data_5I0
#
_chem_comp.id 5I0
_chem_comp.name "[(2~{S},3~{S},4~{S},5~{R},6~{S})-2-[(2~{R},3~{R},4~{R},5~{S})-2-[(1~{R},2~{S},3~{R},4~{R},5~{S},6~{R})-2,4-bis[[azaniumylidene(azanyl)methyl]amino]-3,5,6-tris(oxidanyl)cyclohexyl]oxy-4-[bis(oxidanyl)methyl]-5-methyl-4-oxidanyl-oxolan-3-yl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-methyl-azanium"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C21 H44 N7 O13"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "hydrated form of streptomycin"
_chem_comp.pdbx_formal_charge 3
_chem_comp.pdbx_initial_date 2021-07-09
_chem_comp.pdbx_modified_date 2022-11-23
_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 602.613
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 5I0
_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 7P2E
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
5I0 C11 C1 C 0 1 N N R 194.104 212.271 211.776 4.607 -0.124 -0.202 C11 5I0 1
5I0 C12 C2 C 0 1 N N R 193.048 207.097 210.913 -0.621 0.589 -0.267 C12 5I0 2
5I0 C13 C3 C 0 1 N N S 194.470 204.965 209.017 -3.455 -0.784 0.621 C13 5I0 3
5I0 NB1 N1 N 0 1 N N N 195.877 214.714 211.881 6.889 1.414 -0.508 NB1 5I0 4
5I0 CG2 C4 C 0 1 N N N 193.574 204.403 213.392 -1.829 3.263 1.678 CG2 5I0 5
5I0 CD1 C5 C 0 1 N N N 195.914 209.348 208.425 2.040 -2.344 2.833 CD1 5I0 6
5I0 NE1 N2 N 0 1 N N N 197.034 209.980 208.709 3.025 -1.801 3.547 NE1 5I0 7
5I0 CH2 C6 C 0 1 N N N 190.801 206.315 213.631 -1.010 3.983 -1.541 CH2 5I0 8
5I0 C21 C7 C 0 1 N N R 194.204 211.614 210.402 3.797 -1.288 0.373 C21 5I0 9
5I0 C22 C8 C 0 1 N N R 193.592 205.686 211.151 -1.883 1.022 0.512 C22 5I0 10
5I0 C23 C9 C 0 1 N N S 194.565 203.615 208.262 -4.885 -1.139 0.207 C23 5I0 11
5I0 C31 C10 C 0 1 N N S 194.644 210.160 210.553 2.528 -0.747 1.035 C31 5I0 12
5I0 C32 C11 C 0 1 N N R 192.746 205.154 212.336 -1.931 2.555 0.325 C32 5I0 13
5I0 C33 C12 C 0 1 N N S 193.220 203.284 207.594 -4.920 -1.412 -1.300 C33 5I0 14
5I0 C41 C13 C 0 1 N N R 193.657 209.400 211.434 1.686 -0.005 -0.005 C41 5I0 15
5I0 C42 C14 C 0 1 N N S 192.081 206.454 212.842 -0.693 2.867 -0.544 C42 5I0 16
5I0 C43 C15 C 0 1 N N R 192.900 204.444 206.662 -3.925 -2.529 -1.629 C43 5I0 17
5I0 C51 C16 C 0 1 N N R 193.527 210.065 212.797 2.496 1.158 -0.580 C51 5I0 18
5I0 C53 C17 C 0 1 N N S 192.855 205.751 207.447 -2.532 -2.120 -1.144 C53 5I0 19
