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.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
RPO C1 C1 C 0 1 N N S N N N 190.255 87.059 -11.126 2.260 -0.995 1.765 C1 YKR 1
RPO O1 O1 O 0 1 N N N 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 N N N 188.865 87.213 -10.475 1.942 0.499 1.870 C2 YKR 3
RPO N2 N2 N 0 1 N N N 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 N N N 189.037 87.614 -9.001 2.816 1.270 0.877 C3 YKR 5
RPO O3 O3 O 0 1 N N N 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 N N N 189.875 86.543 -8.274 4.289 0.969 1.169 C4 YKR 7
RPO O4 O4 O 0 1 N N N 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 N N N 191.258 86.409 -9.007 4.517 -0.543 1.091 C5 YKR 9
RPO O5 O5 O 0 1 N N N 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 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 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 N 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 N 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 N 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 N 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 N 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 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 N 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 N N N 193.089 90.683 -13.889 0.994 -5.261 -1.151 C1 CYY 20
RPO CAT CAT C 0 1 N N N 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 N N N 192.834 89.662 -11.594 2.692 -3.610 -0.353 C3 CYY 22
RPO CBT CBT C 0 1 N N R N N N 191.830 88.632 -12.125 1.597 -2.846 0.394 C4 CYY 23
RPO CBW CBW C 0 1 N N R N N N 191.047 89.235 -13.290 0.266 -3.012 -0.341 C5 CYY 24
RPO CBI CBI C 0 1 N N S N N N 192.115 89.600 -14.435 -0.101 -4.496 -0.403 C6 CYY 25
RPO NAB NAB N 0 1 N N N 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 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 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 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 N N N 186.846 88.077 -14.706 -2.483 -0.006 -1.737 C4 BDR 30
RPO "O4'" "O4'" O 0 1 N N N 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 N N N 189.128 88.526 -14.658 -1.800 -1.805 -0.486 C1 BDR 32
RPO "C2'" "C2'" C 0 1 N N R N N N 188.904 87.384 -15.628 -2.917 -1.160 0.364 C2 BDR 33
RPO "O2'" "O2'" O 0 1 N N N 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 N N N 187.439 87.523 -16.001 -3.377 0.051 -0.478 C3 BDR 35
RPO "O3'" "O3'" O 0 1 N N N 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 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 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 N N N 183.558 88.660 -17.466 -6.383 2.649 0.930 C5 IDG 39
RPO OAV OAV O 0 1 N N N 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 N N N 186.011 88.514 -17.733 -5.656 0.522 0.094 C1 IDG 41
