data_AYD
# 
_chem_comp.id                                    AYD 
_chem_comp.name                                  
;4-{[(4'-AMINO-2'-METHYLPYRIMIDIN-5'-YL)METHYL]AMINO}PENT-3-ENYL DIPHOSPHATE
;
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H20 N4 O7 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2002-10-31 
_chem_comp.pdbx_modified_date                    2012-01-05 
_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                        382.247 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     AYD 
_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        1N0H 
_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 
AYD "N1'"  "N1'"  N 0 1 Y N N 3.781  105.275 52.542 -7.878  0.633  -0.737 "N1'"  AYD 1  
AYD "C2'"  "C2'"  C 0 1 Y N N 3.931  106.077 53.701 -8.173  -0.565 -0.273 "C2'"  AYD 2  
AYD CM2    CM2    C 0 1 N N N 5.039  107.035 53.864 -9.510  -1.172 -0.609 CM2    AYD 3  
AYD "N3'"  "N3'"  N 0 1 Y N N 3.017  105.977 54.737 -7.331  -1.246 0.477  "N3'"  AYD 4  
AYD "C4'"  "C4'"  C 0 1 Y N N 1.885  105.065 54.682 -6.142  -0.741 0.793  "C4'"  AYD 5  
AYD "N4'"  "N4'"  N 0 1 N N N 1.039  105.032 55.740 -5.258  -1.460 1.582  "N4'"  AYD 6  
AYD "C5'"  "C5'"  C 0 1 Y N N 1.682  104.189 53.461 -5.798  0.527  0.317  "C5'"  AYD 7  
AYD "C6'"  "C6'"  C 0 1 Y N N 2.693  104.337 52.384 -6.713  1.203  -0.465 "C6'"  AYD 8  
AYD "C7'"  "C7'"  C 0 1 N N N 0.483  103.187 53.336 -4.463  1.140  0.650  "C7'"  AYD 9  
AYD N3     N3     N 0 1 N N N -0.009 102.378 54.563 -3.435  0.580  -0.231 N3     AYD 10 
AYD C5     C5     C 0 1 N N N 0.993  101.092 56.636 -1.189  0.491  -0.905 C5     AYD 11 
AYD C4     C4     C 0 1 N N N 0.839  101.359 55.096 -2.115  0.996  -0.111 C4     AYD 12 
AYD CM4    CM4    C 0 1 N N N 1.609  100.508 54.136 -1.740  2.025  0.924  CM4    AYD 13 
AYD C6     C6     C 0 1 N N N 1.842  100.062 57.370 0.218   1.030  -0.859 C6     AYD 14 
AYD C7     C7     C 0 1 N N N 2.877  98.880  57.166 1.196   -0.120 -0.609 C7     AYD 15 
AYD O7     O7     O 0 1 N N N 4.140  98.065  57.711 2.530   0.391  -0.566 O7     AYD 16 
AYD PA     PA     P 0 1 N N R 5.122  97.978  58.844 3.819   -0.542 -0.320 PA     AYD 17 
AYD O1A    O1A    O 0 1 N N N 6.097  96.958  58.702 3.640   -1.309 0.933  O1A    AYD 18 
AYD O2A    O2A    O 0 1 N N N 5.827  99.149  58.996 3.986   -1.563 -1.554 O2A    AYD 19 
AYD O3A    O3A    O 0 1 N N N 4.358  97.620  60.160 5.134   0.379  -0.203 O3A    AYD 20 
AYD PB     PB     P 0 1 N N N 3.419  96.455  60.630 6.633   0.126  0.327  PB     AYD 21 
AYD O1B    O1B    O 0 1 N N N 2.090  96.940  60.360 6.590   -0.713 1.546  O1B    AYD 22 
AYD O2B    O2B    O 0 1 N N N 3.764  96.295  62.012 7.485   -0.627 -0.813 O2B    AYD 23 
AYD O3B    O3B    O 0 1 N N N 3.881  95.329  59.800 7.326   1.538  0.671  O3B    AYD 24 
AYD HM21   1HM2   H 0 0 N N N 5.157  107.665 54.775 -9.427  -1.745 -1.533 HM21   AYD 25 
AYD HM22   2HM2   H 0 0 N N N 5.992  106.475 53.716 -9.824  -1.831 0.200  HM22   AYD 26 
AYD HM23   3HM2   H 0 0 N N N 5.026  107.717 52.982 -10.247 -0.379 -0.738 HM23   AYD 27 
AYD "H4'1" "1H4'" H 0 0 N N N 0.245  104.392 55.701 -5.505  -2.339 1.908  "H4'1" AYD 28 
AYD "H4'2" "2H4'" H 0 0 N N N 0.698  105.975 55.924 -4.393  -1.084 1.808  "H4'2" AYD 29 
AYD "H6'"  "H6'"  H 0 1 N N N 2.635  103.743 51.456 -6.482  2.185  -0.851 "H6'"  AYD 30 
AYD "H7'1" "1H7'" H 0 0 N N N -0.388 103.739 52.912 -4.513  2.220  0.508  "H7'1" AYD 31 
AYD "H7'2" "2H7'" H 0 0 N N N 0.716  102.467 52.516 -4.210  0.922  1.688  "H7'2" AYD 32 
AYD HN3    HN3    H 0 1 N N N -0.919 101.971 54.347 -3.676  -0.083 -0.897 HN3    AYD 33 
AYD H5     H5     H 0 1 N N N 0.407  101.734 57.314 -1.439  -0.308 -1.587 H5     AYD 34 
AYD HM41   1HM4   H 0 0 N N N 2.270  99.712  54.551 -2.611  2.257  1.537  HM41   AYD 35 
AYD HM42   2HM4   H 0 0 N N N 0.901  100.048 53.407 -0.945  1.631  1.557  HM42   AYD 36 
AYD HM43   3HM4   H 0 0 N N N 2.208  101.166 53.464 -1.394  2.931  0.427  HM43   AYD 37 
AYD H61    1H6    H 0 1 N N N 2.415  100.721 58.062 0.455   1.508  -1.810 H61    AYD 38 