5I0 C61 C18 C 0 1 N N S 193.098 211.518 212.642 3.765 0.618 -1.242 C61 5I0 20
5I0 C63 C19 C 0 1 N N N 192.588 206.948 206.565 -1.543 -3.257 -1.415 C63 5I0 21
5I0 CA1 C20 C 0 1 N N N 194.577 214.782 211.676 6.922 0.162 -0.962 CA1 5I0 22
5I0 CI3 C21 C 0 1 N N N 196.195 201.774 208.816 -5.833 0.169 1.980 CI3 5I0 23
5I0 N11 N3 N 0 1 N N N 193.727 213.668 211.646 5.822 -0.641 -0.836 N11 5I0 24
5I0 N23 N4 N 1 1 N N N 194.955 202.498 209.188 -5.781 -0.019 0.524 N23 5I0 25
5I0 N31 N5 N 0 1 N N N 194.774 209.526 209.252 1.752 -1.862 1.586 N31 5I0 26
5I0 NC1 N6 N 1 1 N N N 193.991 215.946 211.448 8.027 -0.308 -1.538 NC1 5I0 27
5I0 NF1 N7 N 1 1 N N N 195.834 208.561 207.366 1.335 -3.357 3.334 NF1 5I0 28
5I0 O13 O1 O 0 1 N N N 193.467 204.839 209.994 -3.049 0.413 -0.046 O13 5I0 29
5I0 O21 O2 O 0 1 N N N 195.135 212.328 209.597 4.583 -1.980 1.345 O21 5I0 30
5I0 O32 O3 O 0 1 N N N 191.742 204.259 211.855 -3.129 2.940 -0.353 O32 5I0 31
5I0 O33 O4 O 0 1 N N N 193.473 202.099 206.849 -6.236 -1.814 -1.683 O33 5I0 32
5I0 O41 O5 O 0 1 N N N 193.846 207.993 211.647 0.500 0.499 0.613 O41 5I0 33
5I0 O42 O6 O 0 1 N N N 191.839 207.201 211.634 -0.412 1.634 -1.242 O42 5I0 34
5I0 O43 O7 O 0 1 N N N 191.637 204.240 206.037 -3.896 -2.742 -3.042 O43 5I0 35
5I0 O51 O8 O 0 1 N N N 192.579 209.368 213.598 1.709 1.851 -1.552 O51 5I0 36
5I0 O53 O9 O 0 1 N N N 194.120 205.977 208.091 -2.576 -1.852 0.259 O53 5I0 37
5I0 O61 O10 O 0 1 N N N 193.017 212.140 213.920 4.521 1.705 -1.780 O61 5I0 38
5I0 O63 O11 O 0 1 N N N 192.461 208.140 207.325 -0.223 -2.832 -1.070 O63 5I0 39
5I0 OG2A O12 O 0 0 N N N 194.577 205.284 213.803 -1.875 4.678 1.480 OG2A 5I0 40
5I0 OG2B O13 O 0 0 N N N 192.765 203.994 214.456 -2.920 2.862 2.509 OG2B 5I0 41
5I0 H11 H1 H 0 1 N N N 195.090 212.207 212.260 4.879 0.561 0.600 H11 5I0 42
5I0 H12 H2 H 0 1 N N N 192.960 207.337 209.843 -0.792 -0.366 -0.765 H12 5I0 43
5I0 H13 H3 H 0 1 N N N 195.444 205.182 209.481 -3.416 -0.631 1.699 H13 5I0 44
5I0 HB11 H4 H 0 0 N N N 196.314 213.827 212.028 6.084 1.756 -0.088 HB11 5I0 45
5I0 HB12 H5 H 0 0 N N N 196.426 215.550 211.890 7.669 1.983 -0.597 HB12 5I0 46
5I0 HE12 H6 H 0 0 N N N 197.080 210.583 209.505 3.538 -1.064 3.182 HE12 5I0 47
5I0 HE11 H7 H 0 0 N N N 197.839 209.857 208.128 3.229 -2.144 4.431 HE11 5I0 48
