data_6YB
# 
_chem_comp.id                                    6YB 
_chem_comp.name                                  "(2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-carbamimidamidoethyl)amino]-2-azanyl-butanoic acid" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H28 N10 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2016-07-22 
_chem_comp.pdbx_modified_date                    2017-08-11 
_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                        452.468 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     6YB 
_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        5LKJ 
_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.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 
6YB N1     N1  N 0 1 Y N N 50.574 42.021 126.715 -6.469 -0.498 1.643  N1     6YB 1  
6YB C2     C1  C 0 1 Y N N 50.387 41.983 128.044 -6.026 -1.536 0.958  C2     6YB 2  
6YB N3     N2  N 0 1 Y N N 50.245 40.807 128.704 -4.821 -1.572 0.429  N3     6YB 3  
6YB C4     C2  C 0 1 Y N N 50.287 39.647 128.020 -3.990 -0.544 0.567  C4     6YB 4  
6YB C6     C3  C 0 1 Y N N 50.628 40.877 125.993 -5.709 0.576  1.833  C6     6YB 5  
6YB N10    N3  N 0 1 N N N 51.790 31.058 129.882 4.693  -2.760 0.865  N10    6YB 6  
6YB C11    C4  C 0 1 N N N 52.338 32.202 130.714 3.889  -1.541 0.740  C11    6YB 7  
6YB C10    C5  C 0 1 N N N 51.308 32.619 131.749 3.151  -1.553 -0.600 C10    6YB 8  
6YB ND     N4  N 0 1 N N N 51.349 34.042 132.133 2.346  -0.331 -0.726 ND     6YB 9  
6YB "C5'"  C6  C 0 1 N N N 51.235 34.943 130.920 1.443  -0.412 -1.883 "C5'"  6YB 10 
6YB "C4'"  C7  C 0 1 N N R 50.497 36.241 131.301 0.272  -1.338 -1.551 "C4'"  6YB 11 
6YB "O4'"  O1  O 0 1 N N N 51.059 37.331 130.549 -0.456 -0.822 -0.425 "O4'"  6YB 12 
6YB "C1'"  C8  C 0 1 N N R 49.978 37.990 129.827 -1.846 -1.152 -0.634 "C1'"  6YB 13 
6YB N9     N5  N 0 1 Y N N 50.164 38.355 128.415 -2.710 -0.270 0.155  N9     6YB 14 
6YB C5     C9  C 0 1 Y N N 50.483 39.651 126.639 -4.415 0.586  1.288  C5     6YB 15 
6YB N6     N6  N 0 1 N N N 50.837 40.911 124.520 -6.183 1.659  2.553  N6     6YB 16 
6YB N7     N7  N 0 1 Y N N 50.485 38.360 126.235 -3.391 1.473  1.278  N7     6YB 17 
6YB C8     C10 C 0 1 Y N N 50.304 37.564 127.328 -2.390 0.973  0.614  C8     6YB 18 
6YB "C2'"  C11 C 0 1 N N R 48.812 37.012 129.825 -2.052 -0.909 -2.150 "C2'"  6YB 19 
6YB "O2'"  O2  O 0 1 N N N 47.528 37.677 129.861 -3.139 -1.690 -2.650 "O2'"  6YB 20 
6YB "C3'"  C12 C 0 1 N N S 49.025 36.209 131.038 -0.704 -1.396 -2.743 "C3'"  6YB 21 
6YB "O3'"  O3  O 0 1 N N N 48.377 36.800 132.111 -0.826 -2.734 -3.230 "O3'"  6YB 22 
6YB CG     C13 C 0 1 N N N 52.494 34.350 132.989 3.203  0.859  -0.810 CG     6YB 23 
6YB CB     C14 C 0 1 N N N 52.019 35.132 134.197 2.365  2.112  -0.550 CB     6YB 24 
6YB CA     C15 C 0 1 N N S 53.079 35.481 135.284 3.279  3.338  -0.510 CA     6YB 25 
6YB C      C16 C 0 1 N N N 52.986 34.552 136.461 2.441  4.585  -0.386 C      6YB 26 
6YB O      O4  O 0 1 N N N 53.957 33.803 136.754 2.285  5.104  0.694  O      6YB 27 
