data_ADP # _chem_comp.id ADP _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H15 N5 O10 P2" _chem_comp.mon_nstd_parent_comp_id A _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2025-01-22 _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 427.201 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ADP _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 1PHP _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 ADP PB PB P 0 1 N N N N N N 44.669 2.928 38.556 1.162 -0.221 -5.685 PB ADP 1 ADP O1B O1B O 0 1 N N N N N N 46.021 3.508 38.317 1.725 1.133 -5.492 O1B ADP 2 ADP O2B O2B O 0 1 N N N N N N 43.709 3.812 37.905 2.190 -1.112 -6.546 O2B ADP 3 ADP O3B O3B O 0 1 N N N N N N 44.459 1.449 38.382 -0.240 -0.113 -6.467 O3B ADP 4 ADP PA PA P 0 1 N N S N N N 43.230 2.955 41.110 -0.105 0.025 -3.446 PA ADP 5 ADP O1A O1A O 0 1 N N N N N N 41.975 3.497 40.573 0.476 1.376 -3.288 O1A ADP 6 ADP O2A O2A O 0 1 N N N N N N 42.962 1.501 41.401 -1.487 0.129 -4.266 O2A ADP 7 ADP O3A O3A O 0 1 N N N N N N 44.522 3.210 40.212 0.925 -0.913 -4.250 O3A ADP 8 ADP "O5'" O5* O 0 1 N N N N N N 43.462 3.832 42.407 -0.389 -0.609 -1.994 "O5'" ADP 9 ADP "C5'" C5* C 0 1 N N N N N N 43.735 5.246 42.335 -1.307 0.264 -1.333 "C5'" ADP 10 ADP "C4'" C4* C 0 1 N N R N N N 43.095 5.810 43.626 -1.620 -0.284 0.059 "C4'" ADP 11 ADP "O4'" O4* O 0 1 N N N N N N 43.764 5.261 44.779 -0.417 -0.348 0.857 "O4'" ADP 12 ADP "C3'" C3* C 0 1 N N S N N N 43.337 7.325 43.617 -2.550 0.683 0.825 "C3'" ADP 13 ADP "O3'" O3* O 0 1 N N N N N N 42.056 7.988 43.560 -3.907 0.245 0.739 "O3'" ADP 14 ADP "C2'" C2* C 0 1 N N R N N N 43.946 7.593 45.083 -2.047 0.611 2.286 "C2'" ADP 15 ADP "O2'" O2* O 0 1 N N N N N N 43.554 8.726 45.877 -3.080 0.129 3.148 "O2'" ADP 16 ADP "C1'" C1* C 0 1 N N R N N N 43.613 6.275 45.813 -0.871 -0.388 2.227 "C1'" ADP 17 ADP N9 N9 N 0 1 Y N N N N N 44.375 5.781 46.991 0.201 0.031 3.132 N9 ADP 18 ADP C8 C8 C 0 1 Y N N N N N 45.711 5.486 47.062 1.231 0.870 2.827 C8 ADP 19 ADP N7 N7 N 0 1 Y N N N N N 46.202 5.379 48.282 2.000 1.027 3.865 N7 ADP 20 ADP C5 C5 C 0 1 Y N N N N N 45.067 5.597 49.064 1.509 0.305 4.902 C5 ADP 21 ADP C6 C6 C 0 1 Y N N N N N 44.883 5.623 50.499 1.910 0.087 6.231 C6 ADP 22 ADP N6 N6 N 0 1 N N N N N N 45.912 5.433 51.325 3.044 0.697 6.738 N6 ADP 23 ADP N1 N1 N 0 1 Y N N N N N 43.626 5.852 50.896 1.171 -0.714 6.991 N1 ADP 24 ADP C2 C2 C 0 1 Y N N N N N 42.590 6.076 50.067 0.088 -1.300 6.516 C2 ADP 25 ADP N3 N3 N 0 1 Y N N N N N 42.675 6.067 48.735 -0.321 -1.130 5.277 N3 ADP 26 ADP C4 C4 C 0 1 Y N N N N N 43.951 5.821 48.304 0.353 -0.346 4.442 C4 ADP 27 ADP HOB2 2HOB H 0 0 N N N N N N 42.847 3.442 38.057 2.304 -0.664 -7.396 HOB2 ADP 28 ADP HOB3 3HOB H 0 0 N N N N N N 43.597 1.079 38.534 -0.572 -1.016 -6.571 HOB3 ADP 29 ADP HOA2 2HOA H 0 0 N N N N N N 43.773 1.150 41.748 -1.833 -0.770 -4.346 HOA2 ADP 30 ADP "H5'1" 1H5* H 0 0 N N N N N N 44.812 5.500 42.206 -2.227 0.330 -1.913 "H5'1" ADP 31 ADP "H5'2" 2H5* H 0 0 N N N N N N 43.385 5.735 41.396 -0.862 1.255 -1.242 "H5'2" ADP 32 ADP "H4'" H4* H 0 1 N N N