 10.224 5.027 -1.716 -0.690 HN3 RIO 53
RIO HN3A HN3A H 0 0 N N N N N N 18.076 30.938 11.438 6.335 -1.692 0.337 HN3A RIO 54
RIO H13 H13 H 0 1 N N N N N N 16.358 33.688 14.233 4.229 2.480 0.939 H13 RIO 55
RIO HO7 HO7 H 0 1 N N N N N N 14.887 32.009 15.612 4.462 3.467 -1.224 HO7 RIO 56
RIO H14 H14 H 0 1 N N N N N N 17.184 31.499 16.207 1.860 2.093 -0.951 H14 RIO 57
RIO HO8 HO8 H 0 1 N N N N N N 16.415 32.906 17.647 2.684 4.330 -0.766 HO8 RIO 58
RIO H15 H15 H 0 1 N N N N N N 18.653 34.040 15.222 1.962 2.347 2.091 H15 RIO 59
RIO HN4 HN4 H 0 1 N N N N N N 20.361 32.936 16.734 -0.393 1.900 1.857 HN4 RIO 60
RIO HN4A HN4A H 0 0 N N N N N N 19.150 33.752 17.465 -0.000 3.261 0.985 HN4A RIO 61
RIO H16 H16 H 0 1 N N N N N N 20.719 32.687 11.879 -2.695 1.341 1.896 H16 RIO 62
RIO HO9 HO9 H 0 1 N N N N N N 19.005 32.024 10.639 -3.831 -0.645 2.687 HO9 RIO 63
RIO H17 H17 H 0 1 N N N N N N 23.082 32.051 11.223 -4.210 2.762 0.797 H17 RIO 64
RIO HO10 HO10 H 0 0 N N N N N N 22.232 33.601 9.768 -6.093 1.336 1.158 HO10 RIO 65
#
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
RIO O1 C1 SING N N 1
RIO C1 C2 SING N N 2
RIO C2 O2 SING N N 3
RIO C2 C17 SING N N 4
RIO O2 C3 SING N N 5
RIO C3 O3 SING N N 6
RIO C3 C16 SING N N 7
RIO O3 C4 SING N N 8
RIO C4 C5 SING N N 9
RIO C4 C9 SING N N 10
RIO C5 O4 SING N N 11
RIO C5 C6 SING N N 12
RIO C6 N1 SING N N 13
RIO C6 C7 SING N N 14
RIO C7 C8 SING N N 15
RIO C8 N2 SING N N 16
RIO C8 C9 SING N N 17
RIO C9 O5 SING N N 18
RIO O5 C10 SING N N 19
RIO C10 O6 SING N N 20
RIO C10 C15 SING N N 21
RIO O6 C11 SING N N 22
RIO C11 C12 SING N N 23
RIO C11 C13 SING N N 24
RIO C12 N3 SING N N 25
RIO C13 O7 SING N N 26
RIO C13 C14 SING N N 27
RIO C14 O8 SING N N 28
RIO C14 C15 SING N N 29
RIO C15 N4 SING N N 30
RIO C16 O9 SING N N 31
RIO C16 C17 SING N N 32
RIO C17 O10 SING N N 33
RIO O1 HO1 SING N N 34
RIO C1 H1 SING N N 35
RIO C1 H1A SING N N 36
RIO C2 H2 SING N N 37
RIO C3 H3 SING N N 38
RIO C4 H4 SING N N 39
RIO C5 H5 SING N N 40
RIO O4 HO4 SING N N 41
RIO C6 H6 SING N N 42
RIO N1 HN1 SING N N 43
RIO N1 HN1A SING N N 44
RIO C7 H7 SING N N 45
RIO C7 H7A SING N N 46
RIO C8 H8 SING N N 47
RIO N2 HN2 SING N N 48
RIO N2 HN2A SING N N 49
RIO C9 H9 SING N N 50
RIO C10 H10 SING N N 51
RIO C11 H11 SING N N 52
RIO C12 H12 SING N N 53
RIO C12 H12A SING N N 54
RIO N3 HN3 SING N N 55
RIO N3 HN3A SING N N 56
RIO C13 H13 SING N N 57
RIO O7 HO7 SING N N 58
RIO C14 H14 SING N N 59
RIO O8 HO8 SING N N 60
RIO C15 H15 SING N N 61
RIO N4 HN4 SING N N 62
RIO N4 HN4A SING N N 63
RIO C16 H16 SING N N 64
RIO O9 HO9 SING N N 65
RIO C17 H17 SING N N 66
RIO O10 HO10 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
RIO SMILES ACDLabs 10.04 O(C2C(OC1OC(CN)C(O)C(O)C1N)C(N)CC(N)C2O)C3OC(C(O)C3O)CO
RIO SMILES_CANONICAL CACTVS 3.341 NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O)[C@H]2O[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)[C@H](N)[C@@H](O)[C@@H]1O