6YB N      N8  N 0 1 N N N 54.409 35.502 134.762 4.181  3.238  0.645  N      6YB 28 
6YB C12    C17 C 0 1 N N N 52.012 29.678 130.271 5.448  -2.972 1.994  C12    6YB 29 
6YB N12    N9  N 0 1 N N N 52.768 29.364 131.455 6.163  -4.056 2.105  N12    6YB 30 
6YB N11    N10 N 0 1 N N N 51.524 28.709 129.540 5.450  -2.041 3.005  N11    6YB 31 
6YB OXT    O5  O 0 1 N N N 51.913 34.532 137.173 1.868  5.119  -1.476 OXT    6YB 32 
6YB H21    H1  H 0 1 N N N 50.349 42.909 128.599 -6.676 -2.388 0.827  H21    6YB 33 
6YB H103   H2  H 0 0 N N N 51.268 31.258 129.053 4.692  -3.417 0.152  H103   6YB 34 
6YB H112   H3  H 0 0 N N N 53.257 31.877 131.223 3.165  -1.498 1.553  H112   6YB 35 
6YB H111   H4  H 0 0 N N N 52.564 33.056 130.058 4.542  -0.669 0.788  H111   6YB 36 
6YB H102   H5  H 0 0 N N N 50.309 32.404 131.341 3.875  -1.596 -1.414 H102   6YB 37 
6YB H101   H6  H 0 0 N N N 51.472 32.017 132.655 2.499  -2.425 -0.648 H101   6YB 38 
6YB "H5'2" H8  H 0 0 N N N 50.674 34.422 130.130 1.065  0.583  -2.118 "H5'2" 6YB 39 
6YB "H5'1" H9  H 0 0 N N N 52.242 35.190 130.553 1.987  -0.806 -2.741 "H5'1" 6YB 40 
6YB "H4'1" H10 H 0 0 N N N 50.657 36.420 132.375 0.642  -2.338 -1.327 "H4'1" 6YB 41 
6YB "H1'1" H11 H 0 0 N N N 49.671 38.886 130.386 -2.035 -2.196 -0.383 "H1'1" 6YB 42 
6YB H62    H12 H 0 1 N N N 50.919 41.860 124.216 -5.618 2.437  2.686  H62    6YB 43 
6YB H61    H13 H 0 1 N N N 51.674 40.414 124.291 -7.078 1.641  2.924  H61    6YB 44 
6YB H81    H14 H 0 1 N N N 50.277 36.484 127.325 -1.445 1.469  0.451  H81    6YB 45 
6YB "H2'1" H15 H 0 0 N N N 48.882 36.369 128.935 -2.209 0.150  -2.357 "H2'1" 6YB 46 
6YB "H2'2" H16 H 0 0 N N N 46.834 37.028 129.858 -3.307 -1.572 -3.595 "H2'2" 6YB 47 
6YB "H3'1" H17 H 0 0 N N N 48.691 35.173 130.878 -0.373 -0.729 -3.539 "H3'1" 6YB 48 
6YB "H3'2" H18 H 0 0 N N N 48.517 36.278 132.892 -1.472 -2.836 -3.942 "H3'2" 6YB 49 
6YB HG3    H19 H 0 1 N N N 52.968 33.414 133.320 3.994  0.790  -0.063 HG3    6YB 50 
6YB HG2    H20 H 0 1 N N N 53.223 34.951 132.426 3.646  0.918  -1.804 HG2    6YB 51 
6YB HB3    H21 H 0 1 N N N 51.596 36.079 133.832 1.632  2.231  -1.348 HB3    6YB 52 
6YB HB2    H22 H 0 1 N N N 51.229 34.541 134.684 1.848  2.012  0.405  HB2    6YB 53 
6YB HA     H23 H 0 1 N N N 52.837 36.491 135.646 3.866  3.384  -1.427 HA     6YB 54 
6YB H      H24 H 0 1 N N N 55.051 35.730 135.494 3.661  3.194  1.508  H      6YB 55 
6YB H2     H25 H 0 1 N N N 54.635 34.602 134.389 4.798  2.445  0.554  H2     6YB 56 
6YB H121   H27 H 0 0 N N N 53.087 30.187 131.925 6.162  -4.714 1.392  H121   6YB 57 
6YB H113   H28 H 0 0 N N N 51.677 27.757 129.805 4.918  -1.234 2.922  H113   6YB 58 
6YB H4     H29 H 0 1 N N N 50.998 28.920 128.716 5.983  -2.190 3.802  H4     6YB 59 
6YB H5     H30 H 0 1 N N N 52.012 33.903 137.878 1.340  5.919  -1.347 H5     6YB 60 
# 
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 
6YB N6    C6     SING N N 1  
6YB C6    C5     DOUB Y N 2  
6YB C6    N1     SING Y N 3  
6YB N7    C5     SING Y N 4  
