data_RPO # _chem_comp.id RPO _chem_comp.name "(1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-4-O-benzyl-2-deoxy-alpha-D-glucopyranoside" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C30 H51 N5 O14" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-07-31 _chem_comp.pdbx_modified_date 2013-08-02 _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 705.751 _chem_comp.one_letter_code ? _chem_comp.three_letter_code RPO _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 ? _chem_comp.pdbx_subcomponent_list "YKR CYY BDR IDG" _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.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 RPO C1 C1 C 0 1 N N S 190.255 87.059 -11.126 2.260 -0.995 1.765 C1 YKR 1 RPO O1 O1 O 0 1 N N N 190.932 88.324 -11.034 1.939 -1.460 0.453 O1 YKR 2 RPO C2 C2 C 0 1 N N R 188.865 87.213 -10.475 1.942 0.499 1.870 C2 YKR 3 RPO N2 N2 N 0 1 N N N 188.082 88.225 -11.188 0.525 0.722 1.553 N2 YKR 4 RPO C3 C3 C 0 1 N N R 189.037 87.614 -9.001 2.816 1.270 0.877 C3 YKR 5 RPO O3 O3 O 0 1 N N N 187.753 87.768 -8.372 2.578 2.672 1.020 O3 YKR 6 RPO C4 C4 C 0 1 N N S 189.875 86.543 -8.274 4.289 0.969 1.169 C4 YKR 7 RPO O4 O4 O 0 1 N N N 190.075 86.925 -6.894 5.112 1.626 0.203 O4 YKR 8 RPO C5 C5 C 0 1 N N R 191.258 86.409 -9.007 4.517 -0.543 1.091 C5 YKR 9 RPO O5 O5 O 0 1 N N N 191.041 86.054 -10.423 3.652 -1.203 2.018 O5 YKR 10 RPO C6 C6 C 0 1 N N N 192.133 85.326 -8.322 5.973 -0.858 1.441 C6 YKR 11 RPO O6 O6 O 0 1 N N N 192.709 84.442 -9.290 6.279 -0.327 2.731 O6 YKR 12 RPO CAL CAL C 0 1 Y N N 189.193 86.691 -2.354 7.567 4.834 -1.637 CAL YKR 13 RPO CAM CAM C 0 1 Y N N 188.958 86.378 -3.725 6.855 4.208 -0.631 CAM YKR 14 RPO CAN CAN C 0 1 Y N N 190.536 86.777 -1.865 8.506 4.126 -2.363 CAN YKR 15 RPO CAO CAO C 0 1 Y N N 190.059 86.147 -4.604 7.083 2.873 -0.351 CAO YKR 16 RPO CAP CAP C 0 1 Y N N 191.639 86.546 -2.746 8.733 2.791 -2.083 CAP YKR 17 RPO CAU CAU C 0 1 N N N 189.847 85.852 -5.947 6.307 2.191 0.746 CAU YKR 18 RPO CBC CBC C 0 1 Y N N 191.399 86.233 -4.112 8.022 2.165 -1.077 CBC YKR 19 RPO CBD CBD C 0 1 N N R 193.089 90.683 -13.889 0.994 -5.261 -1.151 C1 CYY 20 RPO CAT CAT C 0 1 N N N 193.840 90.100 -12.677 2.325 -5.095 -0.415 C2 CYY 21 RPO CBE CBE C 0 1 N N S 192.834 89.662 -11.594 2.692 -3.610 -0.353 C3 CYY 22 RPO CBT CBT C 0 1 N N R 191.830 88.632 -12.125 1.597 -2.846 0.394 C4 CYY 23 RPO CBW CBW C 0 1 N N R 191.047 89.235 -13.290 0.266 -3.012 -0.341 C5 CYY 24 RPO CBI CBI C 0 1 N N S 192.115 89.600 -14.435 -0.101 -4.496 -0.403 C6 CYY 25 RPO NAB NAB N 0 1 N N N 194.071 91.081 -14.898 0.642 -6.686 -1.211 N1 