data_YGP
# 
_chem_comp.id                                    YGP 
_chem_comp.name                                  "5'-O-[(R)-[(3,6-dimethyl-2-oxo-1,2-dihydropyridin-4-yl)oxy](hydroxy)phosphoryl]guanosine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H21 N6 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2013-05-30 
_chem_comp.pdbx_modified_date                    2014-01-31 
_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                        484.357 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YGP 
_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        3WB2 
_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 
YGP C2    C2  C 0 1 N N N 24.457 -49.407 10.945 6.996  -0.232 1.306  C2    YGP 1  
YGP N2    N2  N 0 1 N N N 24.788 -50.456 11.691 7.821  0.552  2.072  N2    YGP 2  
YGP C4    C4  C 0 1 Y N N 24.306 -48.319 8.866  4.947  -0.532 0.282  C4    YGP 3  
YGP C5    C5  C 0 1 Y N N 23.716 -47.225 9.415  5.354  -1.782 -0.197 C5    YGP 4  
YGP C6    C6  C 0 1 N N N 23.499 -47.192 10.737 6.659  -2.234 0.112  C6    YGP 5  
YGP O6    O6  O 0 1 N N N 22.991 -46.211 11.259 7.056  -3.316 -0.284 O6    YGP 6  
YGP N1    N1  N 0 1 N N N 23.843 -48.301 11.559 7.450  -1.440 0.868  N1    YGP 7  
YGP N3    N3  N 0 1 N N N 24.660 -49.382 9.600  5.788  0.201  1.021  N3    YGP 8  
YGP N7    N7  N 0 1 Y N N 23.488 -46.309 8.454  4.320  -2.298 -0.905 N7    YGP 9  
YGP C8    C8  C 0 1 Y N N 23.903 -46.871 7.317  3.326  -1.459 -0.888 C8    YGP 10 
YGP N9    N9  N 0 1 Y N N 24.401 -48.101 7.572  3.664  -0.355 -0.162 N9    YGP 11 
YGP "C1'" C1* C 0 1 N N R 24.973 -49.102 6.599  2.814  0.811  0.090  "C1'" YGP 12 
YGP "O4'" O4* O 0 1 N N N 25.176 -48.541 5.243  1.422  0.463  -0.074 "O4'" YGP 13 
YGP "C2'" C2* C 0 1 N N R 23.956 -50.235 6.454  3.076  1.906  -0.967 "C2'" YGP 14 
YGP "O2'" O2* O 0 1 N N N 24.626 -51.424 6.160  3.969  2.896  -0.452 "O2'" YGP 15 
YGP "C3'" C3* C 0 1 N N S 23.151 -49.781 5.266  1.681  2.516  -1.231 "C3'" YGP 16 
YGP "O3'" O3* O 0 1 N N N 22.482 -50.879 4.623  1.669  3.904  -0.888 "O3'" YGP 17 
YGP "C4'" C4* C 0 1 N N R 24.219 -49.183 4.343  0.740  1.716  -0.299 "C4'" YGP 18 
YGP "C5'" C5* C 0 1 N N N 23.557 -48.099 3.524  -0.608 1.474  -0.982 "C5'" YGP 19 
YGP "O5'" O5* O 0 1 N N N 22.742 -47.252 4.377  -1.475 0.772  -0.088 "O5'" YGP 20 
YGP PBG   PBG P 0 1 N N N 21.932 -46.049 3.674  -2.979 0.350  -0.477 PBG   YGP 21 
YGP OAI   OAI O 0 1 N N N 21.332 -45.117 4.751  -2.941 -0.724 -1.677 OAI   YGP 22 
YGP OAF   OAF O 0 1 N N N 20.877 -46.525 2.771  -3.732 1.548  -0.911 OAF   YGP 23 
YGP OAR   OAR O 0 1 N N N 23.074 -45.177 2.855  -3.701 -0.303 0.805  OAR   YGP 24 
YGP CAW   CAW C 0 1 N N N 24.302 -44.766 3.306  -5.013 -0.583 0.615  CAW   YGP 25 
YGP CAK   CAK C 0 1 N N N 24.523 -44.167 4.559  -5.407 -1.567 -0.314 CAK   YGP 26 
