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
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
APR N1 N 6.335 9.068 1
APR C2 C 7.706 8.460 2
APR N3 N 7.865 6.968 3
APR C4 C 6.654 6.085 4
APR C5 C 5.282 6.692 5
APR C6 C 5.123 8.184 6
APR N6 N 3.752 8.792 7
APR N7 N 4.289 5.580 8
APR C8 C 5.038 4.291 9
APR N9 N 6.496 4.602 10
APR "C1'" C 7.611 3.598 11
APR "C2'" C 9.078 3.910 12
APR "O2'" O 9.688 5.280 13
APR "C3'" C 9.828 2.611 14
APR "O3'" O 11.320 2.454 15
APR "O4'" O 7.454 2.107 16
APR "C4'" C 8.825 1.496 17
APR "C5'" C 9.136 0.029 18
APR "O5'" O 10.563 -0.434 19
APR PA P 10.875 -1.902 20
APR O1A O 9.408 -2.214 21
APR O2A O 12.342 -1.590 22
APR O3A O 11.187 -3.369 23
APR PB P 12.614 -3.833 24
APR O1B O 13.077 -2.406 25
APR O2B O 12.150 -5.259 26
APR O5D O 14.040 -4.296 27
APR C5D C 14.352 -5.763 28
APR O4D O 16.992 -5.345 29
APR O1D O 19.632 -5.763 30
APR C1D C 18.206 -6.227 31
APR O2D O 18.624 -8.867 32
APR C2D C 17.742 -7.653 33
APR O3D O 15.360 -8.867 34
APR C3D C 16.242 -7.653 35
APR C4D C 15.778 -6.227 36
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
APR N1 C2 DOUBLE NONE 1
APR N1 C6 SINGLE NONE 2
APR C2 N3 SINGLE NONE 3
APR N3 C4 DOUBLE NONE 4
APR C4 C5 SINGLE NONE 5
APR C4 N9 SINGLE NONE 6
APR C5 C6 DOUBLE NONE 7
APR C5 N7 SINGLE NONE 8
APR C6 N6 SINGLE NONE 9
APR N7 C8 DOUBLE NONE 10
APR C8 N9 SINGLE NONE 11
APR "C1'" N9 SINGLE BEGINWEDGE 12
APR "C1'" "C2'" SINGLE NONE 13
APR "C1'" "O4'" SINGLE NONE 14
APR "C2'" "O2'" SINGLE BEGINDASH 15
APR "C2'" "C3'" SINGLE NONE 16
APR "C3'" "O3'" SINGLE BEGINDASH 17
APR "C3'" "C4'" SINGLE NONE 18
APR "O4'" "C4'" SINGLE NONE 19
APR "C4'" "C5'" SINGLE BEGINWEDGE 20
APR "C5'" "O5'" SINGLE NONE 21
APR "O5'" PA SINGLE NONE 22
APR PA O1A DOUBLE NONE 23
APR PA O2A SINGLE BEGINWEDGE 24
APR PA O3A SINGLE NONE 25
APR O3A PB SINGLE NONE 26
APR PB O1B DOUBLE NONE 27
APR PB O2B SINGLE BEGINDASH 28
APR PB O5D SINGLE NONE 29
APR O5D C5D SINGLE NONE 30
APR C4D C5D SINGLE BEGINWEDGE 31
APR O4D C1D SINGLE NONE 32
APR O4D C4D SINGLE NONE 33
APR C1D O1D SINGLE BEGINWEDGE 34
APR C1D C2D SINGLE NONE 35
APR C2D O2D SINGLE BEGINDASH 36
APR C2D C3D SINGLE NONE 37
APR C3D O3D SINGLE BEGINDASH 38
APR C3D C4D SINGLE NONE 39
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
APR MurckoScaffold S1 scaffold 'O=[PH](OC[C@@H]1CCCO1)O[PH](=O)OC[C@@H]1CC[C@H](n2cnc3cncnc32)O1' InChI=1S/C15H22N4O7P2/c20-27(23-7-11-2-1-5-22-11)26-28(21)24-8-12-3-4-14(25-12)19-10-18-13-6-16-9-17-15(13)19/h6,9-12,14,27-28H,1-5,7-8H2/t11-,12-,14+/m0/s1 UJUHCPFOMLEXIT-SGMGOOAPSA-N
APR adenine F1 fragment 'Nc1ncnc2nc[nH]c12' InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10) GFFGJBXGBJISGV-UHFFFAOYSA-N
APR furanose F2 fragment OC1CCCO1 InChI=1S/C4H8O2/c5-4-2-1-3-6-4/h4-5H,1-3H2 JNODDICFTDYODH-UHFFFAOYSA-N
APR imidazole F3 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
APR phosphate F4 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