6YB N7    C8     DOUB Y N 5  
6YB C5    C4     SING Y N 6  
6YB N1    C2     DOUB Y N 7  
6YB C8    N9     SING Y N 8  
6YB C4    N9     SING Y N 9  
6YB C4    N3     DOUB Y N 10 
6YB C2    N3     SING Y N 11 
6YB N9    "C1'"  SING N N 12 
6YB N11   C12    SING N N 13 
6YB "C2'" "C1'"  SING N N 14 
6YB "C2'" "O2'"  SING N N 15 
6YB "C2'" "C3'"  SING N N 16 
6YB "C1'" "O4'"  SING N N 17 
6YB N10   C12    SING N N 18 
6YB N10   C11    SING N N 19 
6YB C12   N12    DOUB N N 20 
6YB "O4'" "C4'"  SING N N 21 
6YB C11   C10    SING N N 22 
6YB "C5'" "C4'"  SING N N 23 
6YB "C5'" ND     SING N N 24 
6YB "C3'" "C4'"  SING N N 25 
6YB "C3'" "O3'"  SING N N 26 
6YB C10   ND     SING N N 27 
6YB ND    CG     SING N N 28 
6YB CG    CB     SING N N 29 
6YB CB    CA     SING N N 30 
6YB N     CA     SING N N 31 
6YB CA    C      SING N N 32 
6YB C     O      DOUB N N 33 
6YB C     OXT    SING N N 34 
6YB C2    H21    SING N N 35 
6YB N10   H103   SING N N 36 
6YB C11   H112   SING N N 37 
6YB C11   H111   SING N N 38 
6YB C10   H102   SING N N 39 
6YB C10   H101   SING N N 40 
6YB "C5'" "H5'2" SING N N 41 
6YB "C5'" "H5'1" SING N N 42 
6YB "C4'" "H4'1" SING N N 43 
6YB "C1'" "H1'1" SING N N 44 
6YB N6    H62    SING N N 45 
6YB N6    H61    SING N N 46 
6YB C8    H81    SING N N 47 
6YB "C2'" "H2'1" SING N N 48 
6YB "O2'" "H2'2" SING N N 49 
6YB "C3'" "H3'1" SING N N 50 
6YB "O3'" "H3'2" SING N N 51 
6YB CG    HG3    SING N N 52 
6YB CG    HG2    SING N N 53 
6YB CB    HB3    SING N N 54 
6YB CB    HB2    SING N N 55 
6YB CA    HA     SING N N 56 
6YB N     H      SING N N 57 
6YB N     H2     SING N N 58 
6YB N12   H121   SING N N 59 
6YB N11   H113   SING N N 60 
6YB N11   H4     SING N N 61 
6YB OXT   H5     SING N N 62 
# 
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 
6YB InChI            InChI                1.03  
"InChI=1S/C17H28N10O5/c18-8(16(30)31)1-3-26(4-2-22-17(20)21)5-9-11(28)12(29)15(32-9)27-7-25-10-13(19)23-6-24-14(10)27/h6-9,11-12,15,28-29H,1-5,18H2,(H,30,31)(H2,19,23,24)(H4,20,21,22)/t8-,9+,11+,12+,15+/m0/s1" 
6YB InChIKey         InChI                1.03  JNOBHECZYPSIIL-OPYVMVOTSA-N 
6YB SMILES_CANONICAL CACTVS               3.385 "N[C@@H](CCN(CCNC(N)=N)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O" 
6YB SMILES           CACTVS               3.385 "N[CH](CCN(CCNC(N)=N)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O" 
6YB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.5 "[H]/N=C(\N)/NCCN(CC[C@@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O" 
6YB SMILES           "OpenEye OEToolkits" 2.0.5 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCC(C(=O)O)N)CCNC(=N)N)O)O)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 
6YB "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.5 "(2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-carbamimidamidoethyl)amino]-2-azanyl-butanoic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
6YB "Create component" 2016-07-22 EBI  
6YB "Initial release"  2017-08-16 RCSB 
# 
