data_D3Y
# 
_chem_comp.id                                    D3Y 
_chem_comp.name                                  "3'-deoxy-3'-(D-tyrosylamino)adenosine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C19 H23 N7 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2013-11-06 
_chem_comp.pdbx_modified_date                    2013-12-13 
_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                        429.430 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     D3Y 
_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        4NBI 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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 
D3Y CD1   CD1   C 0 1 Y N N -33.745 1.861  -25.292 -5.105 1.911  0.302  CD1   D3Y 1  
D3Y CE1   CE1   C 0 1 Y N N -34.979 1.659  -25.909 -6.284 2.501  0.715  CE1   D3Y 2  
D3Y CZ    CZ    C 0 1 Y N N -35.287 0.414  -26.454 -7.501 1.983  0.296  CZ    D3Y 3  
D3Y OH    OH    O 0 1 N N N -36.497 0.220  -27.053 -8.662 2.562  0.701  OH    D3Y 4  
D3Y CE2   CE2   C 0 1 Y N N -34.359 -0.627 -26.380 -7.531 0.874  -0.536 CE2   D3Y 5  
D3Y CD2   CD2   C 0 1 Y N N -33.123 -0.422 -25.765 -6.349 0.288  -0.947 CD2   D3Y 6  
D3Y CG    CG    C 0 1 Y N N -32.810 0.826  -25.226 -5.137 0.805  -0.528 CG    D3Y 7  
D3Y CB    CB    C 0 1 N N N -31.454 1.028  -24.536 -3.850 0.168  -0.983 CB    D3Y 8  
D3Y CA    CA    C 0 1 N N R -30.507 2.055  -25.171 -3.436 -0.914 0.017  CA    D3Y 9  
D3Y N     N     N 0 1 N N N -30.342 1.777  -26.614 -4.430 -1.995 0.008  N     D3Y 10 
D3Y C     C     C 0 1 N N N -31.044 3.479  -24.948 -2.088 -1.466 -0.370 C     D3Y 11 
D3Y O     O     O 0 1 N N N -31.307 3.916  -23.821 -2.013 -2.519 -0.967 O     D3Y 12 
D3Y N8    N8    N 0 1 N N N -31.218 4.161  -26.072 -0.966 -0.791 -0.052 N8    D3Y 13 
D3Y "C3'" "C3'" C 0 1 N N S -31.753 5.522  -26.093 0.344  -1.328 -0.429 "C3'" D3Y 14 
D3Y "C2'" "C2'" C 0 1 N N R -30.624 6.543  -26.094 1.393  -0.196 -0.502 "C2'" D3Y 15 
D3Y "O2'" "O2'" O 0 1 N N N -29.542 6.133  -26.944 0.794  1.063  -0.186 "O2'" D3Y 16 
D3Y "C4'" "C4'" C 0 1 N N S -32.418 5.757  -27.449 0.879  -2.269 0.673  "C4'" D3Y 17 
D3Y "C5'" "C5'" C 0 1 N N N -33.890 5.308  -27.505 0.604  -3.729 0.306  "C5'" D3Y 18 
D3Y "O5'" "O5'" O 0 1 N N N -34.680 6.130  -26.648 1.002  -4.575 1.388  "O5'" D3Y 19 
D3Y "O4'" "O4'" O 0 1 N N N -32.304 7.199  -27.683 2.301  -2.018 0.714  "O4'" D3Y 20 
D3Y "C1'" "C1'" C 0 1 N N R -31.319 7.739  -26.744 2.440  -0.584 0.565  "C1'" D3Y 21 
D3Y N9    N9    N 0 1 Y N N -32.074 8.656  -25.830 3.789  -0.247 0.106  N9    D3Y 22 
D3Y C8    C8    C 0 1 Y N N -33.313 9.102  -26.069 4.637  -1.067 -0.577 C8    D3Y 23 
D3Y N7    N7    N 0 1 Y N N -33.692 9.914  -25.089 5.753  -0.445 -0.826 N7    D3Y 24 
D3Y C5    C5    C 0 1 Y N N -32.681 9.992  -24.212 5.691  0.811  -0.321 C5    D3Y 25 
D3Y C4    C4    C 0 1 Y N N -31.646 9.193  -24.684 4.429  0.955  0.278  C4    D3Y 26 
D3Y N3    N3    N 0 1 Y N N -30.501 9.093  -23.967 4.113  2.113  0.849  N3    D3Y 27 
D3Y C2    C2    C 0 1 Y N N -30.362 9.753  -22.818 4.967  3.114  0.853  C2    D3Y 28 
D3Y N1    N1    N 0 1 Y N N -31.337 10.520 -22.339 6.164  3.027  0.301  N1    D3Y 29 