CYY 26 RPO NAC NAC N 0 1 N N N 193.563 89.079 -10.463 3.970 -3.451 0.353 N3 CYY 27 RPO "O1'" "O1'" O 0 1 N N N 190.100 88.187 -13.687 -0.756 -2.298 0.357 O5 CYY 28 RPO OAH OAH O 0 1 N N N 191.490 90.170 -15.576 -1.344 -4.651 -1.090 O6 CYY 29 RPO "C4'" "C4'" C 0 1 N N R 186.846 88.077 -14.706 -2.483 -0.006 -1.737 C4 BDR 30 RPO "O4'" "O4'" O 0 1 N N N 187.903 88.699 -13.955 -1.308 -0.736 -1.322 O BDR 31 RPO "C1'" "C1'" C 0 1 N N S 189.128 88.526 -14.658 -1.800 -1.805 -0.486 C1 BDR 32 RPO "C2'" "C2'" C 0 1 N N R 188.904 87.384 -15.628 -2.917 -1.160 0.364 C2 BDR 33 RPO "O2'" "O2'" O 0 1 N N N 189.780 87.542 -16.724 -3.996 -2.077 0.552 O2 BDR 34 RPO "C3'" "C3'" C 0 1 N N S 187.439 87.523 -16.001 -3.377 0.051 -0.478 C3 BDR 35 RPO "O3'" "O3'" O 0 1 N N N 187.306 88.536 -17.057 -4.754 -0.081 -0.836 O3 BDR 36 RPO "C5'" "C5'" C 0 1 N N N 186.250 86.960 -13.847 -2.102 1.407 -2.184 C5 BDR 37 RPO "O5'" "O5'" O 0 1 N N N 185.718 87.534 -12.645 -1.312 1.334 -3.372 O5 BDR 38 RPO CBM CBM C 0 1 N N S 183.558 88.660 -17.466 -6.383 2.649 0.930 C5 IDG 39 RPO OAV OAV O 0 1 N N N 184.873 88.678 -16.798 -5.538 1.944 0.018 O5 IDG 40 RPO CBQ CBQ C 0 1 N N R 186.011 88.514 -17.733 -5.656 0.522 0.094 C1 IDG 41 RPO CBF CBF C 0 1 N N R 185.989 89.628 -18.822 -7.091 0.112 -0.248 C2 IDG 42 RPO NAD NAD N 0 1 N N N 186.210 90.937 -18.167 -7.400 0.511 -1.628 N2 IDG 43 RPO CBH CBH C 0 1 N N R 184.613 89.622 -19.544 -8.057 0.810 0.714 C3 IDG 44 RPO OAG OAG O 0 1 N N N 184.429 88.348 -20.200 -7.799 0.373 2.050 O3 IDG 45 RPO CBJ CBJ C 0 1 N N S 183.470 89.791 -18.522 -7.847 2.324 0.622 C4 IDG 46 RPO OAI OAI O 0 1 N N N 183.593 91.048 -17.854 -8.168 2.771 -0.698 O4 IDG 47 RPO CAQ CAQ C 0 1 N N N 182.414 88.833 -16.455 -6.152 4.154 0.781 C6 IDG 48 RPO NAA NAA N 0 1 N N N 182.881 88.617 -15.068 -4.747 4.465 1.076 N6 IDG 49 RPO H1 H1 H 0 1 N N N 190.126 86.769 -12.179 1.672 -1.545 2.500 H1 YKR 50 RPO H2 H2 H 0 1 N N N 188.346 86.244 -10.519 2.147 0.845 2.884 H2 YKR 51 RPO HN2 HN2 H 0 1 N N N 187.184 88.316 -10.758 -0.072 0.218 2.192 HN2 YKR 52 RPO HN2A HN2A H 0 0 N N N 188.560 89.103 -11.151 0.305 1.706 1.553 HN2A YKR 53 RPO H3 H3 H 0 1 N N N 189.585 88.567 -8.963 2.573 0.961 -0.139 H3 YKR 54 RPO HO3 HO3 H 0 1 N N N 187.873 88.016 -7.463 1.662 2.934 0.856 HO3 YKR 55 RPO H4 H4 H 0 1 N N N 189.351 85.578 -8.332 4.543 1.325 2.167 H4 YKR 56 RPO H5 H5 H 0 1 N N N 191.780 87.375 -8.944 4.302 -0.892 0.081 H5 YKR 57 RPO H6 H6 H 0 1 N N N 192.940 85.819 -7.760 6.120 -1.938 1.448 H6 YKR 58 RPO H6A H6A H 0 1 N N N 191.507 84.743 -7.630 6.631 -0.408 0.697 H6A YKR 59 RPO HO6 HO6 H 0 1 N N N 