AYD H62    2H6    H 0 1 N N N 1.063  99.551  57.984 0.301   1.760  -0.054 H62    AYD 39 
AYD H71    1H7    H 0 1 N N N 2.161  98.035  57.035 0.959   -0.598 0.341  H71    AYD 40 
AYD H72    2H7    H 0 1 N N N 3.260  99.150  56.154 1.112   -0.850 -1.414 H72    AYD 41 
AYD H2A    H2A    H 0 1 N N N 6.448  99.094  59.712 4.107   -1.129 -2.409 H2A    AYD 42 
AYD H2B    H2B    H 0 1 N N N 3.195  95.589  62.296 7.555   -0.133 -1.642 H2B    AYD 43 
AYD H3B    H3B    H 0 1 N N N 3.312  94.623  60.084 8.233   1.462  0.997  H3B    AYD 44 
# 
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 
AYD "N1'" "C2'"  DOUB Y N 1  
AYD "N1'" "C6'"  SING Y N 2  
AYD "C2'" CM2    SING N N 3  
AYD "C2'" "N3'"  SING Y N 4  
AYD CM2   HM21   SING N N 5  
AYD CM2   HM22   SING N N 6  
AYD CM2   HM23   SING N N 7  
AYD "N3'" "C4'"  DOUB Y N 8  
AYD "C4'" "N4'"  SING N N 9  
AYD "C4'" "C5'"  SING Y N 10 
AYD "N4'" "H4'1" SING N N 11 
AYD "N4'" "H4'2" SING N N 12 
AYD "C5'" "C6'"  DOUB Y N 13 
AYD "C5'" "C7'"  SING N N 14 
AYD "C6'" "H6'"  SING N N 15 
AYD "C7'" N3     SING N N 16 
AYD "C7'" "H7'1" SING N N 17 
AYD "C7'" "H7'2" SING N N 18 
AYD N3    C4     SING N N 19 
AYD N3    HN3    SING N N 20 
AYD C5    C4     DOUB N E 21 
AYD C5    C6     SING N N 22 
AYD C5    H5     SING N N 23 
AYD C4    CM4    SING N N 24 
AYD CM4   HM41   SING N N 25 
AYD CM4   HM42   SING N N 26 
AYD CM4   HM43   SING N N 27 
AYD C6    C7     SING N N 28 
AYD C6    H61    SING N N 29 
AYD C6    H62    SING N N 30 
AYD C7    O7     SING N N 31 
AYD C7    H71    SING N N 32 
AYD C7    H72    SING N N 33 
AYD O7    PA     SING N N 34 
AYD PA    O1A    DOUB N N 35 
AYD PA    O2A    SING N N 36 
AYD PA    O3A    SING N N 37 
AYD O2A   H2A    SING N N 38 
AYD O3A   PB     SING N N 39 
AYD PB    O1B    DOUB N N 40 
AYD PB    O2B    SING N N 41 
AYD PB    O3B    SING N N 42 
AYD O2B   H2B    SING N N 43 
AYD O3B   H3B    SING N N 44 
# 
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 
AYD SMILES           ACDLabs              10.04 "O=P(O)(O)OP(=O)(O)OCC/C=C(/NCc1cnc(nc1N)C)C"                                                                                                               
AYD InChI            InChI                1.03  "InChI=1S/C11H20N4O7P2/c1-8(13-6-10-7-14-9(2)15-11(10)12)4-3-5-21-24(19,20)22-23(16,17)18/h4,7,13H,3,5-6H2,1-2H3,(H,19,20)(H2,12,14,15)(H2,16,17,18)/b8-4+" 
AYD InChIKey         InChI                1.03  DPGNBHAKLFOOJK-XBXARRHUSA-N                                                                                                                                 
AYD SMILES_CANONICAL CACTVS               3.385 "CC(\NCc1cnc(C)nc1N)=C/CCO[P](O)(=O)O[P](O)(O)=O"                                                                                                           
AYD SMILES           CACTVS               3.385 "CC(NCc1cnc(C)nc1N)=CCCO[P](O)(=O)O[P](O)(O)=O"                                                                                                             
AYD SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 "Cc1ncc(c(n1)N)CN/C(=C/CCO[P@@](=O)(O)OP(=O)(O)O)/C"                                                                                                        
AYD SMILES           "OpenEye OEToolkits" 1.7.5 "Cc1ncc(c(n1)N)CNC(=CCCOP(=O)(O)OP(=O)(O)O)C"                                                                                                               
# 
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 
AYD "SYSTEMATIC NAME" ACDLabs              10.04 "(3E)-4-{[(4-amino-2-methylpyrimidin-5-yl)methyl]amino}pent-3-en-1-yl trihydrogen diphosphate"   
AYD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(E)-4-[(4-amino-2-methyl-pyrimidin-5-yl)methylamino]pent-3-enyl] phosphono 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 
AYD "Create component"   2002-10-31 RCSB 
AYD "Modify descriptor"  2011-06-04 RCSB 
AYD "Modify descriptor"  2012-01-05 RCSB 
AYD "Modify coordinates" 2012-01-05 RCSB 
# 
