data_9BG # _chem_comp.id 9BG _chem_comp.name "2',5'-GpAp" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H26 N10 O14 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl [(2~{R},3~{R},4~{R},5~{R})-2-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-04-17 _chem_comp.pdbx_modified_date 2021-03-13 _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 692.427 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 9BG _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 5VDQ _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 9BG C10 C1 C 0 1 Y N N -25.527 -7.298 -27.175 6.372 -1.113 0.799 C10 9BG 1 9BG C17 C2 C 0 1 N N R -27.287 -8.434 -30.657 4.890 2.359 -1.289 C17 9BG 2 9BG C24 C3 C 0 1 N N R -28.466 -12.209 -24.787 -2.100 1.507 -0.090 C24 9BG 3 9BG C02 C4 C 0 1 N N N -24.680 -9.655 -24.423 4.313 -3.681 2.293 C02 9BG 4 9BG C04 C5 C 0 1 N N N -24.621 -11.715 -25.838 2.454 -3.310 0.962 C04 9BG 5 9BG C07 C6 C 0 1 Y N N -25.155 -9.448 -26.911 4.345 -1.934 0.577 C07 9BG 6 9BG C08 C7 C 0 1 Y N N -25.027 -8.831 -25.670 5.018 -2.605 1.590 C08 9BG 7 9BG C12 C8 C 0 1 N N R -25.657 -8.688 -29.113 4.947 -0.058 -0.997 C12 9BG 8 9BG C14 C9 C 0 1 N N R -26.060 -7.313 -30.914 5.860 1.635 -2.249 C14 9BG 9 9BG C19 C10 C 0 1 N N R -27.157 -8.871 -29.441 4.275 1.219 -0.447 C19 9BG 10 9BG C23 C11 C 0 1 N N N -28.976 -12.397 -26.204 -0.847 1.556 0.786 C23 9BG 11 9BG C25 C12 C 0 1 N N S -29.751 -12.026 -23.731 -3.342 1.855 0.753 C25 9BG 12 9BG N34 N1 N 0 1 Y N N -28.401 -9.162 -23.588 -4.011 -1.481 -0.691 N34 9BG 13 9BG O01 O1 O 0 1 N N N -24.571 -9.122 -23.363 4.860 -4.302 3.192 O01 9BG 14 9BG N03 N2 N 0 1 N N N -24.487 -11.072 -24.538 3.055 -3.970 1.928 N03 9BG 15 9BG N05 N3 N 0 1 N N N -24.432 -13.116 -25.964 1.168 -3.649 0.633 N05 9BG 16 9BG N06 N4 N 0 1 N N N -24.955 -10.911 -27.030 3.059 -2.304 0.278 N06 9BG 17 9BG N09 N5 N 0 1 Y N N -25.257 -7.517 -25.843 6.252 -2.058 1.688 N09 9BG 18 9BG N11 N6 N 0 1 Y N N -25.463 -8.497 -27.817 5.212 -1.004 0.090 N11 9BG 19 9BG O13 O2 O 0 1 N N N -25.239 -7.396 -29.942 6.187 0.398 -1.579 O13 9BG 20 9BG C15 C13 C 0 1 N N N -26.628 -5.915 -30.982 7.122 2.475 -2.463 C15 9BG 21 9BG O16 O3 O 0 1 N N N -26.431 -5.282 -29.691 7.952 1.845 -3.441 O16 9BG 22 9BG O18 O4 O 0 1 N N N -27.162 -9.516 -31.580 3.872 3.043 -2.024 O18 9BG 23 9BG O20 O5 O 0 1 N N N -27.516 -10.353 -29.368 2.860 1.162 -0.638 O20 9BG 24 9BG P21 P1 P 0 1 N N N -28.715 -10.794 -28.300 1.805 1.312 