193.239 83.789 -8.848 7.188 -0.490 3.019 HO6 YKR 60 RPO HAL HAL H 0 1 N N N 188.361 86.863 -1.687 7.386 5.876 -1.859 HAL YKR 61 RPO HAM HAM H 0 1 N N N 187.947 86.316 -4.099 6.121 4.761 -0.064 HAM YKR 62 RPO HAN HAN H 0 1 N N N 190.717 87.017 -0.828 9.062 4.615 -3.149 HAN YKR 63 RPO HAP HAP H 0 1 N N N 192.651 86.609 -2.375 9.467 2.238 -2.651 HAP YKR 64 RPO HAU HAU H 0 1 N N N 188.801 85.528 -6.056 6.049 2.918 1.515 HAU YKR 65 RPO HAUA HAUA H 0 0 N N N 190.518 85.022 -6.216 6.916 1.400 1.184 HAUA YKR 66 RPO HBC HBC H 0 1 N N N 192.230 86.060 -4.779 8.200 1.123 -0.859 HBC YKR 67 RPO HBD HBD H 0 1 N N N 192.505 91.556 -13.564 1.086 -4.866 -2.163 H1 CYY 68 RPO HAT HAT H 0 1 N N N 194.431 89.230 -12.999 2.233 -5.489 0.597 H21 CYY 69 RPO HATA HATA H 0 0 N N N 194.512 90.866 -12.262 3.105 -5.639 -0.948 H22 CYY 70 RPO HBE HBE H 0 1 N N N 192.279 90.549 -11.254 2.784 -3.216 -1.365 H3 CYY 71 RPO HBT HBT H 0 1 N N N 192.365 87.731 -12.461 1.505 -3.240 1.406 H4 CYY 72 RPO HBW HBW H 0 1 N N N 190.524 90.149 -12.971 0.358 -2.618 -1.353 H5 CYY 73 RPO HBI HBI H 0 1 N N N 192.681 88.694 -14.696 -0.193 -4.891 0.609 H6 CYY 74 RPO HNAC HNAC H 0 0 N N N 193.598 91.462 -15.692 1.350 -7.213 -1.700 HN11 CYY 75 RPO HNAD HNAD H 0 0 N N N 194.684 91.771 -14.513 0.488 -7.059 -0.286 HN12 CYY 76 RPO HNAE HNAE H 0 0 N N N 192.913 88.794 -9.758 4.680 -4.048 -0.044 HN31 CYY 77 RPO HNAF HNAF H 0 0 N N N 194.085 88.285 -10.776 4.266 -2.487 0.351 HN32 CYY 78 RPO HOAH HOAH H 0 0 N N N 190.881 89.544 -15.950 -1.639 -5.569 -1.168 HO6 CYY 79 RPO "H4'" "H4'" H 0 1 N N N 186.061 88.808 -14.948 -2.993 -0.533 -2.543 H4 BDR 80 RPO "H1'" "H1'" H 0 1 N N N 189.407 89.437 -15.207 -2.206 -2.611 -1.097 H1 BDR 81 RPO "H2'" "H2'" H 0 1 N N N 189.069 86.423 -15.118 -2.524 -0.831 1.326 H2 BDR 82 RPO "HO2'" "HO2'" H 0 0 N N N 189.649 86.831 -17.340 -3.749 -2.885 1.023 HO2 BDR 83 RPO "H3'" "H3'" H 0 1 N N N 186.990 86.558 -16.277 -3.213 0.980 0.068 H3 BDR 84 RPO "H5'" "H5'" H 0 1 N N N 185.446 86.455 -14.403 -3.007 1.981 -2.384 H51 BDR 85 RPO "H5'A" "H5'A" H 0 0 N N N 187.034 86.231 -13.593 -1.529 1.895 -1.396 H52 BDR 86 RPO "HO5'" "HO5'" H 0 0 N N N 185.345 86.848 -12.104 -1.034 2.195 -3.714 H5 BDR 87 RPO HBM HBM H 0 1 N N N 183.426 87.697 -17.980 -6.151 2.345 1.951 H5 IDG 88 RPO HBQ HBQ H 0 1 N N N 185.900 87.548 -18.248 -5.414 0.190 1.103 H1 IDG 89 RPO HBF HBF H 0 1 N N N 186.784 89.431 -19.556 -7.195 -0.969 -0.149 H2 IDG 90 RPO HNAG HNAG H 0 0 N N N 187.097 90.933 -17.705 -6.776 0.063 -2.282 HN21 IDG 91 RPO HNAH HNAH H 0 0 N N N 186.197 91.661 -18.857 -8.363 0.313 -1.854 HN22 IDG 92 RPO HBH