RIO SMILES CACTVS 3.341 NC[CH]1O[CH](O[CH]2[CH](N)C[CH](N)[CH](O)[CH]2O[CH]3O[CH](CO)[CH](O)[CH]3O)[CH](N)[CH](O)[CH]1O
RIO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CN)O)O)N)O[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)O)N
RIO SMILES "OpenEye OEToolkits" 1.5.0 C1C(C(C(C(C1N)OC2C(C(C(C(O2)CN)O)O)N)OC3C(C(C(O3)CO)O)O)O)N
RIO InChI InChI 1.03 InChI=1S/C17H34N4O10/c18-2-6-10(24)12(26)8(21)16(28-6)30-14-5(20)1-4(19)9(23)15(14)31-17-13(27)11(25)7(3-22)29-17/h4-17,22-27H,1-3,18-21H2/t4-,5+,6-,7-,8-,9+,10-,11-,12-,13-,14-,15-,16-,17+/m1/s1
RIO InChIKey InChI 1.03 NSKGQURZWSPSBC-VVPCINPTSA-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
RIO "SYSTEMATIC NAME" ACDLabs 10.04 "(1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside"
RIO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(1R,2R,3S,4R,6S)-4,6-diamino-2-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-3-hydroxy-cyclohexyl]oxy-oxane-3,4-diol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
RIO 'Create component' 2002-07-08 RCSB
RIO 'Modify descriptor' 2011-06-04 RCSB
RIO 'Modify synonyms' 2020-06-05 PDBE
#
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 RIO 5-AMINO-2-AMINOMETHYL-6-[4,6-DIAMINO-2-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-3-HYDROXY-CYCLOHEXYLOXY]-TETRAHYDRO-PYRAN-3,4-DIOL ? ?
2 RIO "(1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside" ? ?
#
_pdbe_chem_comp_drugbank_details.comp_id RIO
_pdbe_chem_comp_drugbank_details.drugbank_id DB03615
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Ribostamycin
_pdbe_chem_comp_drugbank_details.description
"Ribostamycin is an aminoglycoside antibiotic[A187166] isolated from _Streptomyces ribosidificus_[A187178] listed as one of the World Health Organization's critically important antimicrobials.[L9071]"
_pdbe_chem_comp_drugbank_details.cas_number 25546-65-0
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth. However, their exact mechanism of action is not fully known.'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
RIO '5-AMINO-2-AMINOMETHYL-6-[4,6-DIAMINO-2-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-3-HYDROXY-CYCLOHEXYLOXY]-TETRAHYDRO-PYRAN-3,4-DIOL' wwPDB ?
RIO '(1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside' wwPDB ?
RIO Ribostamycin DrugBank ?
RIO 'Ribostamycin A' DrugBank ?
RIO Ribostamycinum DrugBank ?
RIO Vistamycin DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id RIO
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03615
_pdbe_chem_comp_drugbank_classification.parent '4,5-disubstituted 2-deoxystreptamines'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Organooxygen compounds'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic oxygen compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as 4,5-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that a glycosidically linked to a pyranose of furanose unit at the C4- and C5-positions.'