RPO CBF CBF C 0 1 N N R N N N 185.989 89.628 -18.822 -7.091 0.112 -0.248 C2 IDG 42
RPO NAD NAD N 0 1 N N N 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 N N N 184.613 89.622 -19.544 -8.057 0.810 0.714 C3 IDG 44
RPO OAG OAG O 0 1 N N N 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 N N N 183.470 89.791 -18.522 -7.847 2.324 0.622 C4 IDG 46
RPO OAI OAI O 0 1 N N N 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
#
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
RPO C1 C 12.093 -1.126 1
RPO O1 O 13.392 -0.376 2
RPO C2 C 12.093 -2.626 3
RPO N2 N 13.392 -3.376 4
RPO C3 C 10.794 -3.376 5
RPO O3 O 10.794 -4.876 6
RPO C4 C 9.495 -2.626 7
RPO O4 O 8.196 -3.376 8
RPO C5 C 9.495 -1.126 9
RPO O5 O 10.794 -0.376 10
RPO C6 C 8.196 -0.376 11
RPO O6 O 8.196 1.124 12
RPO CAL C 3.000 -3.376 13
RPO CAM C 4.299 -2.626 14
RPO CAN C 3.000 -4.876 15
RPO CAO C 5.598 -3.376 16
RPO CAP C 4.299 -5.626 17
RPO CAU C 6.897 -2.626 18
RPO CBC C 5.598 -4.876 19
RPO CBD C 15.642 3.521 20
RPO CAT C 14.142 3.521 21
RPO CBE C 13.392 2.222 22
RPO CBT C 14.142 0.923 23
RPO CBW C 15.642 0.923 24
RPO CBI C 16.392 2.222 25
RPO NAB N 16.392 4.820 26
RPO NAC N 11.892 2.222 27
RPO "O1'" O 16.392 -0.376 28
RPO OAH O 17.892 2.222 29
RPO "C4'" C 20.201 0.374 30
RPO "O4'" O 18.774 0.838 31
RPO "C1'" C 17.892 -0.376 32
RPO "C2'" C 18.774 -1.589 33
RPO "O2'" O 18.311 -3.016 34
RPO "C3'" C 20.201 -1.126 35
RPO "O3'" O 21.414 -2.007 36
RPO "C5'" C 21.414 1.256 37
RPO "O5'" O 21.257 2.748 38
RPO CBM C 24.311 0.705 39
RPO OAV O 22.941 0.095 40
RPO CBQ C 22.784 -1.397 41
RPO CBF C 23.998 -2.279 42
RPO NAD N 23.841 -3.771 43
RPO CBH C 25.368 -1.669 44
RPO OAG O 26.582 -2.551 45
RPO CBJ C 25.525 -0.177 46
RPO OAI O 26.895 0.433 47
RPO CAQ C 24.468 2.196 48
RPO NAA N 25.839 2.807 49
#
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
RPO C1 O1 SINGLE BEGINDASH 1
RPO C1 C2 SINGLE NONE 2
RPO C1 O5 SINGLE NONE 3
RPO CBT O1 SINGLE BEGINDASH 4
RPO C2 N2 SINGLE BEGINDASH 5
RPO C2 C3 SINGLE NONE 6
RPO C3 O3 SINGLE BEGINWEDGE 7
RPO C3 C4 SINGLE NONE 8
RPO C4 O4 SINGLE BEGINDASH 9
RPO C4 C5 SINGLE NONE 10
RPO O4 CAU SINGLE NONE 11
RPO C5 O5 SINGLE NONE 12
RPO C5 C6 SINGLE BEGINWEDGE 13
RPO C6 O6 SINGLE NONE 14
RPO "C1'" "O1'" SINGLE BEGINDASH 15
RPO "C1'" "C2'" SINGLE NONE 16
RPO "C1'" "O4'" SINGLE NONE 17
RPO CBW "O1'" SINGLE BEGINWEDGE 18
RPO "C2'" "O2'" SINGLE BEGINWEDGE 19
RPO "C2'" "C3'" SINGLE NONE 20
RPO "C3'" "O3'" SINGLE BEGINWEDGE 21
RPO "C3'" "C4'" SINGLE NONE 22
RPO CBQ "O3'" SINGLE BEGINWEDGE 23
RPO "C4'" "O4'" SINGLE NONE 24
RPO "C4'" "C5'" SINGLE BEGINDASH 25
RPO "C5'" "O5'" SINGLE NONE 26
RPO NAA CAQ SINGLE NONE 27
RPO CBD NAB SINGLE BEGINWEDGE 28
RPO CBE NAC SINGLE BEGINWEDGE 29