HBH H 0 1 N N N 184.580 90.446 -20.272 -9.084 0.566 0.441 H3 IDG 93 RPO HOAG HOAG H 0 0 N N N 183.589 88.338 -20.644 -8.376 0.775 2.714 HO3 IDG 94 RPO HBJ HBJ H 0 1 N N N 182.505 89.720 -19.045 -8.492 2.826 1.344 H4 IDG 95 RPO HOAI HOAI H 0 0 N N N 182.886 91.144 -17.227 -9.081 2.593 -0.962 HO4 IDG 96 RPO HAQ HAQ H 0 1 N N N 181.622 88.105 -16.683 -6.384 4.458 -0.240 H61 IDG 97 RPO HAQA HAQA H 0 0 N N N 182.011 89.853 -16.542 -6.797 4.692 1.476 H62 IDG 98 RPO HNAA HNAA H 0 0 N N N 182.116 88.736 -14.436 -4.127 3.930 0.488 HN61 IDG 99 RPO HNAB HNAB H 0 0 N N N 183.245 87.690 -14.980 -4.568 5.454 0.984 HN62 IDG 100 # 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 RPO C1 O1 SING N N 1 RPO C1 C2 SING N N 2 RPO C1 O5 SING N N 3 RPO O1 CBT SING N N 4 RPO C2 N2 SING N N 5 RPO C2 C3 SING N N 6 RPO C3 O3 SING N N 7 RPO C3 C4 SING N N 8 RPO C4 O4 SING N N 9 RPO C4 C5 SING N N 10 RPO O4 CAU SING N N 11 RPO C5 O5 SING N N 12 RPO C5 C6 SING N N 13 RPO C6 O6 SING N N 14 RPO "C1'" "O1'" SING N N 15 RPO "C1'" "C2'" SING N N 16 RPO "C1'" "O4'" SING N N 17 RPO "O1'" CBW SING N N 18 RPO "C2'" "O2'" SING N N 19 RPO "C2'" "C3'" SING N N 20 RPO "C3'" "O3'" SING N N 21 RPO "C3'" "C4'" SING N N 22 RPO "O3'" CBQ SING N N 23 RPO "C4'" "O4'" SING N N 24 RPO "C4'" "C5'" SING N N 25 RPO "C5'" "O5'" SING N N 26 RPO NAA CAQ SING N N 27 RPO NAB CBD SING N N 28 RPO NAC CBE SING N N 29 RPO NAD CBF SING N N 30 RPO OAG CBH SING N N 31 RPO OAH CBI SING N N 32 RPO OAI CBJ SING N N 33 RPO CAL CAM DOUB Y N 34 RPO CAL CAN SING Y N 35 RPO CAM CAO SING Y N 36 RPO CAN CAP DOUB Y N 37 RPO CAO CAU SING N N 38 RPO CAO CBC DOUB Y N 39 RPO CAP CBC SING Y N 40 RPO CAQ CBM SING N N 41 RPO CAT CBD SING N N 42 RPO CAT CBE SING N N 43 RPO OAV CBM SING N N 44 RPO OAV CBQ SING N N 45 RPO CBD CBI SING N N 46 RPO CBE CBT SING N N 47 RPO CBF CBH SING N N 48 RPO CBF CBQ SING N N 49 RPO CBH CBJ SING N N 50 RPO CBI CBW SING N N 51 RPO CBJ CBM SING N N 52 RPO CBT CBW SING N N 53 RPO C1 H1 SING N N 54 RPO C2 H2 SING N N 55 RPO N2 HN2 SING N N 56 RPO N2 HN2A SING N N 57 RPO C3 H3 SING N N 58 RPO O3 HO3 SING N N 59 RPO C4 H4 SING N N 60 RPO C5 H5 SING N N 61 RPO C6 H6 SING N N 62 RPO C6 H6A SING N N 63 RPO O6 HO6 SING N N 64 RPO "C1'" "H1'" SING N N 65 RPO "C2'" "H2'" SING N N 66 RPO "O2'" "HO2'" SING N N 67 RPO "C3'" "H3'" SING N N 68 RPO "C4'" "H4'" SING N N 69 RPO "C5'" "H5'" SING N N 70 RPO "C5'" "H5'A" SING N N 71 RPO "O5'" "HO5'" SING N N 72 RPO NAA HNAA SING N N 73 RPO NAA HNAB SING N N 74 RPO NAB HNAC SING N N 75 RPO NAB HNAD SING N N 76 RPO NAC HNAE SING N N 77 RPO NAC HNAF SING N N 78 