N N N 42.010 5.556 43.668 -2.078 -1.270 -0.015 "H4'" ADP 33 ADP "H3'" H3* H 0 1 N N N N N N 43.978 7.672 42.773 -2.451 1.696 0.435 "H3'" ADP 34 ADP "HO3'" *HO3 H 0 0 N N N N N N 42.205 8.926 43.554 -4.439 0.884 1.233 "HO3'" ADP 35 ADP "H2'" H2* H 0 1 N N N N N N 45.014 7.879 44.941 -1.699 1.589 2.618 "H2'" ADP 36 ADP "HO2'" *HO2 H 0 0 N N N N N N 43.913 8.884 46.742 -3.807 0.764 3.094 "HO2'" ADP 37 ADP "H1'" H1* H 0 1 N N N N N N 42.621 6.482 46.279 -1.212 -1.391 2.485 "H1'" ADP 38 ADP H8 H8 H 0 1 N N N N N N 46.358 5.341 46.181 1.387 1.335 1.865 H8 ADP 39 ADP HN61 1HN6 H 0 0 N N N N N N 45.782 5.451 52.336 3.308 0.542 7.658 HN61 ADP 40 ADP HN62 2HN6 H 0 0 N N N N N N 46.639 6.107 51.086 3.577 1.277 6.172 HN62 ADP 41 ADP H2 H2 H 0 1 N N N N N N 41.601 6.281 50.510 -0.482 -1.944 7.169 H2 ADP 42 # 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 ADP PB O1B DOUB N N 1 ADP PB O2B SING N N 2 ADP PB O3B SING N N 3 ADP PB O3A SING N N 4 ADP O2B HOB2 SING N N 5 ADP O3B HOB3 SING N N 6 ADP PA O1A DOUB N N 7 ADP PA O2A SING N N 8 ADP PA O3A SING N N 9 ADP PA "O5'" SING N N 10 ADP O2A HOA2 SING N N 11 ADP "O5'" "C5'" SING N N 12 ADP "C5'" "C4'" SING N N 13 ADP "C5'" "H5'1" SING N N 14 ADP "C5'" "H5'2" SING N N 15 ADP "C4'" "O4'" SING N N 16 ADP "C4'" "C3'" SING N N 17 ADP "C4'" "H4'" SING N N 18 ADP "O4'" "C1'" SING N N 19 ADP "C3'" "O3'" SING N N 20 ADP "C3'" "C2'" SING N N 21 ADP "C3'" "H3'" SING N N 22 ADP "O3'" "HO3'" SING N N 23 ADP "C2'" "O2'" SING N N 24 ADP "C2'" "C1'" SING N N 25 ADP "C2'" "H2'" SING N N 26 ADP "O2'" "HO2'" SING N N 27 ADP "C1'" N9 SING N N 28 ADP "C1'" "H1'" SING N N 29 ADP N9 C8 SING Y N 30 ADP N9 C4 SING Y N 31 ADP C8 N7 DOUB Y N 32 ADP C8 H8 SING N N 33 ADP N7 C5 SING Y N 34 ADP C5 C6 SING Y N 35 ADP C5 C4 DOUB Y N 36 ADP C6 N6 SING N N 37 ADP C6 N1 DOUB Y N 38 ADP N6 HN61 SING N N 39 ADP N6 HN62 SING N N 40 ADP N1 C2 SING Y N 41 ADP C2 N3 DOUB Y N 42 ADP C2 H2 SING N N 43 ADP N3 C4 SING Y 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 ADP SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O" ADP SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O" ADP SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O" ADP 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)OP(=O)(O)O)O)O)N" ADP SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N" ADP InChI InChI 1.03 "InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1" ADP InChIKey InChI 1.03 XTWYTFMLZFPYCI-KQYNXXCUSA-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 ADP "SYSTEMATIC NAME" ACDLabs 10.04 ;adenosine 5'-(trihydrogen diphosphate) ; ADP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl 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 ADP "Create component" 1999-07-08 RCSB ADP "Modify descriptor" 2011-06-04 RCSB ADP "Modify PCM" 2025-01-22 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 ADP LYS None "Covalent chemical modification" "Amino-acid side chain" "Any position" O3B NZ ? ? 2 ADP GLY None "Covalent chemical modification" "Amino-acid side chain" "Any position" O1B N ? ? #