data_APR
# 
_chem_comp.id                                    APR 
_chem_comp.name                                  ADENOSINE-5-DIPHOSPHORIBOSE 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C15 H23 N5 O14 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1999-07-08 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        559.316 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     APR 
_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        1G9Q 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              Y 
# 
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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
APR N1     N1   N 0 1 Y N N N N N 57.304 21.677 3.126  2.348  -0.932 9.041   N1     APR 1  
APR C2     C2   C 0 1 Y N N N N N 58.333 20.780 2.780  1.265  -1.622 8.731   C2     APR 2  
APR N3     N3   N 0 1 Y N N N N N 58.815 19.783 3.523  0.592  -1.418 7.618   N3     APR 3  
APR C4     C4   C 0 1 Y N N N N N 58.161 19.655 4.774  0.984  -0.493 6.749   C4     APR 4  
APR C5     C5   C 0 1 Y N N N N N 57.100 20.441 5.267  2.128  0.271  7.035   C5     APR 5  
APR C6     C6   C 0 1 Y N N N N N 56.684 21.562 4.396  2.816  0.012  8.233   C6     APR 6  
APR N6     N6   N 0 1 N N N N N N 55.837 22.531 4.767  3.952  0.730  8.566   N6     APR 7  
APR N7     N7   N 0 1 Y N N N N N 56.714 19.987 6.521  2.307  1.124  5.999   N7     APR 8  
APR C8     C8   C 0 1 Y N N N N N 57.592 19.016 6.814  1.365  0.943  5.120   C8     APR 9  
APR N9     N9   N 0 1 Y N N N N N 58.523 18.831 5.825  0.523  -0.044 5.537   N9     APR 10 
APR "C1'"  C1*  C 0 1 N N R N N N 59.925 18.013 5.799  -0.656 -0.537 4.822   "C1'"  APR 11 
APR "C2'"  C2*  C 0 1 N N R N N N 60.873 18.577 6.883  -1.902 0.290  5.207   "C2'"  APR 12 
APR "O2'"  O2*  O 0 1 N N N N N N 62.159 18.740 6.323  -2.672 -0.385 6.202   "O2'"  APR 13 
APR "C3'"  C3*  C 0 1 N N S N N N 60.931 17.488 8.019  -2.700 0.400  3.886   "C3'"  APR 14 
APR "O3'"  O3*  O 0 1 N N N N N N 62.274 17.237 8.416  -3.986 -0.206 4.025   "O3'"  APR 15 
APR "O4'"  O4*  O 0 1 N N N N N N 59.714 16.695 6.161  -0.502 -0.338 3.400   "O4'"  APR 16 
APR "C4'"  C4*  C 0 1 N N R N N N 60.320 16.270 7.470  -1.842 -0.377 2.863   "C4'"  APR 17 
APR "C5'"  C5*  C 0 1 N N N N N N 59.249 15.847 8.393  -1.888 0.307  1.496   "C5'"  APR 18 
APR "O5'"  O5*  O 0 1 N N N N N N 58.071 15.548 7.636  -1.032 -0.386 0.586   "O5'"  APR 19 
APR PA     PA   P 0 1 N N S N N N 56.778 15.038 8.330  -1.129 0.384  -0.823  PA     APR 20 
APR O1A    O1A  O 0 1 N N N N N N 56.709 13.669 8.178  -0.686 1.786  -0.651  O1A    APR 21 
APR O2A    O2A  O 0 1 N N N N N N 55.711 15.657 7.705  -2.652 0.362  -1.343  O2A    APR 22 
APR O3A    O3A  O 0 1 N N N N N N 56.727 15.443 9.983  -0.183 -0.348 -1.901  O3A    APR 23 
APR PB     PB   P 0 1 N N R N N N 56.585 16.854 10.752 -0.328 0.470  -3.280  PB     APR 24 
APR O1B    O1B  O 0 1 N N N N N N 57.185 17.940 9.929  0.101  1.871  -3.069  O1B    APR 25 
APR O2B    O2B  O 0 1 N N N N N N 57.257 16.795 12.071 -1.865 0.447  -3.758  O2B    APR 26 
APR O5D    RO5* O 0 1 N N N N N N 54.938 17.195 10.904 0.595  -0.210 -4.408  O5D    APR 27 
APR C5D    RC5* C 0 1 N N N N N N 54.343 16.628 12.167 0.423  0.556  -5.601  C5D    APR 28 
APR O4D    RO4* O 0 1 N N N N N N 54.107 19.129 12.819 0.853  -1.385 -6.996  O4D    APR 29 
APR O1D    RO1* O 0 1 N N N N N N 52.862 20.438 11.386 0.208  -2.680 -8.863  O1D    APR 30 
APR C1D    RC1* C 0 1 N N R N N N 52.834 19.759 12.610 1.030  -1.602 -8.412  C1D    APR 31 
APR O2D    RO2* O 0 1 N N N N N N 50.542 19.075 13.137 1.185  -0.064 -10.319 O2D    APR 32 
APR C2D    RC2* C 0 1 N N R N N N 51.779 18.629 12.553 0.574  -0.261 -9.042  C2D    APR 33 
APR O3D    RO3* O 0 1 N N N N N N 51.951 17.595 14.816 2.341  1.326  -8.446  O3D    APR 34 