RPO NAD HNAG SING N N 79 RPO NAD HNAH SING N N 80 RPO OAG HOAG SING N N 81 RPO OAH HOAH SING N N 82 RPO OAI HOAI SING N N 83 RPO CAL HAL SING N N 84 RPO CAM HAM SING N N 85 RPO CAN HAN SING N N 86 RPO CAP HAP SING N N 87 RPO CAQ HAQ SING N N 88 RPO CAQ HAQA SING N N 89 RPO CAT HAT SING N N 90 RPO CAT HATA SING N N 91 RPO CAU HAU SING N N 92 RPO CAU HAUA SING N N 93 RPO CBC HBC SING N N 94 RPO CBD HBD SING N N 95 RPO CBE HBE SING N N 96 RPO CBF HBF SING N N 97 RPO CBH HBH SING N N 98 RPO CBI HBI SING N N 99 RPO CBJ HBJ SING N N 100 RPO CBM HBM SING N N 101 RPO CBQ HBQ SING N N 102 RPO CBT HBT SING N N 103 RPO CBW HBW SING N N 104 # 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 RPO InChI InChI 1.03 ;InChI=1S/C30H51N5O14/c31-7-14-20(39)21(40)17(34)28(44-14)48-26-16(9-37)46-30(23(26)42)49-27-19(38)12(32)6-13(33)24(27)47-29-18(35)22(41)25(15(8-36)45-29)43-10-11-4-2-1-3-5-11/h1-5,12-30,36-42H,6-10,31-35H2/t12-,13+,14+,15-,16-,17-,18-,19+,20-,21-,22-,23-,24-,25-,26-,27-,28-,29-,30+/m1/s1 ; RPO InChIKey InChI 1.03 DRHDMQJFWDZMND-JCNXQQRHSA-N RPO SMILES ACDLabs 12.01 "O(C3C(OC2OC(CO)C(OCc1ccccc1)C(O)C2N)C(N)CC(N)C3O)C5OC(C(OC4OC(CN)C(O)C(O)C4N)C5O)CO" RPO SMILES_CANONICAL CACTVS 3.370 "NC[C@@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@@H](O[C@@H]3[C@@H](O)[C@H](N)C[C@H](N)[C@H]3O[C@H]4O[C@H](CO)[C@@H](OCc5ccccc5)[C@H](O)[C@H]4N)[C@@H]2O)[C@H](N)[C@@H](O)[C@@H]1O" RPO SMILES CACTVS 3.370 "NC[CH]1O[CH](O[CH]2[CH](CO)O[CH](O[CH]3[CH](O)[CH](N)C[CH](N)[CH]3O[CH]4O[CH](CO)[CH](OCc5ccccc5)[CH](O)[CH]4N)[CH]2O)[CH](N)[CH](O)[CH]1O" RPO SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1ccc(cc1)CO[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)N)O[C@@H]3[C@H](C[C@H]([C@@H]([C@H]3O[C@H]4[C@@H]([C@@H]([C@H](O4)CO)O[C@@H]5[C@@H]([C@H]([C@@H]([C@@H](O5)CN)O)O)N)O)O)N)N)CO" RPO SMILES "OpenEye OEToolkits" 1.7.6 "c1ccc(cc1)COC2C(OC(C(C2O)N)OC3C(CC(C(C3OC4C(C(C(O4)CO)OC5C(C(C(C(O5)CN)O)O)N)O)O)N)N)CO" # 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 RPO "SYSTEMATIC NAME" ACDLabs 12.01 "(1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-4-O-benzyl-2-deoxy-alpha-D-glucopyranoside" RPO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 ;(2S,3S,4R,5R,6R)-2-(aminomethyl)-5-azanyl-6-[(2R,3S,4R,5S)-5-[(1R,2R,3S,5R,6S)-3,5-bis(azanyl)-2-[(2S,3R,4R,5S,6R)-3-azanyl-6-(hydroxymethyl)-4-oxidanyl-5-phenylmethoxy-oxan-2-yl]oxy-6-oxidanyl-cyclohexyl]oxy-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]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 RPO "Create component" 2012-07-31 EBI RPO "Initial release" 2013-08-07 RCSB #