RPO CBF NAD SINGLE BEGINWEDGE 30
RPO CBH OAG SINGLE BEGINDASH 31
RPO CBI OAH SINGLE BEGINDASH 32
RPO CBJ OAI SINGLE BEGINWEDGE 33
RPO CAL CAM DOUBLE NONE 34
RPO CAL CAN SINGLE NONE 35
RPO CAM CAO SINGLE NONE 36
RPO CAN CAP DOUBLE NONE 37
RPO CAO CAU SINGLE NONE 38
RPO CAO CBC DOUBLE NONE 39
RPO CAP CBC SINGLE NONE 40
RPO CBM CAQ SINGLE BEGINWEDGE 41
RPO CAT CBD SINGLE NONE 42
RPO CAT CBE SINGLE NONE 43
RPO OAV CBM SINGLE NONE 44
RPO OAV CBQ SINGLE NONE 45
RPO CBD CBI SINGLE NONE 46
RPO CBE CBT SINGLE NONE 47
RPO CBF CBH SINGLE NONE 48
RPO CBF CBQ SINGLE NONE 49
RPO CBH CBJ SINGLE NONE 50
RPO CBI CBW SINGLE NONE 51
RPO CBJ CBM SINGLE NONE 52
RPO CBT CBW SINGLE NONE 53
#
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
RPO MurckoScaffold S1 scaffold 'c1ccc(CO[C@H]2CC[C@@H](O[C@@H]3CCCC[C@H]3O[C@H]3C[C@H](O[C@@H]4CCCCO4)CO3)OC2)cc1' InChI=1S/C27H40O7/c1-2-8-20(9-3-1)17-29-21-13-14-26(30-18-21)33-23-10-4-5-11-24(23)34-27-16-22(19-31-27)32-25-12-6-7-15-28-25/h1-3,8-9,21-27H,4-7,10-19H2/t21-,22-,23+,24+,25+,26+,27-/m0/s1 RYIUORNZYNVTGO-VMZVVKDESA-N
RPO cyclohexane F1 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N
RPO furanose F2 fragment OC1CCCO1 InChI=1S/C4H8O2/c5-4-2-1-3-6-4/h4-5H,1-3H2 JNODDICFTDYODH-UHFFFAOYSA-N
RPO phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
RPO pyranose F4 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N
RPO ribose F5 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
RPO C1 S1 1
RPO O1 S1 1
RPO C2 S1 1
RPO C3 S1 1
RPO C4 S1 1
RPO O4 S1 1
RPO C5 S1 1
RPO O5 S1 1
RPO CAL S1 1
RPO CAM S1 1
RPO CAN S1 1
RPO CAO S1 1
RPO CAP S1 1
RPO CAU S1 1
RPO CBC S1 1
RPO CBD S1 1
RPO CAT S1 1
RPO CBE S1 1
RPO CBT S1 1
RPO CBW S1 1
RPO CBI S1 1
RPO "O1'" S1 1
RPO "C4'" S1 1
RPO "O4'" S1 1
RPO "C1'" S1 1
RPO "C2'" S1 1
RPO "C3'" S1 1
RPO "O3'" S1 1
RPO CBM S1 1
RPO OAV S1 1
RPO CBQ S1 1
RPO CBF S1 1
RPO CBH S1 1
RPO CBJ S1 1
RPO CBD F1 1
RPO CAT F1 1
RPO CBE F1 1
RPO CBT F1 1
RPO CBW F1 1
RPO CBI F1 1
RPO "C3'" F2 1
RPO "C4'" F2 1
RPO "O4'" F2 1
RPO "C1'" F2 1
RPO "C2'" F2 1
RPO "O1'" F2 1
RPO CAL F3 1
RPO CAM F3 1
RPO CAO F3 1
RPO CBC F3 1
RPO CAP F3 1
RPO CAN F3 1
RPO C4 F4 1
RPO C5 F4 1
RPO O5 F4 1
RPO C1 F4 1
RPO C2 F4 1
RPO C3 F4 1
RPO O1 F4 1
RPO CBJ F4 2
RPO CBM F4 2
RPO OAV F4 2
RPO CBQ F4 2
RPO CBF F4 2
RPO CBH F4 2
RPO "O3'" F4 2
RPO "C2'" F5 1
RPO "C3'" F5 1
RPO "C4'" F5 1
RPO "O4'" F5 1
RPO "C1'" F5 1
RPO "C5'" F5 1
RPO "O5'" F5 1
RPO "O3'" F5 1
RPO "O2'" F5 1
#
_pdbe_chem_comp_rdkit_properties.comp_id RPO
_pdbe_chem_comp_rdkit_properties.exactmw 705.343
_pdbe_chem_comp_rdkit_properties.amw 705.759
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 19
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 17
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 24