5I0 HH23 H8 H 0 0 N N N 190.997 205.744 214.550 -1.299 4.884 -0.999 HH23 5I0 49
5I0 HH22 H9 H 0 0 N N N 190.422 207.314 213.894 -0.127 4.191 -2.146 HH22 5I0 50
5I0 HH21 H10 H 0 0 N N N 190.052 205.787 213.024 -1.829 3.671 -2.189 HH21 5I0 51
5I0 H21 H11 H 0 1 N N N 193.210 211.632 209.932 3.524 -1.973 -0.430 H21 5I0 52
5I0 H22 H12 H 0 1 N N N 194.644 205.753 211.466 -1.786 0.769 1.567 H22 5I0 53
5I0 H23 H13 H 0 1 N N N 195.330 203.711 207.477 -5.210 -2.029 0.746 H23 5I0 54
5I0 H31 H14 H 0 1 N N N 195.623 210.152 211.054 2.800 -0.062 1.838 H31 5I0 55
5I0 H33 H15 H 0 1 N N N 192.430 203.151 208.347 -4.643 -0.507 -1.841 H33 5I0 56
5I0 H41 H16 H 0 1 N N N 192.676 209.517 210.951 1.413 -0.691 -0.808 H41 5I0 57
5I0 H42 H17 H 0 1 N N N 192.814 206.991 213.461 0.151 3.149 0.085 H42 5I0 58
5I0 H43 H18 H 0 1 N N N 193.691 204.516 205.901 -4.230 -3.448 -1.127 H43 5I0 59
5I0 H51 H19 H 0 1 N N N 194.512 210.045 213.287 2.768 1.843 0.222 H51 5I0 60
5I0 H53 H20 H 0 1 N N N 192.058 205.681 208.202 -2.210 -1.224 -1.676 H53 5I0 61
5I0 H61 H21 H 0 1 N N N 192.117 211.545 212.146 3.493 -0.067 -2.045 H61 5I0 62
5I0 H631 H22 H 0 0 N N N 191.655 206.779 206.007 -1.814 -4.124 -0.814 H631 5I0 63
5I0 H632 H23 H 0 0 N N N 193.422 207.063 205.857 -1.575 -3.522 -2.471 H632 5I0 64
5I0 HI33 H24 H 0 0 N N N 196.392 200.981 209.552 -4.833 0.386 2.354 HI33 5I0 65
5I0 HI31 H25 H 0 0 N N N 196.073 201.326 207.819 -6.498 1.001 2.215 HI31 5I0 66
5I0 HI32 H26 H 0 0 N N N 197.040 202.478 208.801 -6.208 -0.740 2.450 HI32 5I0 67
5I0 HN11 H27 H 0 0 N N N 192.753 213.856 211.521 5.846 -1.553 -1.167 HN11 5I0 68
5I0 HN24 H28 H 0 0 N N N 195.084 202.884 210.101 -5.433 0.823 0.088 HN24 5I0 69
5I0 HN23 H29 H 0 0 N N N 194.205 201.837 209.209 -6.707 -0.220 0.177 HN23 5I0 70
5I0 HN31 H30 H 0 0 N N N 193.923 209.155 208.879 1.035 -2.257 1.067 HN31 5I0 71
5I0 HC12 H31 H 0 0 N N N 194.535 216.785 211.430 8.052 -1.220 -1.869 HC12 5I0 72
5I0 HF11 H32 H 0 0 N N N 194.975 208.096 207.152 1.539 -3.700 4.219 HF11 5I0 73
5I0 HO21 H33 H 0 0 N N N 194.852 213.231 209.510 5.405 -2.350 0.994 HO21 5I0 74
5I0 HO32 H34 H 0 0 N N N 191.228 203.937 212.586 -3.211 3.893 -0.496 HO32 5I0 75
5I0 HO33 H35 H 0 0 N N N 193.671 201.386 207.445 -6.331 -2.003 -2.627 HO33 5I0 76
5I0 HO43 H36 H 0 0 N N N 191.654 203.428 205.545 -3.282 -3.435 -3.322 HO43 5I0 77