APR purine F5 fragment 'c1ncc2[nH]cnc2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N
APR pyrimidine F6 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
APR ribose F7 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
APR N1 S1 1
APR C2 S1 1
APR N3 S1 1
APR C4 S1 1
APR C5 S1 1
APR C6 S1 1
APR N7 S1 1
APR C8 S1 1
APR N9 S1 1
APR "C1'" S1 1
APR "C2'" S1 1
APR "C3'" S1 1
APR "O4'" S1 1
APR "C4'" S1 1
APR "C5'" S1 1
APR "O5'" S1 1
APR PA S1 1
APR O1A S1 1
APR O3A S1 1
APR PB S1 1
APR O1B S1 1
APR O5D S1 1
APR C5D S1 1
APR O4D S1 1
APR C1D S1 1
APR C2D S1 1
APR C3D S1 1
APR C4D S1 1
APR N1 F1 1
APR C6 F1 1
APR C5 F1 1
APR C4 F1 1
APR N3 F1 1
APR C2 F1 1
APR N9 F1 1
APR C8 F1 1
APR N7 F1 1
APR N6 F1 1
APR C3D F2 1
APR C4D F2 1
APR O4D F2 1
APR C1D F2 1
APR C2D F2 1
APR O1D F2 1
APR C4 F3 1
APR C5 F3 1
APR N7 F3 1
APR C8 F3 1
APR N9 F3 1
APR "O5'" F4 1
APR PA F4 1
APR O1A F4 1
APR O2A F4 1
APR O3A F4 1
APR O3A F4 2
APR PB F4 2
APR O1B F4 2
APR O2B F4 2
APR O5D F4 2
APR N7 F5 1
APR C8 F5 1
APR N9 F5 1
APR C4 F5 1
APR C5 F5 1
APR C6 F5 1
APR N1 F5 1
APR C2 F5 1
APR N3 F5 1
APR C5 F6 1
APR C4 F6 1
APR N3 F6 1
APR C2 F6 1
APR N1 F6 1
APR C6 F6 1
APR "C2'" F7 1
APR "C3'" F7 1
APR "C4'" F7 1
APR "O4'" F7 1
APR "C1'" F7 1
APR "C5'" F7 1
APR "O5'" F7 1
APR "O3'" F7 1
APR "O2'" F7 1
APR C2D F7 2
APR C3D F7 2
APR C4D F7 2
APR O4D F7 2
APR C1D F7 2
APR C5D F7 2
APR O5D F7 2
APR O3D F7 2
APR O2D F7 2
#
_pdbe_chem_comp_rdkit_properties.comp_id APR
_pdbe_chem_comp_rdkit_properties.exactmw 559.072
_pdbe_chem_comp_rdkit_properties.amw 559.318
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 19
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 9
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 17
_pdbe_chem_comp_rdkit_properties.NumHBD 8
_pdbe_chem_comp_rdkit_properties.NumHBA 19
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 36
_pdbe_chem_comp_rdkit_properties.NumAtoms 59
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 21
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.667
_pdbe_chem_comp_rdkit_properties.NumRings 4
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 4
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 10
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 233.433
_pdbe_chem_comp_rdkit_properties.tpsa 291.520
_pdbe_chem_comp_rdkit_properties.CrippenClogP -4.092
_pdbe_chem_comp_rdkit_properties.CrippenMR 108.162
_pdbe_chem_comp_rdkit_properties.chi0v 18.135
_pdbe_chem_comp_rdkit_properties.chi1v 11.363
_pdbe_chem_comp_rdkit_properties.chi2v 5.940
_pdbe_chem_comp_rdkit_properties.chi3v 5.940
_pdbe_chem_comp_rdkit_properties.chi4v 3.909
_pdbe_chem_comp_rdkit_properties.chi0n 39.346
_pdbe_chem_comp_rdkit_properties.chi1n 19.194
_pdbe_chem_comp_rdkit_properties.chi2n 3.710
_pdbe_chem_comp_rdkit_properties.chi3n 3.710
_pdbe_chem_comp_rdkit_properties.chi4n 2.273
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.670