_pdbe_chem_comp_rdkit_properties.NumHBD 12
_pdbe_chem_comp_rdkit_properties.NumHBA 19
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 49
_pdbe_chem_comp_rdkit_properties.NumAtoms 100
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 19
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.800
_pdbe_chem_comp_rdkit_properties.NumRings 5
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 4
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 4
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 19
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 355.061
_pdbe_chem_comp_rdkit_properties.tpsa 336.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP -6.692
_pdbe_chem_comp_rdkit_properties.CrippenMR 165.134
_pdbe_chem_comp_rdkit_properties.chi0v 22.952
_pdbe_chem_comp_rdkit_properties.chi1v 12.155
_pdbe_chem_comp_rdkit_properties.chi2v 5.530
_pdbe_chem_comp_rdkit_properties.chi3v 5.530
_pdbe_chem_comp_rdkit_properties.chi4v 3.374
_pdbe_chem_comp_rdkit_properties.chi0n 73.952
_pdbe_chem_comp_rdkit_properties.chi1n 36.485
_pdbe_chem_comp_rdkit_properties.chi2n 5.530
_pdbe_chem_comp_rdkit_properties.chi3n 5.530
_pdbe_chem_comp_rdkit_properties.chi4n 3.374
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.540
_pdbe_chem_comp_rdkit_properties.kappa1 9.758
_pdbe_chem_comp_rdkit_properties.kappa2 16.862
_pdbe_chem_comp_rdkit_properties.kappa3 8.257
_pdbe_chem_comp_rdkit_properties.Phi 3.358
#
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
RPO UniChem ZINC ZINC000098209374
RPO UniChem PubChem 71627367
#
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
RPO C1 -2.800 1.255 -1.057 ETKDGv3 1
RPO O1 -2.633 2.588 -0.608 ETKDGv3 2
RPO C2 -3.759 1.252 -2.264 ETKDGv3 3
RPO N2 -5.038 1.903 -1.954 ETKDGv3 4
RPO C3 -3.990 -0.193 -2.752 ETKDGv3 5
RPO O3 -2.845 -0.663 -3.418 ETKDGv3 6
RPO C4 -4.332 -1.145 -1.586 ETKDGv3 7
RPO O4 -5.686 -0.932 -1.205 ETKDGv3 8
RPO C5 -3.428 -0.906 -0.344 ETKDGv3 9
RPO O5 -3.326 0.468 0.002 ETKDGv3 10
RPO C6 -2.051 -1.599 -0.421 ETKDGv3 11
RPO O6 -2.210 -2.988 -0.322 ETKDGv3 12
RPO CAL -6.371 -3.531 2.166 ETKDGv3 13
RPO CAM -6.633 -2.705 1.146 ETKDGv3 14
RPO CAN -5.668 -4.807 1.923 ETKDGv3 15
RPO CAO -6.220 -3.065 -0.233 ETKDGv3 16
RPO CAP -5.290 -5.138 0.682 ETKDGv3 17
RPO CAU -6.472 -2.099 -1.360 ETKDGv3 18
RPO CBC -5.575 -4.227 -0.446 ETKDGv3 19
RPO CBD -1.429 5.426 -0.532 ETKDGv3 20
RPO CAT -1.407 5.201 0.984 ETKDGv3 21
RPO CBE -1.850 3.765 1.362 ETKDGv3 22
RPO CBT -1.517 2.709 0.265 ETKDGv3 23
RPO CBW -0.252 3.099 -0.548 ETKDGv3 24
RPO CBI -0.408 4.489 -1.239 ETKDGv3 25
RPO NAB -1.155 6.834 -0.832 ETKDGv3 26
RPO NAC -1.237 3.386 2.639 ETKDGv3 27
RPO "O1'" 0.873 3.141 0.319 ETKDGv3 28
RPO OAH -0.743 4.341 -2.598 ETKDGv3 29
RPO "C4'" 3.260 1.085 1.653 ETKDGv3 30