5I0 HO51 H37 H 0 0 N N N 192.507 209.792 214.445 2.161 2.603 -1.959 HO51 5I0 78
5I0 HO61 H38 H 0 0 N N N 192.391 211.673 214.461 4.048 2.221 -2.447 HO61 5I0 79
5I0 HO63 H39 H 0 0 N N N 192.294 208.871 206.742 0.457 -3.503 -1.216 HO63 5I0 80
5I0 HG2A H40 H 0 0 N N N 195.119 204.863 214.460 -1.815 5.191 2.297 HG2A 5I0 81
5I0 HG2B H41 H 0 0 N N N 193.293 203.533 215.097 -3.790 3.071 2.144 HG2B 5I0 82
5I0 HG21 H42 H 0 0 N N N 194.025 203.524 212.907 -0.888 2.995 2.158 HG21 5I0 83
5I0 HC11 H43 H 0 0 N N N 193.004 215.987 211.294 8.807 0.261 -1.628 HC11 5I0 84
5I0 HF12 H44 H 0 0 N N N 196.633 208.431 206.779 0.618 -3.753 2.815 HF12 5I0 85
#
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
5I0 O43 C43 SING N N 1
5I0 C63 O63 SING N N 2
5I0 C63 C53 SING N N 3
5I0 C43 C53 SING N N 4
5I0 C43 C33 SING N N 5
5I0 O33 C33 SING N N 6
5I0 NF1 CD1 DOUB N N 7
5I0 C53 O53 SING N N 8
5I0 C33 C23 SING N N 9
5I0 O53 C13 SING N N 10
5I0 C23 C13 SING N N 11
5I0 C23 N23 SING N N 12
5I0 CD1 NE1 SING N N 13
5I0 CD1 N31 SING N N 14
5I0 CI3 N23 SING N N 15
5I0 C13 O13 SING N N 16
5I0 N31 C31 SING N N 17
5I0 O21 C21 SING N N 18
5I0 O13 C22 SING N N 19
5I0 C21 C31 SING N N 20
5I0 C21 C11 SING N N 21
5I0 C31 C41 SING N N 22
5I0 C12 C22 SING N N 23
5I0 C12 O42 SING N N 24
5I0 C12 O41 SING N N 25
5I0 C22 C32 SING N N 26
5I0 C41 O41 SING N N 27
5I0 C41 C51 SING N N 28
5I0 NC1 CA1 DOUB N N 29
5I0 O42 C42 SING N N 30
5I0 N11 CA1 SING N N 31
5I0 N11 C11 SING N N 32
5I0 CA1 NB1 SING N N 33
5I0 C11 C61 SING N N 34
5I0 O32 C32 SING N N 35
5I0 C32 C42 SING N N 36
5I0 C32 CG2 SING N N 37
5I0 C61 C51 SING N N 38
5I0 C61 O61 SING N N 39
5I0 C51 O51 SING N N 40
5I0 C42 CH2 SING N N 41
5I0 CG2 OG2A SING N N 42
5I0 CG2 OG2B SING N N 43
5I0 C11 H11 SING N N 44
5I0 C12 H12 SING N N 45
5I0 C13 H13 SING N N 46
5I0 NB1 HB11 SING N N 47
5I0 NB1 HB12 SING N N 48
5I0 NE1 HE12 SING N N 49
5I0 NE1 HE11 SING N N 50
5I0 CH2 HH23 SING N N 51
5I0 CH2 HH22 SING N N 52
5I0 CH2 HH21 SING N N 53
5I0 C21 H21 SING N N 54
5I0 C22 H22 SING N N 55
5I0 C23 H23 SING N N 56
5I0 C31 H31 SING N N 57
5I0 C33 H33 SING N N 58
5I0 C41 H41 SING N N 59
5I0 C42 H42 SING N N 60
5I0 C43 H43 SING N N 61
5I0 C51 H51 SING N N 62
5I0 C53 H53 SING N N 63
5I0 C61 H61 SING N N 64
5I0 C63 H631 SING N N 65
5I0 C63 H632 SING N N 66
5I0 CI3 HI33 SING N N 67
5I0 CI3 HI31 SING N N 68
5I0 CI3 HI32 SING N N 69
