data_YMP
# 
_chem_comp.id                                    YMP 
_chem_comp.name                                  "O-(ADENOSINE-5'-O-YL)-N-(L-TYROSYL)PHOSPHORAMIDATE" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C19 H24 N7 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "TYROSYL-ADENYLATE ANALOGUE; TYR-AMP ANALOGUE" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2006-05-02 
_chem_comp.pdbx_modified_date                    2020-05-26 
_chem_comp.pdbx_ambiguous_flag                   ? 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        509.410 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YMP 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        ? 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
YMP N      N    N 0 1 N N N 8.261  30.255 160.434 5.465   1.361  1.720  N      YMP 1  
YMP CA     CA   C 0 1 N N S 8.118  31.568 159.734 4.723   1.142  0.471  CA     YMP 2  
YMP CB     CB   C 0 1 N N N 9.501  32.146 159.423 4.558   -0.360 0.232  CB     YMP 3  
YMP CG     CG   C 0 1 Y N N 10.268 32.506 160.675 5.911   -0.984 0.007  CG     YMP 4  
YMP CD1    CD1  C 0 1 Y N N 9.699  33.340 161.639 6.635   -1.469 1.080  CD1    YMP 5  
YMP CE1    CE1  C 0 1 Y N N 10.416 33.674 162.784 7.876   -2.041 0.876  CE1    YMP 6  
YMP CZ     CZ   C 0 1 Y N N 11.704 33.173 162.975 8.395   -2.130 -0.407 CZ     YMP 7  
YMP OH     OH   O 0 1 N N N 12.372 33.494 164.078 9.615   -2.693 -0.610 OH     YMP 8  
YMP CE2    CE2  C 0 1 Y N N 12.280 32.337 162.015 7.666   -1.643 -1.483 CE2    YMP 9  
YMP CD2    CD2  C 0 1 Y N N 11.558 32.003 160.869 6.424   -1.077 -1.274 CD2    YMP 10 
YMP C      C    C 0 1 N N N 7.308  31.413 158.469 3.365   1.787  0.574  C      YMP 11 
YMP O      O    O 0 1 N N N 6.785  30.344 158.202 2.898   2.046  1.663  O      YMP 12 
YMP N3P    N3P  N 0 1 N N N 7.213  32.502 157.702 2.669   2.075  -0.544 N3P    YMP 13 
YMP P      P    P 0 1 N N S 6.429  32.648 156.226 1.191   2.777  -0.431 P      YMP 14 
YMP O1P    O1P  O 0 1 N N N 5.777  31.383 155.759 0.641   2.988  -1.789 O1P    YMP 15 
YMP O2P    O2P  O 0 1 N N N 7.390  33.312 155.279 1.325   4.194  0.320  O2P    YMP 16 
YMP "O5'"  O5*  O 0 1 N N N 5.212  33.669 156.482 0.204   1.818  0.405  "O5'"  YMP 17 
YMP "C5'"  C5*  C 0 1 N N N 5.441  34.972 157.013 -0.061  0.680  -0.419 "C5'"  YMP 18 
YMP "C4'"  C4*  C 0 1 N N R 4.272  35.381 157.902 -0.999  -0.277 0.321  "C4'"  YMP 19 
YMP "O4'"  O4*  O 0 1 N N N 3.176  35.859 157.108 -2.290  0.334  0.485  "O4'"  YMP 20 
YMP "C1'"  C1*  C 0 1 N N R 1.997  35.110 157.408 -3.270  -0.723 0.398  "C1'"  YMP 21 
YMP "C2'"  C2*  C 0 1 N N R 2.359  33.977 158.365 -2.730  -1.623 -0.742 "C2'"  YMP 22 
YMP "C3'"  C3*  C 0 1 N N S 3.796  34.222 158.762 -1.198  -1.560 -0.509 "C3'"  YMP 23 
YMP "O3'"  O3*  O 0 1 N N N 3.815  34.722 160.090 -0.755  -2.708 0.219  "O3'"  YMP 24 
YMP "O2'"  O2*  O 0 1 N N N 1.441  33.780 159.426 -3.211  -2.962 -0.606 "O2'"  YMP 25 
YMP N9     N9   N 0 1 Y N N 1.201  34.584 156.285 -4.585  -0.179 0.052  N9     YMP 26 
YMP C4     C4   C 0 1 Y N N -0.089 34.816 156.131 -5.799  -0.764 0.309  C4     YMP 27 
YMP N3     N3   N 0 1 Y N N -0.846 35.595 156.952 -6.193  -1.887 0.901  N3     YMP 28 
YMP C5     C5   C 0 1 Y N N -0.577 34.175 155.035 -6.769  0.117  -0.198 C5     YMP 29 
YMP N7     N7   N 0 1 Y N N 0.468  33.518 154.494 -6.109  1.171  -0.736 N7     YMP 30 
YMP C8     C8   C 0 1 Y N N 1.556  33.767 155.274 -4.827  0.999  -0.590 C8     YMP 31 