#
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
RIO DB03615 '30S ribosomal protein S12' 'Escherichia coli (strain K12)' P0A7S3 yes 1
RIO DB03615 'Protein disulfide-isomerase' Humans P07237 unknown 2
RIO DB03615 "Aminoglycoside N(6')-acetyltransferase type 1" 'Salmonella enteritidis' Q9R381 unknown 3
RIO DB03615 "Aminoglycoside 2'-N-acetyltransferase" 'Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)' P9WQG9 unknown 4
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
RIO O1 O 19.693 0.503 1
RIO C1 C 18.322 1.113 2
RIO C2 C 17.109 0.232 3
RIO O2 O 15.682 0.695 4
RIO C3 C 14.801 -0.518 5
RIO O3 O 13.301 -0.518 6
RIO C4 C 12.551 0.781 7
RIO C5 C 13.301 2.080 8
RIO O4 O 14.801 2.080 9
RIO C6 C 12.551 3.379 10
RIO N1 N 13.301 4.678 11
RIO C7 C 11.051 3.379 12
RIO C8 C 10.301 2.080 13
RIO N2 N 8.801 2.080 14
RIO C9 C 11.051 0.781 15
RIO O5 O 10.301 -0.518 16
RIO C10 C 9.002 -1.268 17
RIO O6 O 7.702 -0.518 18
RIO C11 C 6.404 -1.268 19
RIO C12 C 5.104 -0.518 20
RIO N3 N 3.805 -1.268 21
RIO C13 C 6.404 -2.768 22
RIO O7 O 5.104 -3.518 23
RIO C14 C 7.702 -3.518 24
RIO O8 O 7.702 -5.018 25
RIO C15 C 9.002 -2.768 26
RIO N4 N 10.301 -3.518 27
RIO C16 C 15.682 -1.732 28
RIO O9 O 15.219 -3.158 29
RIO C17 C 17.109 -1.268 30
RIO O10 O 18.322 -2.150 31
#
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
RIO O1 C1 SINGLE NONE 1
RIO C2 C1 SINGLE BEGINDASH 2
RIO C2 O2 SINGLE NONE 3
RIO C2 C17 SINGLE NONE 4
RIO O2 C3 SINGLE NONE 5
RIO C3 O3 SINGLE BEGINDASH 6
RIO C3 C16 SINGLE NONE 7
RIO C4 O3 SINGLE BEGINWEDGE 8
RIO C4 C5 SINGLE NONE 9
RIO C4 C9 SINGLE NONE 10
RIO C5 O4 SINGLE BEGINDASH 11
RIO C5 C6 SINGLE NONE 12
RIO C6 N1 SINGLE BEGINWEDGE 13
RIO C6 C7 SINGLE NONE 14
RIO C7 C8 SINGLE NONE 15
RIO C8 N2 SINGLE BEGINWEDGE 16
RIO C8 C9 SINGLE NONE 17
RIO C9 O5 SINGLE BEGINDASH 18
RIO C10 O5 SINGLE BEGINDASH 19
RIO C10 O6 SINGLE NONE 20
RIO C10 C15 SINGLE NONE 21
RIO O6 C11 SINGLE NONE 22
RIO C11 C12 SINGLE BEGINWEDGE 23
RIO C11 C13 SINGLE NONE 24
RIO C12 N3 SINGLE NONE 25
RIO C13 O7 SINGLE BEGINDASH 26
RIO C13 C14 SINGLE NONE 27
RIO C14 O8 SINGLE BEGINWEDGE 28
RIO C14 C15 SINGLE NONE 29
RIO C15 N4 SINGLE BEGINDASH 30
RIO C16 O9 SINGLE BEGINWEDGE 31
RIO C16 C17 SINGLE NONE 32
RIO C17 O10 SINGLE BEGINWEDGE 33
#
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
RIO MurckoScaffold S1 scaffold 'C1CC[C@@H](O[C@@H]2CCCC[C@H]2O[C@H]2CCCO2)OC1' InChI=1S/C15H26O4/c1-2-7-13(19-15-9-5-11-17-15)12(6-1)18-14-8-3-4-10-16-14/h12-15H,1-11H2/t12-,13-,14-,15+/m1/s1 QHKOMLCENKQGLA-TUVASFSCSA-N
RIO cyclohexane F1 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N
RIO furanose F2 fragment OC1CCCO1 InChI=1S/C4H8O2/c5-4-2-1-3-6-4/h4-5H,1-3H2 JNODDICFTDYODH-UHFFFAOYSA-N