YGP CAT   CAT C 0 1 N N N 25.818 -43.778 4.938  -6.719 -1.835 -0.492 CAT   YGP 27 
YGP CAA   CAA C 0 1 N N N 26.078 -43.204 6.191  -7.134 -2.888 -1.487 CAA   YGP 28 
YGP NAO   NAO N 0 1 N N N 26.885 -43.961 3.997  -7.669 -1.168 0.215  NAO   YGP 29 
YGP CAX   CAX C 0 1 N N N 26.657 -44.547 2.743  -7.332 -0.222 1.111  CAX   YGP 30 
YGP OAD   OAD O 0 1 N N N 27.631 -44.670 1.983  -8.203 0.364  1.735  OAD   YGP 31 
YGP CAV   CAV C 0 1 N N N 25.339 -44.955 2.385  -5.985 0.087  1.334  CAV   YGP 32 
YGP CAB   CAB C 0 1 N N N 25.013 -45.565 1.125  -5.600 1.145  2.336  CAB   YGP 33 
YGP H1    H1  H 0 1 N N N 25.201 -51.262 11.266 8.714  0.244  2.294  H1    YGP 34 
YGP H2    H2  H 0 1 N N N 24.624 -50.440 12.677 7.512  1.415  2.391  H2    YGP 35 
YGP H3    H3  H 0 1 N N N 23.654 -48.294 12.541 8.345  -1.732 1.100  H3    YGP 36 
YGP H4    H4  H 0 1 N N N 23.849 -46.412 6.341  2.373  -1.617 -1.371 H4    YGP 37 
YGP H5    H5  H 0 1 N N N 25.919 -49.504 6.990  2.992  1.201  1.092  H5    YGP 38 
YGP H6    H6  H 0 1 N N N 23.327 -50.311 7.353  3.480  1.467  -1.880 H6    YGP 39 
YGP H7    H7  H 0 1 N N N 25.130 -51.700 6.917  4.169  3.608  -1.075 H7    YGP 40 
YGP H8    H8  H 0 1 N N N 22.437 -49.000 5.566  1.395  2.379  -2.274 H8    YGP 41 
YGP H9    H9  H 0 1 N N N 21.825 -51.237 5.208  2.286  4.441  -1.403 H9    YGP 42 
YGP H10   H10 H 0 1 N N N 24.683 -49.952 3.708  0.600  2.246  0.642  H10   YGP 43 
YGP H11   H11 H 0 1 N N N 24.331 -47.487 3.038  -1.057 2.431  -1.248 H11   YGP 44 
YGP H12   H12 H 0 1 N N N 22.920 -48.562 2.756  -0.457 0.880  -1.883 H12   YGP 45 
YGP H13   H13 H 0 1 N N N 20.395 -45.037 4.615  -2.397 -1.501 -1.492 H13   YGP 46 
YGP H14   H14 H 0 1 N N N 23.694 -44.006 5.232  -4.663 -2.104 -0.882 H14   YGP 47 
YGP H16   H16 H 0 1 N N N 25.144 -43.146 6.769  -7.188 -3.856 -0.989 H16   YGP 48 
YGP H17   H17 H 0 1 N N N 26.807 -43.823 6.734  -8.112 -2.635 -1.896 H17   YGP 49 
YGP H18   H18 H 0 1 N N N 26.487 -42.192 6.053  -6.403 -2.934 -2.293 H18   YGP 50 
YGP H19   H19 H 0 1 N N N 23.936 -45.786 1.092  -6.500 1.623  2.724  H19   YGP 51 
YGP H20   H20 H 0 1 N N N 25.272 -44.877 0.307  -5.051 0.685  3.157  H20   YGP 52 
YGP H21   H21 H 0 1 N N N 25.582 -46.499 1.012  -4.972 1.893  1.852  H21   YGP 53 
YGP H15   H15 H 0 1 N N N 27.809 -43.665 4.239  -8.605 -1.377 0.071  H15   YGP 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 
YGP CAB   CAV   SING N N 1  
YGP OAD   CAX   DOUB N N 2  
YGP CAV   CAX   SING N N 3  
YGP CAV   CAW   DOUB N N 4  
YGP CAX   NAO   SING N N 5  
YGP OAF   PBG   DOUB N N 6  
YGP OAR   CAW   SING N N 7  
YGP OAR   PBG   SING N N 8  
YGP CAW   CAK   SING N N 9  
YGP "C5'" "C4'" SING N N 10 
YGP "C5'" "O5'" SING N N 11 
YGP PBG   "O5'" SING N N 12 
YGP PBG   OAI   SING N N 13 
YGP NAO   CAT   SING N N 14 
YGP "C4'" "O4'" SING N N 15 
YGP "C4'" "C3'" SING N N 16 