RPO "O4'" 2.008 1.737 1.739 ETKDGv3 31
RPO "C1'" 1.502 1.875 0.433 ETKDGv3 32
RPO "C2'" 2.671 1.777 -0.530 ETKDGv3 33
RPO "O2'" 2.261 1.297 -1.784 ETKDGv3 34
RPO "C3'" 3.588 0.812 0.178 ETKDGv3 35
RPO "O3'" 3.219 -0.521 -0.152 ETKDGv3 36
RPO "C5'" 4.323 1.961 2.327 ETKDGv3 37
RPO "O5'" 5.543 1.276 2.388 ETKDGv3 38
RPO CBM 6.219 -2.160 0.895 ETKDGv3 39
RPO OAV 5.007 -1.435 1.009 ETKDGv3 40
RPO CBQ 4.350 -1.365 -0.248 ETKDGv3 41
RPO CBF 3.881 -2.775 -0.690 ETKDGv3 42
RPO NAD 2.787 -3.270 0.155 ETKDGv3 43
RPO CBH 5.055 -3.786 -0.681 ETKDGv3 44
RPO OAG 5.831 -3.676 -1.850 ETKDGv3 45
RPO CBJ 5.936 -3.651 0.586 ETKDGv3 46
RPO OAI 5.287 -4.254 1.678 ETKDGv3 47
RPO CAQ 7.051 -1.978 2.178 ETKDGv3 48
RPO NAA 6.273 -2.289 3.376 ETKDGv3 49
RPO H1 -1.822 0.857 -1.407 ETKDGv3 50
RPO H2 -3.278 1.821 -3.091 ETKDGv3 51
RPO HN2 -5.383 1.599 -1.015 ETKDGv3 52
RPO HN2A -4.882 2.936 -1.899 ETKDGv3 53
RPO H3 -4.846 -0.202 -3.468 ETKDGv3 54
RPO HO3 -2.834 -0.235 -4.314 ETKDGv3 55
RPO H4 -4.144 -2.186 -1.948 ETKDGv3 56
RPO H5 -3.943 -1.391 0.514 ETKDGv3 57
RPO H6 -1.420 -1.241 0.423 ETKDGv3 58
RPO H6A -1.529 -1.360 -1.371 ETKDGv3 59
RPO HO6 -1.297 -3.374 -0.353 ETKDGv3 60
RPO HAL -6.671 -3.266 3.171 ETKDGv3 61
RPO HAM -7.143 -1.768 1.331 ETKDGv3 62
RPO HAN -5.458 -5.473 2.750 ETKDGv3 63
RPO HAP -4.772 -6.071 0.502 ETKDGv3 64
RPO HAU -6.329 -2.565 -2.363 ETKDGv3 65
RPO HAUA -7.540 -1.798 -1.321 ETKDGv3 66
RPO HBC -5.246 -4.504 -1.440 ETKDGv3 67
RPO HBD -2.458 5.197 -0.891 ETKDGv3 68
RPO HAT -0.376 5.394 1.360 ETKDGv3 69
RPO HATA -2.082 5.932 1.480 ETKDGv3 70
RPO HBE -2.956 3.778 1.501 ETKDGv3 71
RPO HBT -1.313 1.744 0.789 ETKDGv3 72
RPO HBW -0.097 2.354 -1.363 ETKDGv3 73
RPO HBI 0.591 4.979 -1.214 ETKDGv3 74
RPO HNAC -1.206 6.971 -1.868 ETKDGv3 75
RPO HNAD -0.182 7.074 -0.531 ETKDGv3 76
RPO HNAE -1.668 2.489 2.961 ETKDGv3 77
RPO HNAF -1.501 4.099 3.358 ETKDGv3 78
RPO HOAH -1.613 3.867 -2.644 ETKDGv3 79
RPO "H4'" 3.194 0.129 2.218 ETKDGv3 80
RPO "H1'" 0.802 1.020 0.263 ETKDGv3 81
RPO "H2'" 3.164 2.773 -0.632 ETKDGv3 82
RPO "HO2'" 3.042 1.390 -2.388 ETKDGv3 83
RPO "H3'" 4.645 1.060 -0.087 ETKDGv3 84
RPO "H5'" 4.446 2.911 1.758 ETKDGv3 85
RPO "H5'A" 3.987 2.208 3.359 ETKDGv3 86
RPO "HO5'" 6.184 1.893 2.826 ETKDGv3 87
RPO HBM 6.848 -1.737 0.078 ETKDGv3 88
RPO HBQ 5.029 -0.960 -1.037 ETKDGv3 89
RPO HBF 3.500 -2.703 -1.734 ETKDGv3 90
RPO HNAG 1.917 -2.735 -0.069 ETKDGv3 91
RPO HNAH 3.005 -3.097 1.163 ETKDGv3 92
RPO HBH 4.624 -4.812 -0.695 ETKDGv3 93
RPO HOAG 6.215 -2.764 -1.887 ETKDGv3 94
RPO HBJ 6.910 -4.163 0.406 ETKDGv3 95
RPO HOAI 5.413 -5.234 1.583 ETKDGv3 96
RPO HAQ 7.946 -2.637 2.135 ETKDGv3 97
RPO HAQA 7.412 -0.927 2.234 ETKDGv3 98
RPO HNAA 5.587 -1.515 3.534 ETKDGv3 99
RPO HNAB 6.926 -2.273 4.192 ETKDGv3 100
#