RIO pyranose F3 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N
RIO ribose F4 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-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
RIO C2 S1 1
RIO O2 S1 1
RIO C3 S1 1
RIO O3 S1 1
RIO C4 S1 1
RIO C5 S1 1
RIO C6 S1 1
RIO C7 S1 1
RIO C8 S1 1
RIO C9 S1 1
RIO O5 S1 1
RIO C10 S1 1
RIO O6 S1 1
RIO C11 S1 1
RIO C13 S1 1
RIO C14 S1 1
RIO C15 S1 1
RIO C16 S1 1
RIO C17 S1 1
RIO C4 F1 1
RIO C5 F1 1
RIO C6 F1 1
RIO C7 F1 1
RIO C8 F1 1
RIO C9 F1 1
RIO C17 F2 1
RIO C2 F2 1
RIO O2 F2 1
RIO C3 F2 1
RIO C16 F2 1
RIO O3 F2 1
RIO C13 F3 1
RIO C11 F3 1
RIO O6 F3 1
RIO C10 F3 1
RIO C15 F3 1
RIO C14 F3 1
RIO O5 F3 1
RIO C16 F4 1
RIO C17 F4 1
RIO C2 F4 1
RIO O2 F4 1
RIO C3 F4 1
RIO C1 F4 1
RIO O1 F4 1
RIO O10 F4 1
RIO O9 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id RIO
_pdbe_chem_comp_rdkit_properties.exactmw 454.227
_pdbe_chem_comp_rdkit_properties.amw 454.477
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 14
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 14
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 16
_pdbe_chem_comp_rdkit_properties.NumHBD 10
_pdbe_chem_comp_rdkit_properties.NumHBA 14
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 31
_pdbe_chem_comp_rdkit_properties.NumAtoms 65
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 14
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 3
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 14
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 226.893
_pdbe_chem_comp_rdkit_properties.tpsa 262.380
_pdbe_chem_comp_rdkit_properties.CrippenClogP -6.652
_pdbe_chem_comp_rdkit_properties.CrippenMR 101.785
_pdbe_chem_comp_rdkit_properties.chi0v 14.371
_pdbe_chem_comp_rdkit_properties.chi1v 7.502
_pdbe_chem_comp_rdkit_properties.chi2v 3.471
_pdbe_chem_comp_rdkit_properties.chi3v 3.471
_pdbe_chem_comp_rdkit_properties.chi4v 2.066
_pdbe_chem_comp_rdkit_properties.chi0n 48.371
_pdbe_chem_comp_rdkit_properties.chi1n 23.529
_pdbe_chem_comp_rdkit_properties.chi2n 3.471
_pdbe_chem_comp_rdkit_properties.chi3n 3.471
_pdbe_chem_comp_rdkit_properties.chi4n 2.066
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.560
_pdbe_chem_comp_rdkit_properties.kappa1 5.977
_pdbe_chem_comp_rdkit_properties.kappa2 10.148
_pdbe_chem_comp_rdkit_properties.kappa3 4.874
_pdbe_chem_comp_rdkit_properties.Phi 1.957
#
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
RIO UniChem DrugBank DB03615
RIO UniChem 'KEGG LIGAND' C01759
RIO UniChem ChEBI 45257
RIO UniChem ZINC ZINC000053255716
RIO UniChem fdasrs 2Q5JOU7T53
RIO UniChem SureChEMBL SCHEMBL1649929
RIO UniChem PharmGKB PA166292902
RIO UniChem NMRShiftDB 60145872