D3Y C6    C6    C 0 1 Y N N -32.505 10.668 -23.010 6.571  1.906  -0.287 C6    D3Y 30 
D3Y N6    N6    N 0 1 N N N -33.484 11.437 -22.530 7.826  1.826  -0.865 N6    D3Y 31 
D3Y H1    H1    H 0 1 N N N -33.511 2.824  -24.863 -4.157 2.316  0.623  H1    D3Y 32 
D3Y H2    H2    H 0 1 N N N -35.695 2.466  -25.964 -6.258 3.364  1.363  H2    D3Y 33 
D3Y H3    H3    H 0 1 N N N -37.002 1.024  -27.016 -9.016 2.200  1.525  H3    D3Y 34 
D3Y H4    H4    H 0 1 N N N -34.598 -1.593 -26.800 -8.477 0.469  -0.863 H4    D3Y 35 
D3Y H5    H5    H 0 1 N N N -32.409 -1.230 -25.706 -6.372 -0.576 -1.595 H5    D3Y 36 
D3Y H6    H6    H 0 1 N N N -31.650 1.349  -23.502 -3.994 -0.282 -1.965 H6    D3Y 37 
D3Y H7    H7    H 0 1 N N N -30.936 0.057  -24.527 -3.069 0.926  -1.041 H7    D3Y 38 
D3Y H8    H8    H 0 1 N N N -29.528 1.974  -24.676 -3.378 -0.482 1.016  H8    D3Y 39 
D3Y H9    H9    H 0 1 N N N -29.993 0.848  -26.737 -5.328 -1.664 0.326  H9    D3Y 40 
D3Y H10   H10   H 0 1 N N N -31.226 1.864  -27.073 -4.502 -2.412 -0.908 H10   D3Y 41 
D3Y H12   H12   H 0 1 N N N -30.974 3.728  -26.939 -1.026 0.051  0.425  H12   D3Y 42 
D3Y H13   H13   H 0 1 N N N -32.457 5.705  -25.268 0.281  -1.853 -1.382 H13   D3Y 43 
D3Y H14   H14   H 0 1 N N N -30.296 6.779  -25.071 1.850  -0.162 -1.491 H14   D3Y 44 
D3Y H15   H15   H 0 1 N N N -29.098 5.389  -26.555 1.408  1.809  -0.217 H15   D3Y 45 
D3Y H16   H16   H 0 1 N N N -31.854 5.211  -28.220 0.424  -2.028 1.633  H16   D3Y 46 
D3Y H17   H17   H 0 1 N N N -34.259 5.396  -28.537 -0.460 -3.861 0.114  H17   D3Y 47 
D3Y H18   H18   H 0 1 N N N -33.965 4.261  -27.177 1.171  -3.992 -0.587 H18   D3Y 48 
D3Y H19   H19   H 0 1 N N N -35.587 5.849  -26.686 0.856  -5.516 1.224  H19   D3Y 49 
D3Y H20   H20   H 0 1 N N N -30.568 8.323  -27.296 2.223  -0.082 1.508  H20   D3Y 50 
D3Y H21   H21   H 0 1 N N N -33.913 8.841  -26.928 4.416  -2.083 -0.868 H21   D3Y 51 
D3Y H22   H22   H 0 1 N N N -29.439 9.663  -22.265 4.679  4.041  1.326  H22   D3Y 52 
D3Y H23   H23   H 0 1 N N N -33.198 11.837 -21.660 8.107  1.005  -1.300 H23   D3Y 53 
D3Y H24   H24   H 0 1 N N N -33.684 12.167 -23.183 8.424  2.589  -0.835 H24   D3Y 54 
# 
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 
D3Y "O4'" "C4'" SING N N 1  
D3Y "O4'" "C1'" SING N N 2  
D3Y "C5'" "C4'" SING N N 3  
D3Y "C5'" "O5'" SING N N 4  
D3Y "C4'" "C3'" SING N N 5  
D3Y OH    CZ    SING N N 6  
D3Y "O2'" "C2'" SING N N 7  
D3Y "C1'" "C2'" SING N N 8  
D3Y "C1'" N9    SING N N 9  
D3Y N     CA    SING N N 10 
D3Y CZ    CE2   DOUB Y N 11 
D3Y CZ    CE1   SING Y N 12 
D3Y CE2   CD2   SING Y N 13 
D3Y "C2'" "C3'" SING N N 14 
D3Y "C3'" N8    SING N N 15 
D3Y N8    C     SING N N 16 
D3Y C8    N9    SING Y N 17 
D3Y C8    N7    DOUB Y N 18 
D3Y CE1   CD1   DOUB Y N 19 
D3Y N9    C4    SING Y N 20 
D3Y CD2   CG    DOUB Y N 21 
D3Y CD1   CG    SING Y N 22 
D3Y CG    CB    SING N N 23 
D3Y CA    C     SING N N 24 
D3Y CA    CB    SING N N 25 
D3Y N7    C5    SING Y N 26 
D3Y C     O     DOUB N N 27 
D3Y C4    C5    DOUB Y N 28 
D3Y C4    N3    SING Y N 29 
D3Y C5    C6    SING Y N 30 
D3Y N3    C2    DOUB Y N 31 