YGP CAK   CAT   DOUB N N 17 
YGP "O3'" "C3'" SING N N 18 
YGP CAT   CAA   SING N N 19 
YGP "O4'" "C1'" SING N N 20 
YGP "C3'" "C2'" SING N N 21 
YGP "O2'" "C2'" SING N N 22 
YGP "C2'" "C1'" SING N N 23 
YGP "C1'" N9    SING N N 24 
YGP C8    N9    SING Y N 25 
YGP C8    N7    DOUB Y N 26 
YGP N9    C4    SING Y N 27 
YGP N7    C5    SING Y N 28 
YGP C4    C5    DOUB Y N 29 
YGP C4    N3    SING N N 30 
YGP C5    C6    SING N N 31 
YGP N3    C2    DOUB N N 32 
YGP C6    O6    DOUB N N 33 
YGP C6    N1    SING N N 34 
YGP C2    N1    SING N N 35 
YGP C2    N2    SING N N 36 
YGP N2    H1    SING N N 37 
YGP N2    H2    SING N N 38 
YGP N1    H3    SING N N 39 
YGP C8    H4    SING N N 40 
YGP "C1'" H5    SING N N 41 
YGP "C2'" H6    SING N N 42 
YGP "O2'" H7    SING N N 43 
YGP "C3'" H8    SING N N 44 
YGP "O3'" H9    SING N N 45 
YGP "C4'" H10   SING N N 46 
YGP "C5'" H11   SING N N 47 
YGP "C5'" H12   SING N N 48 
YGP OAI   H13   SING N N 49 
YGP CAK   H14   SING N N 50 
YGP CAA   H16   SING N N 51 
YGP CAA   H17   SING N N 52 
YGP CAA   H18   SING N N 53 
YGP CAB   H19   SING N N 54 
YGP CAB   H20   SING N N 55 
YGP CAB   H21   SING N N 56 
YGP NAO   H15   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 
YGP SMILES           ACDLabs              12.01 "O=C4NC(=CC(OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O)=C4C)C" 
YGP InChI            InChI                1.03  
"InChI=1S/C17H21N6O9P/c1-6-3-8(7(2)14(26)20-6)32-33(28,29)30-4-9-11(24)12(25)16(31-9)23-5-19-10-13(23)21-17(18)22-15(10)27/h3,5,9,11-12,16,24-25H,4H2,1-2H3,(H,20,26)(H,28,29)(H3,18,21,22,27)/t9-,11-,12-,16-/m1/s1" 
YGP InChIKey         InChI                1.03  SHYVQHDJQQBUQP-UBEDBUPSSA-N 
YGP SMILES_CANONICAL CACTVS               3.385 "CC1=CC(=C(C)C(=O)N1)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC(=Nc34)N" 
YGP SMILES           CACTVS               3.385 "CC1=CC(=C(C)C(=O)N1)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4C(=O)NC(=Nc34)N" 
YGP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1=CC(=C(C(=O)N1)C)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3N=C(NC4=O)N)O)O" 
YGP SMILES           "OpenEye OEToolkits" 1.7.6 "CC1=CC(=C(C(=O)N1)C)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3N=C(NC4=O)N)O)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 
YGP "SYSTEMATIC NAME" ACDLabs              12.01 "5'-O-[(R)-[(3,6-dimethyl-2-oxo-1,2-dihydropyridin-4-yl)oxy](hydroxy)phosphoryl]guanosine"                                                                        
YGP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl (3,6-dimethyl-2-oxidanylidene-1H-pyridin-4-yl) hydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YGP "Create component" 2013-05-30 PDBJ 
YGP "Modify atom id"   2013-06-24 PDBJ 
YGP "Initial release"  2014-02-05 RCSB 
# 