RIO UniChem DrugCentral 3526
RIO UniChem MetaboLights MTBLC45257
RIO UniChem 'Probes And Drugs' PD013549
RIO UniChem Nikkaji J20.066B
RIO UniChem PubChem 33042
#
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
RIO O1 -1.447 4.054 1.824 ETKDGv3 1
RIO C1 -2.010 2.861 2.300 ETKDGv3 2
RIO C2 -3.044 2.321 1.302 ETKDGv3 3
RIO O2 -2.414 2.004 0.077 ETKDGv3 4
RIO C3 -2.828 0.712 -0.317 ETKDGv3 5
RIO O3 -1.737 -0.183 -0.146 ETKDGv3 6
RIO C4 -1.288 -0.745 -1.372 ETKDGv3 7
RIO C5 -2.224 -1.918 -1.799 ETKDGv3 8
RIO O4 -2.250 -2.005 -3.203 ETKDGv3 9
RIO C6 -1.772 -3.267 -1.195 ETKDGv3 10
RIO N1 -1.828 -3.211 0.269 ETKDGv3 11
RIO C7 -0.346 -3.646 -1.667 ETKDGv3 12
RIO C8 0.538 -2.427 -2.035 ETKDGv3 13
RIO N2 1.959 -2.757 -1.904 ETKDGv3 14
RIO C9 0.195 -1.187 -1.182 ETKDGv3 15
RIO O5 1.048 -0.117 -1.577 ETKDGv3 16
RIO C10 1.976 0.257 -0.570 ETKDGv3 17
RIO O6 3.140 0.749 -1.207 ETKDGv3 18
RIO C11 4.198 1.059 -0.298 ETKDGv3 19
RIO C12 5.355 0.060 -0.472 ETKDGv3 20
RIO N3 4.939 -1.299 -0.137 ETKDGv3 21
RIO C13 3.782 1.216 1.194 ETKDGv3 22
RIO O7 4.780 1.926 1.884 ETKDGv3 23
RIO C14 2.445 1.973 1.278 ETKDGv3 24
RIO O8 1.984 1.950 2.605 ETKDGv3 25
RIO C15 1.370 1.367 0.327 ETKDGv3 26
RIO N4 0.797 2.433 -0.503 ETKDGv3 27
RIO C16 -3.980 0.272 0.585 ETKDGv3 28
RIO O9 -5.231 0.549 -0.004 ETKDGv3 29
RIO C17 -3.748 1.077 1.837 ETKDGv3 30
RIO O10 -4.955 1.394 2.480 ETKDGv3 31
RIO HO1 -2.124 4.766 1.969 ETKDGv3 32
RIO H1 -2.484 3.033 3.293 ETKDGv3 33
RIO H1A -1.199 2.115 2.434 ETKDGv3 34
RIO H2 -3.799 3.116 1.106 ETKDGv3 35
RIO H3 -3.198 0.770 -1.368 ETKDGv3 36
RIO H4 -1.294 0.023 -2.184 ETKDGv3 37
RIO H5 -3.260 -1.706 -1.448 ETKDGv3 38
RIO HO4 -3.031 -2.569 -3.445 ETKDGv3 39
RIO H6 -2.475 -4.060 -1.540 ETKDGv3 40
RIO HN1 -2.815 -3.015 0.554 ETKDGv3 41
RIO HN1A -1.613 -4.163 0.646 ETKDGv3 42
RIO H7 0.152 -4.264 -0.888 ETKDGv3 43
RIO H7A -0.428 -4.294 -2.568 ETKDGv3 44
RIO H8 0.351 -2.164 -3.101 ETKDGv3 45
RIO HN2 2.174 -3.570 -2.527 ETKDGv3 46
RIO HN2A 2.158 -3.055 -0.920 ETKDGv3 47
RIO H9 0.314 -1.481 -0.111 ETKDGv3 48
RIO H10 2.265 -0.624 0.050 ETKDGv3 49
RIO H11 4.594 2.049 -0.619 ETKDGv3 50
RIO H12 6.201 0.359 0.185 ETKDGv3 51
RIO H12A 5.719 0.094 -1.523 ETKDGv3 52
RIO HN3 4.367 -1.668 -0.931 ETKDGv3 53
RIO HN3A 5.798 -1.894 -0.096 ETKDGv3 54
RIO H13 3.659 0.208 1.656 ETKDGv3 55
RIO HO7 4.648 1.745 2.851 ETKDGv3 56
RIO H14 2.658 3.029 0.985 ETKDGv3 57
RIO HO8 1.310 2.675 2.684 ETKDGv3 58
RIO H15 0.557 0.905 0.933 ETKDGv3 59
RIO HN4 0.392 3.160 0.128 ETKDGv3 60
RIO HN4A -0.011 2.050 -1.043 ETKDGv3 61
RIO H16 -3.932 -0.815 0.809 ETKDGv3 62
RIO HO9 -5.261 1.515 -0.234 ETKDGv3 63
RIO H17 -3.082 0.494 2.519 ETKDGv3 64
RIO HO10 -4.712 1.764 3.368 ETKDGv3 65
#