YMP C6     C6   C 0 1 Y N N -2.006 34.332 154.710 -8.122  -0.238 -0.064 C6     YMP 32 
YMP N6     N6   N 0 1 N N N -2.543 33.743 153.651 -9.122  0.588  -0.550 N6     YMP 33 
YMP N1     N1   N 0 1 Y N N -2.724 35.096 155.529 -8.420  -1.384 0.538  N1     YMP 34 
YMP C2     C2   C 0 1 Y N N -2.263 35.809 156.718 -7.473  -2.178 1.004  C2     YMP 35 
YMP HN1    1HN  H 0 1 N N N 9.106  30.253 160.969 5.460   2.355  1.890  HN1    YMP 36 
YMP HN2    2HN  H 0 1 N N N 8.293  29.518 159.759 4.922   0.937  2.458  HN2    YMP 37 
YMP HA     HA   H 0 1 N N N 7.583  32.265 160.396 5.273   1.584  -0.360 HA     YMP 38 
YMP HB1    1HB  H 0 1 N N N 9.359  33.066 158.838 4.088   -0.817 1.103  HB1    YMP 39 
YMP HB2    2HB  H 0 1 N N N 10.077 31.393 158.865 3.933   -0.522 -0.646 HB2    YMP 40 
YMP HD1    HD1  H 0 1 N N N 8.701  33.727 161.496 6.231   -1.400 2.079  HD1    YMP 41 
YMP HE1    HE1  H 0 1 N N N 9.974  34.322 163.526 8.441   -2.419 1.715  HE1    YMP 42 
YMP HOH    HOH  H 0 1 N N N 13.297 33.571 163.877 9.466   -3.637 -0.757 HOH    YMP 43 
YMP HE2    HE2  H 0 1 N N N 13.279 31.952 162.159 8.069   -1.711 -2.483 HE2    YMP 44 
YMP HD2    HD2  H 0 1 N N N 11.998 31.352 160.128 5.856   -0.698 -2.111 HD2    YMP 45 
YMP H3P    H3P  H 0 1 N N N 7.661  33.326 158.048 3.043   1.868  -1.414 H3P    YMP 46 
YMP H2P    H2P  H 0 1 N N N 6.964  33.452 154.441 1.686   4.012  1.198  H2P    YMP 47 
YMP "H5'1" 1H5* H 0 0 N N N 5.536  35.690 156.185 -0.532  1.005  -1.347 "H5'1" YMP 48 
YMP "H5'2" 2H5* H 0 0 N N N 6.366  34.966 157.608 0.874   0.169  -0.645 "H5'2" YMP 49 
YMP "H4'"  H4*  H 0 1 N N N 4.630  36.186 158.560 -0.580  -0.527 1.295  "H4'"  YMP 50 
YMP "H1'"  H1*  H 0 1 N N N 1.321  35.854 157.855 -3.320  -1.278 1.335  "H1'"  YMP 51 
YMP "H2'"  H2*  H 0 1 N N N 2.274  32.997 157.872 -2.994  -1.215 -1.718 "H2'"  YMP 52 
YMP "H3'"  H3*  H 0 1 N N N 4.396  33.306 158.659 -0.670  -1.486 -1.459 "H3'"  YMP 53 
YMP H2     H2   H 0 1 N N N 3.819  33.996 160.702 -0.961  -3.480 -0.325 H2     YMP 54 
YMP H1     H1   H 0 1 N N N 1.913  33.736 160.249 -2.841  -3.468 -1.342 H1     YMP 55 
YMP H8     H8   H 0 1 N N N 2.547  33.372 155.108 -4.068  1.688  -0.928 H8     YMP 56 
YMP HN61   1HN6 H 0 0 N N N -2.054 33.162 153.000 -8.892  1.422  -0.988 HN61   YMP 57 
YMP HN62   2HN6 H 0 0 N N N -3.515 33.972 153.607 -10.052 0.332  -0.451 HN62   YMP 58 
YMP H3     H3   H 0 1 N N N -2.897 36.419 157.345 -7.759  -3.100 1.487  H3     YMP 59 
# 
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 
YMP N     CA     SING N N 1  
YMP N     HN1    SING N N 2  
YMP N     HN2    SING N N 3  
YMP CA    CB     SING N N 4  
YMP CA    C      SING N N 5  
YMP CA    HA     SING N N 6  
YMP CB    CG     SING N N 7  
YMP CB    HB1    SING N N 8  
YMP CB    HB2    SING N N 9  
YMP CG    CD1    DOUB Y N 10 
YMP CG    CD2    SING Y N 11 
YMP CD1   CE1    SING Y N 12 
YMP CD1   HD1    SING N N 13 
YMP CE1   CZ     DOUB Y N 14 
YMP CE1   HE1    SING N N 15 
YMP CZ    OH     SING N N 16 
YMP CZ    CE2    SING Y N 17 
YMP OH    HOH    SING N N 18 
YMP CE2   CD2    DOUB Y N 19 
YMP CE2   HE2    SING N N 20 
YMP CD2   HD2    SING N N 21 
YMP C     O      DOUB N N 22 
YMP C     N3P    SING N N 23 
YMP N3P   P      SING N N 24 
YMP N3P   H3P    SING N N 25 
YMP P     O1P    DOUB N N 26 
YMP P     O2P    SING N N 27 
YMP P     "O5'"  SING N N 28 
YMP O2P   H2P    SING N N 29 
YMP "O5'" "C5'"  SING N N 30 
YMP "C5'" "C4'"  SING N N 31 
YMP "C5'" "H5'1" SING N N 32 
YMP "C5'" "H5'2" SING N N 33 
YMP "C4'" "O4'"  SING N N 34 