APR C3D    RC3* C 0 1 N N S N N N 52.364 17.465 13.367 1.096  0.775  -8.014  C3D    APR 35 
APR C4D    RC4* C 0 1 N N R N N N 53.842 17.623 13.261 1.279  -0.041 -6.720  C4D    APR 36 
APR H2     H2   H 0 1 N N N N N N 58.826 20.870 1.797  0.918  -2.381 9.417   H2     APR 37 
APR H61    1H6  H 0 1 N N N N N N 55.391 22.448 5.680  4.416  0.544  9.397   H61    APR 38 
APR H62    2H6  H 0 1 N N N N N N 55.118 22.640 4.051  4.286  1.415  7.966   H62    APR 39 
APR H8     H8   H 0 1 N N N N N N 57.553 18.439 7.753  1.265  1.493  4.196   H8     APR 40 
APR "H'1"  1H*  H 0 1 N N N N N N 60.348 18.101 4.771  -0.819 -1.592 5.042   "H'1"  APR 41 
APR "H'2"  2H*  H 0 1 N N N N N N 60.523 19.560 7.276  -1.608 1.279  5.559   "H'2"  APR 42 
APR "HO'2" 2HO* H 0 0 N N N N N N 62.741 19.086 6.988  -3.464 0.149  6.354   "HO'2" APR 43 
APR "H'3"  3H*  H 0 1 N N N N N N 60.384 17.837 8.926  -2.801 1.443  3.585   "H'3"  APR 44 
APR "HO'3" 3HO* H 0 0 N N N N N N 62.309 16.580 9.101  -4.474 0.319  4.673   "HO'3" APR 45 
APR "H'4"  4H*  H 0 1 N N N N N N 61.043 15.432 7.339  -2.189 -1.407 2.782   "H'4"  APR 46 
APR "H5'1" 1H5* H 0 0 N N N N N N 59.561 14.998 9.044  -2.910 0.293  1.116   "H5'1" APR 47 
APR "H5'2" 2H5* H 0 0 N N N N N N 59.058 16.598 9.194  -1.552 1.340  1.595   "H5'2" APR 48 
APR HOA2   2HOA H 0 0 N N N N N N 54.920 15.345 8.129  -2.901 -0.566 -1.442  HOA2   APR 49 
APR HOB2   2HOB H 0 0 N N N N N N 57.173 17.625 12.523 -2.105 -0.480 -3.884  HOB2   APR 50 
APR H5R1   1H5R H 0 0 N N N N N N 53.512 15.935 11.898 -0.625 0.539  -5.897  H5R1   APR 51 
APR H5R2   2H5R H 0 0 N N N N N N 55.071 15.919 12.626 0.732  1.586  -5.418  H5R2   APR 52 
APR HOR1   1HOR H 0 0 N N N N N N 52.019 20.854 11.247 0.495  -3.469 -8.385  HOR1   APR 53 
APR "HR'1" 1HR* H 0 0 N N N N N N 52.595 20.484 13.422 2.078  -1.797 -8.642  "HR'1" APR 54 
APR HOR2   2HOR H 0 0 N N N N N N 49.894 18.381 13.102 0.892  -0.792 -10.884 HOR2   APR 55 
APR "HR'2" 2HR* H 0 0 N N N N N N 51.559 18.323 11.503 -0.512 -0.219 -9.122  "HR'2" APR 56 
APR HOR3   3HOR H 0 0 N N N N N N 52.312 16.875 15.319 2.172  1.772  -9.288  HOR3   APR 57 
APR "HR'3" 3HR* H 0 0 N N N N N N 52.011 16.474 12.994 0.361  1.567  -7.864  "HR'3" APR 58 
APR "HR'4" 4HR* H 0 0 N N N N N N 54.373 17.409 14.217 2.329  -0.038 -6.425  "HR'4" APR 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 
APR N1    C2     SING Y N 1  
APR N1    C6     DOUB Y N 2  
APR C2    N3     DOUB Y N 3  
APR C2    H2     SING N N 4  
APR N3    C4     SING Y N 5  
APR C4    C5     DOUB Y N 6  
APR C4    N9     SING Y N 7  
APR C5    C6     SING Y N 8  
APR C5    N7     SING Y N 9  
APR C6    N6     SING N N 10 
APR N6    H61    SING N N 11 
APR N6    H62    SING N N 12 
APR N7    C8     DOUB Y N 13 
APR C8    N9     SING Y N 14 
APR C8    H8     SING N N 15 
APR N9    "C1'"  SING N N 16 
APR "C1'" "C2'"  SING N N 17 
APR "C1'" "O4'"  SING N N 18 
APR "C1'" "H'1"  SING N N 19 
APR "C2'" "O2'"  SING N N 20 
APR "C2'" "C3'"  SING N N 21 
APR "C2'" "H'2"  SING N N 22 
APR "O2'" "HO'2" SING N N 23 
APR "C3'" "O3'"  SING N N 24 
APR "C3'" "C4'"  SING N N 25 
APR "C3'" "H'3"  SING N N 26 
APR "O3'" "HO'3" SING N N 27 
APR "O4'" "C4'"  SING N N 28 
APR "C4'" "C5'"  SING N N 29 
APR "C4'" "H'4"  SING N N 30 
APR "C5'" "O5'"  SING N N 31 
APR "C5'" "H5'1" SING N N 32 
APR "C5'" "H5'2" SING N N 33 
APR "O5'" PA     SING N N 34 
APR PA    O1A    DOUB N N 35 
APR PA    O2A    SING N N 36 
APR PA    O3A    SING N N 37 
APR O2A   HOA2   SING N N 38 
APR O3A   PB     SING N N 39 
APR PB    O1B    DOUB N N 40 
APR PB    O2B    SING N N 41 
APR PB    O5D    SING N N 42 
APR O2B   HOB2   SING N N 43 
APR O5D   C5D    SING N N 44 
APR C5D   C4D    SING N N 45 
APR C5D   H5R1   SING N N 46 