D3Y C6    N6    SING N N 32 
D3Y C6    N1    DOUB Y N 33 
D3Y C2    N1    SING Y N 34 
D3Y CD1   H1    SING N N 35 
D3Y CE1   H2    SING N N 36 
D3Y OH    H3    SING N N 37 
D3Y CE2   H4    SING N N 38 
D3Y CD2   H5    SING N N 39 
D3Y CB    H6    SING N N 40 
D3Y CB    H7    SING N N 41 
D3Y CA    H8    SING N N 42 
D3Y N     H9    SING N N 43 
D3Y N     H10   SING N N 44 
D3Y N8    H12   SING N N 45 
D3Y "C3'" H13   SING N N 46 
D3Y "C2'" H14   SING N N 47 
D3Y "O2'" H15   SING N N 48 
D3Y "C4'" H16   SING N N 49 
D3Y "C5'" H17   SING N N 50 
D3Y "C5'" H18   SING N N 51 
D3Y "O5'" H19   SING N N 52 
D3Y "C1'" H20   SING N N 53 
D3Y C8    H21   SING N N 54 
D3Y C2    H22   SING N N 55 
D3Y N6    H23   SING N N 56 
D3Y N6    H24   SING N N 57 
# 
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 
D3Y SMILES           ACDLabs              12.01 "O=C(NC3C(OC(n2cnc1c(ncnc12)N)C3O)CO)C(N)Cc4ccc(O)cc4"                                                                                                                                                       
D3Y InChI            InChI                1.03  "InChI=1S/C19H23N7O5/c20-11(5-9-1-3-10(28)4-2-9)18(30)25-13-12(6-27)31-19(15(13)29)26-8-24-14-16(21)22-7-23-17(14)26/h1-4,7-8,11-13,15,19,27-29H,5-6,20H2,(H,25,30)(H2,21,22,23)/t11-,12-,13-,15-,19-/m1/s1" 
D3Y InChIKey         InChI                1.03  GCCJIIJWAJOTAC-XDJZACDYSA-N                                                                                                                                                                                  
D3Y SMILES_CANONICAL CACTVS               3.385 "N[C@H](Cc1ccc(O)cc1)C(=O)N[C@H]2[C@@H](O)[C@@H](O[C@@H]2CO)n3cnc4c(N)ncnc34"                                                                                                                                
D3Y SMILES           CACTVS               3.385 "N[CH](Cc1ccc(O)cc1)C(=O)N[CH]2[CH](O)[CH](O[CH]2CO)n3cnc4c(N)ncnc34"                                                                                                                                        
D3Y SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1cc(ccc1C[C@H](C(=O)N[C@@H]2[C@H](O[C@H]([C@@H]2O)n3cnc4c3ncnc4N)CO)N)O"                                                                                                                                   
D3Y SMILES           "OpenEye OEToolkits" 1.7.6 "c1cc(ccc1CC(C(=O)NC2C(OC(C2O)n3cnc4c3ncnc4N)CO)N)O"                                                                                                                                                         
# 
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 
D3Y "SYSTEMATIC NAME" ACDLabs              12.01 "3'-deoxy-3'-(D-tyrosylamino)adenosine"                                                                                         
D3Y "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2R)-N-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]-2-azanyl-3-(4-hydroxyphenyl)propanamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
D3Y "Create component" 2013-11-06 PDBJ 
D3Y "Initial release"  2013-12-18 RCSB 
# 