YMP "C4'" "C3'"  SING N N 35 
YMP "C4'" "H4'"  SING N N 36 
YMP "O4'" "C1'"  SING N N 37 
YMP "C1'" "C2'"  SING N N 38 
YMP "C1'" N9     SING N N 39 
YMP "C1'" "H1'"  SING N N 40 
YMP "C2'" "C3'"  SING N N 41 
YMP "C2'" "O2'"  SING N N 42 
YMP "C2'" "H2'"  SING N N 43 
YMP "C3'" "O3'"  SING N N 44 
YMP "C3'" "H3'"  SING N N 45 
YMP "O3'" H2     SING N N 46 
YMP "O2'" H1     SING N N 47 
YMP N9    C4     SING Y N 48 
YMP N9    C8     SING Y N 49 
YMP C4    N3     SING Y N 50 
YMP C4    C5     DOUB Y N 51 
YMP N3    C2     DOUB Y N 52 
YMP C5    N7     SING Y N 53 
YMP C5    C6     SING Y N 54 
YMP N7    C8     DOUB Y N 55 
YMP C8    H8     SING N N 56 
YMP C6    N6     SING N N 57 
YMP C6    N1     DOUB Y N 58 
YMP N6    HN61   SING N N 59 
YMP N6    HN62   SING N N 60 
YMP N1    C2     SING Y N 61 
YMP C2    H3     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 
YMP SMILES           ACDLabs              10.04 "O=C(NP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)Cc4ccc(O)cc4"                                                                                                                                                                     
YMP SMILES_CANONICAL CACTVS               3.341 "N[C@@H](Cc1ccc(O)cc1)C(=O)N[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34"                                                                                                                                           
YMP SMILES           CACTVS               3.341 "N[CH](Cc1ccc(O)cc1)C(=O)N[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34"                                                                                                                                                    
YMP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1cc(ccc1C[C@@H](C(=O)N[P@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)N)O"                                                                                                                                           
YMP SMILES           "OpenEye OEToolkits" 1.5.0 "c1cc(ccc1CC(C(=O)NP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)N)O"                                                                                                                                                                     
YMP InChI            InChI                1.03  "InChI=1S/C19H24N7O8P/c20-11(5-9-1-3-10(27)4-2-9)18(30)25-35(31,32)33-6-12-14(28)15(29)19(34-12)26-8-24-13-16(21)22-7-23-17(13)26/h1-4,7-8,11-12,14-15,19,27-29H,5-6,20H2,(H2,21,22,23)(H2,25,30,31,32)/t11-,12+,14+,15+,19+/m0/s1" 
YMP InChIKey         InChI                1.03  WJKRKCCMHCWYJU-QTOWJTHWSA-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 
YMP "SYSTEMATIC NAME" ACDLabs              10.04 "5'-O-[(S)-hydroxy(L-tyrosylamino)phosphoryl]adenosine"                                                                                     
YMP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "N-[(2S)-2-amino-3-(4-hydroxyphenyl)propanoyl]-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy]phosphonamidic 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 
YMP "Create component"  2006-05-02 RCSB 
YMP "Modify descriptor" 2011-06-04 RCSB 
YMP "Modify synonyms"   2020-05-26 PDBE 
# 
loop_
_pdbx_chem_comp_synonyms.ordinal 
_pdbx_chem_comp_synonyms.comp_id 
_pdbx_chem_comp_synonyms.name 
_pdbx_chem_comp_synonyms.provenance 
_pdbx_chem_comp_synonyms.type 
1 YMP "TYROSYL-ADENYLATE ANALOGUE" ? ? 
2 YMP "TYR-AMP ANALOGUE"           ? ? 
# 