5I0 N11 HN11 SING N N 70
5I0 N23 HN24 SING N N 71
5I0 N23 HN23 SING N N 72
5I0 N31 HN31 SING N N 73
5I0 NC1 HC12 SING N N 74
5I0 NF1 HF11 SING N N 75
5I0 O21 HO21 SING N N 76
5I0 O32 HO32 SING N N 77
5I0 O33 HO33 SING N N 78
5I0 O43 HO43 SING N N 79
5I0 O51 HO51 SING N N 80
5I0 O61 HO61 SING N N 81
5I0 O63 HO63 SING N N 82
5I0 OG2A HG2A SING N N 83
5I0 OG2B HG2B SING N N 84
5I0 CG2 HG21 SING N N 85
5I0 NC1 HC11 SING N N 86
5I0 NF1 HF12 SING N N 87
#
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
5I0 InChI InChI 1.03 "InChI=1S/C21H41N7O13/c1-4-21(37,18(35)36)15(41-16-8(26-2)12(33)9(30)5(3-29)39-16)17(38-4)40-14-7(28-20(24)25)10(31)6(27-19(22)23)11(32)13(14)34/h4-18,26,29-37H,3H2,1-2H3,(H4,22,23,27)(H4,24,25,28)/p+3/t4-,5-,6+,7-,8-,9-,10+,11-,12-,13+,14+,15-,16-,17-,21+/m0/s1"
5I0 InChIKey InChI 1.03 ATLHDHNZEMANQF-UQHZJGBMSA-Q
5I0 SMILES_CANONICAL CACTVS 3.385 "C[NH2+][C@H]1[C@H](O)[C@@H](O)[C@H](CO)O[C@H]1O[C@H]2[C@@H](O[C@@H](C)[C@]2(O)C(O)O)O[C@H]3[C@H](O)[C@@H](O)[C@H](NC(N)=[NH2+])[C@@H](O)[C@@H]3NC(N)=[NH2+]"
5I0 SMILES CACTVS 3.385 "C[NH2+][CH]1[CH](O)[CH](O)[CH](CO)O[CH]1O[CH]2[CH](O[CH](C)[C]2(O)C(O)O)O[CH]3[CH](O)[CH](O)[CH](NC(N)=[NH2+])[CH](O)[CH]3NC(N)=[NH2+]"
5I0 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@H]1[C@@]([C@H]([C@@H](O1)O[C@@H]2[C@H]([C@@H]([C@H]([C@@H]([C@H]2O)O)NC(=[NH2+])N)O)NC(=[NH2+])N)O[C@H]3[C@H]([C@@H]([C@H]([C@@H](O3)CO)O)O)[NH2+]C)(C(O)O)O"
5I0 SMILES "OpenEye OEToolkits" 2.0.7 "CC1C(C(C(O1)OC2C(C(C(C(C2O)O)NC(=[NH2+])N)O)NC(=[NH2+])N)OC3C(C(C(C(O3)CO)O)O)[NH2+]C)(C(O)O)O"
#
_pdbx_chem_comp_identifier.comp_id 5I0
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier "[(2~{S},3~{S},4~{S},5~{R},6~{S})-2-[(2~{R},3~{R},4~{R},5~{S})-2-[(1~{R},2~{S},3~{R},4~{R},5~{S},6~{R})-2,4-bis[[azaniumylidene(azanyl)methyl]amino]-3,5,6-tris(oxidanyl)cyclohexyl]oxy-4-[bis(oxidanyl)methyl]-5-methyl-4-oxidanyl-oxolan-3-yl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-methyl-azanium"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
5I0 "Create component" 2021-07-09 PDBE
5I0 "Initial release" 2022-07-27 RCSB
5I0 "Modify synonyms" 2022-11-23 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 5I0
_pdbx_chem_comp_synonyms.name "hydrated form of streptomycin"
_pdbx_chem_comp_synonyms.provenance AUTHOR
_pdbx_chem_comp_synonyms.type ?
#