APR C5D   H5R2   SING N N 47 
APR O4D   C1D    SING N N 48 
APR O4D   C4D    SING N N 49 
APR O1D   C1D    SING N N 50 
APR O1D   HOR1   SING N N 51 
APR C1D   C2D    SING N N 52 
APR C1D   "HR'1" SING N N 53 
APR O2D   C2D    SING N N 54 
APR O2D   HOR2   SING N N 55 
APR C2D   C3D    SING N N 56 
APR C2D   "HR'2" SING N N 57 
APR O3D   C3D    SING N N 58 
APR O3D   HOR3   SING N N 59 
APR C3D   C4D    SING N N 60 
APR C3D   "HR'3" SING N N 61 
APR C4D   "HR'4" 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 
APR SMILES           ACDLabs              10.04 "O=P(O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)OP(=O)(O)OCC4OC(O)C(O)C4O"                                                                                                                                                                     
APR SMILES_CANONICAL CACTVS               3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O"                                                                                                                         
APR SMILES           CACTVS               3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O"                                                                                                                                         
APR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)O)O)O)O)O)N"                                                                                                                   
APR SMILES           "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N"                                                                                                                                                             
APR InChI            InChI                1.03  "InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1" 
APR InChIKey         InChI                1.03  SRNWOUGRCWSEMX-KEOHHSTQSA-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 
APR "SYSTEMATIC NAME" ACDLabs              10.04 "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5R)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)" 
APR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5R)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] 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 
APR "Create component"  1999-07-08 RCSB 
APR "Modify descriptor" 2011-06-04 RCSB 
APR "Modify PCM"        2024-09-27 PDBE 
# 
loop_
_pdbx_chem_comp_pcm.pcm_id 
_pdbx_chem_comp_pcm.comp_id 
_pdbx_chem_comp_pcm.modified_residue_id 
_pdbx_chem_comp_pcm.type 
_pdbx_chem_comp_pcm.category 
_pdbx_chem_comp_pcm.position 
_pdbx_chem_comp_pcm.polypeptide_position 
_pdbx_chem_comp_pcm.comp_id_linking_atom 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession 
1  APR ARG ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D NH1 ? PTM-0053 
2  APR ASN ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D ND2 ? PTM-0054 
3  APR ASP ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D OD2 ? PTM-0497 
4  APR CYS ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D SG  ? PTM-0055 
5  APR DDE ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D NE2 ? PTM-0672 
6  APR GLU ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D OE2 ? PTM-0646 
7  APR GLY ADP-ribosylation ADP-ribose "Amino-acid backbone"   C-terminal     C1D OXT ? PTM-0671 
8  APR HIS ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D NE2 ? PTM-0720 
9  APR SER ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D OG  ? PTM-0056 
10 APR THR ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D OG1 ? PTM-0721 
11 APR TYR ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D OH  ? PTM-0670 
12 APR LYS ADP-ribosylation ADP-ribose "Amino-acid side chain" "Any position" C1D NZ  ? PTM-0355 
# 