_pdbe_chem_comp_rdkit_properties.kappa1 10.478
_pdbe_chem_comp_rdkit_properties.kappa2 10.239
_pdbe_chem_comp_rdkit_properties.kappa3 5.592
_pdbe_chem_comp_rdkit_properties.Phi 2.980
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
APR UniChem 'KEGG LIGAND' C00301
APR UniChem ChEBI 191409
APR UniChem ZINC ZINC000017654550
APR UniChem PubChem 445794
APR UniChem MetaboLights MTBLC191409
APR UniChem BRENDA 1069
APR UniChem BRENDA 11541
APR UniChem BRENDA 29704
APR UniChem BRENDA 402
APR UniChem BRENDA 43705
APR UniChem BRENDA 6655
APR UniChem BRENDA 7141
APR UniChem BRENDA 95991
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
APR N1 -7.999 3.119 0.559 ETKDGv3 1
APR C2 -7.495 2.626 1.667 ETKDGv3 2
APR N3 -6.167 2.051 1.677 ETKDGv3 3
APR C4 -5.484 2.102 0.575 ETKDGv3 4
APR C5 -6.009 2.619 -0.635 ETKDGv3 5
APR C6 -7.247 3.108 -0.677 ETKDGv3 6
APR N6 -7.835 3.573 -1.892 ETKDGv3 7
APR N7 -5.097 2.343 -1.690 ETKDGv3 8
APR C8 -4.101 1.711 -1.125 ETKDGv3 9
APR N9 -4.227 1.519 0.301 ETKDGv3 10
APR "C1'" -3.551 0.499 1.103 ETKDGv3 11
APR "C2'" -4.159 -0.885 0.844 ETKDGv3 12
APR "O2'" -4.390 -1.578 2.050 ETKDGv3 13
APR "C3'" -3.114 -1.561 -0.014 ETKDGv3 14
APR "O3'" -3.014 -2.937 0.248 ETKDGv3 15
APR "O4'" -2.176 0.481 0.775 ETKDGv3 16
APR "C4'" -1.838 -0.832 0.387 ETKDGv3 17
APR "C5'" -0.812 -0.785 -0.749 ETKDGv3 18
APR "O5'" -0.435 -2.098 -1.095 ETKDGv3 19
APR PA 0.760 -2.014 -2.309 ETKDGv3 20
APR O1A 0.187 -1.337 -3.535 ETKDGv3 21
APR O2A 1.226 -3.585 -2.738 ETKDGv3 22
APR O3A 2.104 -1.118 -1.768 ETKDGv3 23
APR PB 2.896 -2.040 -0.573 ETKDGv3 24
APR O1B 3.588 -3.227 -1.207 ETKDGv3 25
APR O2B 1.796 -2.598 0.588 ETKDGv3 26
APR O5D 4.054 -1.071 0.217 ETKDGv3 27
APR C5D 4.901 -0.503 -0.755 ETKDGv3 28
APR O4D 5.406 1.310 0.754 ETKDGv3 29
APR O1D 5.098 0.697 2.936 ETKDGv3 30
APR C1D 6.016 1.244 2.025 ETKDGv3 31
APR O2D 8.419 1.137 1.711 ETKDGv3 32
APR C2D 7.262 0.363 1.933 ETKDGv3 33
APR O3D 8.101 -0.883 0.049 ETKDGv3 34
APR C3D 6.944 -0.536 0.765 ETKDGv3 35
APR C4D 5.994 0.325 -0.071 ETKDGv3 36
APR H2 -8.081 2.639 2.575 ETKDGv3 37
APR H61 -8.814 3.937 -1.892 ETKDGv3 38
APR H62 -7.303 3.561 -2.791 ETKDGv3 39
APR H8 -3.260 1.342 -1.696 ETKDGv3 40
APR "H'1" -3.652 0.772 2.177 ETKDGv3 41
APR "H'2" -5.122 -0.818 0.290 ETKDGv3 42
APR "HO'2" -3.532 -1.626 2.549 ETKDGv3 43
APR "H'3" -3.344 -1.383 -1.092 ETKDGv3 44
APR "HO'3" -3.808 -3.360 -0.171 ETKDGv3 45
APR "H'4" -1.371 -1.340 1.262 ETKDGv3 46
APR "H5'1" -1.261 -0.258 -1.621 ETKDGv3 47
APR "H5'2" 0.067 -0.204 -0.387 ETKDGv3 48
APR HOA2 0.376 -4.059 -2.922 ETKDGv3 49
APR HOB2 1.536 -1.790 1.098 ETKDGv3 50
APR H5R1 4.325 0.179 -1.421 ETKDGv3 51
APR H5R2 5.391 -1.289 -1.375 ETKDGv3 52
APR HOR1 5.435 0.913 3.845 ETKDGv3 53
APR "HR'1" 6.289 2.277 2.344 ETKDGv3 54
APR HOR2 8.270 1.698 0.904 ETKDGv3 55
APR "HR'2" 7.410 -0.234 2.859 ETKDGv3 56
APR HOR3 7.833 -1.595 -0.589 ETKDGv3 57
APR "HR'3" 6.436 -1.453 1.149 ETKDGv3 58
APR "HR'4" 6.577 0.849 -0.862 ETKDGv3 59
#