0.570 P21 9BG 25 9BG O22 O6 O 0 1 N N N -28.081 -11.798 -27.119 0.309 1.330 -0.024 O22 9BG 26 9BG O26 O7 O 0 1 N N N -30.135 -13.328 -23.127 -3.994 3.014 0.229 O26 9BG 27 9BG P27 P2 P 0 1 N N N -30.583 -14.666 -24.129 -4.202 4.364 1.081 P27 9BG 28 9BG O28 O8 O 0 1 N N N -31.279 -14.177 -25.371 -2.894 4.833 1.590 O28 9BG 29 9BG O29 O9 O 0 1 N N N -31.504 -15.554 -23.370 -4.850 5.499 0.140 O29 9BG 30 9BG O30 O10 O 0 1 N N N -29.332 -15.455 -24.528 -5.186 4.069 2.321 O30 9BG 31 9BG C31 C14 C 0 1 N N R -29.381 -11.217 -22.815 -4.255 0.612 0.616 C31 9BG 32 9BG O32 O11 O 0 1 N N N -28.999 -11.969 -21.556 -5.622 0.998 0.458 O32 9BG 33 9BG C33 C15 C 0 1 N N R -28.123 -10.448 -23.376 -3.714 -0.046 -0.679 C33 9BG 34 9BG C35 C16 C 0 1 Y N N -28.253 -8.129 -22.664 -5.178 -2.064 -1.116 C35 9BG 35 9BG N36 N7 N 0 1 Y N N -27.826 -8.091 -21.351 -6.326 -1.614 -1.611 N36 9BG 36 9BG C37 C17 C 0 1 Y N N -27.792 -6.959 -20.719 -7.290 -2.449 -1.937 C37 9BG 37 9BG N38 N8 N 0 1 Y N N -28.155 -5.832 -21.290 -7.174 -3.757 -1.792 N38 9BG 38 9BG C39 C18 C 0 1 Y N N -28.579 -5.797 -22.558 -6.063 -4.299 -1.305 C39 9BG 39 9BG N40 N9 N 0 1 N N N -28.980 -4.532 -23.179 -5.951 -5.670 -1.157 N40 9BG 40 9BG C41 C19 C 0 1 Y N N -28.632 -6.994 -23.280 -5.005 -3.447 -0.943 C41 9BG 41 9BG N42 N10 N 0 1 Y N N -28.995 -7.312 -24.529 -3.765 -3.634 -0.431 N42 9BG 42 9BG C43 C20 C 0 1 Y N N -28.840 -8.661 -24.691 -3.178 -2.481 -0.287 C43 9BG 43 9BG O44 O12 O 0 1 N N N -27.760 -11.134 -24.718 -2.289 0.176 -0.600 O44 9BG 44 9BG O45 O13 O 0 1 N N N -29.779 -11.486 -29.030 2.063 2.576 1.296 O45 9BG 45 9BG O46 O14 O 0 1 N N N -29.292 -9.506 -27.625 1.967 0.070 1.581 O46 9BG 46 9BG H1 H1 H 0 1 N N N -25.750 -6.344 -27.630 7.252 -0.506 0.650 H1 9BG 47 9BG H2 H2 H 0 1 N N N -28.241 -7.910 -30.813 5.432 3.056 -0.651 H2 9BG 48 9BG H3 H3 H 0 1 N N N -27.911 -13.107 -24.478 -2.005 2.211 -0.917 H3 9BG 49 9BG H4 H4 H 0 1 N N N -25.095 -9.550 -29.501 4.317 -0.522 -1.757 H4 9BG 50 9BG H5 H5 H 0 1 N N N -25.598 -7.559 -31.881 5.372 1.433 -3.202 H5 9BG 51 9BG H6 H6 H 0 1 N N N -27.760 -8.309 -28.712 4.512 1.354 0.608 H6 9BG 52 9BG H7 H7 H 0 1 N N N -29.966 -11.927 -26.301 -0.773 2.534 1.260 H7 9BG 53 9BG H8 H8 H 0 1 N N N -29.057 -13.472 -26.423 -0.910 0.784 1.553 H8 9BG 54 9BG H9 H9 H 0 1 N N N -30.596 -11.637 -24.319 -3.064 2.014 1.795 H9 9BG 55 9BG H10 H10 H 0 1 N N N -24.206 -13.664 -25.159 0.719 -4.364 1.109 H10 9BG 56 9BG H11 H11 H 0 1 N N N -24.525 -13.555 -26.858 0.708 -3.174 -0.076 H11 9BG 57 9BG H12 H12 H 0 1 N N N -25.047 -11.356 -27.921 2.578 -1.844 -0.428 H12 9BG 58 9BG H13 H13 H 0 1 N N N -26.108 -5.339 -31.762 6.841 3.469 -2.810 H13 9BG 59 9BG H14 H14 H 0 1 N N N -27.702 -5.960 -31.214 7.666 2.558 -1.523 H14 9BG 60 9BG H15 H15 H 0 1 N N N -26.782 -4.400 -29.713 8.772 2.323 -3.628 H15 9BG 61 9BG H16 H16 H 0 1 N N N -27.858 -10.144 -31.428 4.203 3.769 -2.571 H16 9BG 62 9BG H17 H17 H 0 1 N N N -32.332 -15.621 -23.832 -5.004 6.341 0.589 H17 9BG 63 9BG H18 H18 H 0 1 N N N -29.256 -15.471 -25.475 -6.063 3.757 2.062 H18 9BG 64 9BG H19 H19 H 0 1 N N N -30.154 -10.475 -22.567 -4.136 -0.053 1.470 H19 9BG 65 9BG H20 H20 H 0 1 N N N -28.727 -11.351 -20.888 -6.233 0.254 0.368 H20 9BG 66 9BG H21 H21 H 0 1 N N N -27.289 -10.581 -22.671 -4.132 0.439 -1.560 H21 9BG 67 9BG H22 H22 H 0 1 N N N -27.455 -6.942 -19.693 -8.211 -2.050 -2.337 H22 9BG 68 9BG H23 H23 H 0 1 N N N -28.877 -3.788 -22.518 -6.688 -6.247 -1.410 H23 9BG 69 9BG H24 H24 H 0 1 N N N -28.401 -4.353 -23.975 -5.135 -6.054 -0.800 H24 9BG 70 9BG H25 H25 H 0 1 N N N -29.051 -9.215 -25.594 -2.181 -2.338 0.101 H25 9BG 71 9BG H26 H26 H 0 1 N N N -30.218 -9.431 -27.824 1.812 -0.793 1.172 H26 9BG 72 # # 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 9BG O18 C17 SING N N 1 9BG C15 C14 SING N N 2 9BG C15 O16 SING N N 3 9BG C14 C17 SING N N 4 9BG C14 O13 SING N N 5 9BG C17 C19 SING N N 6 9BG O13 C12 SING N N 7 9BG C19 O20 SING N N 8 9BG C19 C12 SING N N 9 9BG O20 P21 SING N N 10 9BG C12 N11 SING N N 11 9BG O45 P21 DOUB N N 12 9BG P21 O46 SING N N 13 9BG P21 O22 SING N N 14 9BG N11 C10 SING Y N 15 9BG N11 C07 SING Y N 16 9BG C10 N09 DOUB Y N 17 9BG O22 C23 SING N N 18 9BG N06 C07 SING N N 19 9BG N06 C04 SING N N 20 9BG C07 C08 DOUB Y N 21 9BG C23 C24 SING N N 22 9BG N05 C04 SING N N 23 9BG N09 C08 SING Y N 24 9BG C04 N03 DOUB N N 25 9BG C08 C02 SING N N 26 9BG O28 P27 DOUB N N 27 9BG C24 O44 SING N N 28 9BG C24 C25 SING N N 29 9BG O44 C33 SING N N 30 9BG C43 N42 DOUB Y N 31 9BG C43 N34 SING Y N 32 9BG N03 C02 SING N N 33 9BG N42 C41 SING Y N 34 9BG O30 P27 SING N N 35 9BG C02 O01 DOUB N N 36 9BG P27 O29 SING N N 37 9BG P27 O26 SING N N 38 9BG C25 O26 SING N N 39 9BG C25 C31 SING N N 40 9BG N34 C33 SING N N 41 9BG N34 C35 SING Y N 42 9BG C33 C31 SING N N 43 9BG C41 C35 DOUB Y N 44 9BG C41 C39 SING Y N 45 9BG N40 C39 SING N N 46 9BG C31 O32 SING N N 47 9BG C35 N36 SING Y N 48 9BG C39 N38 DOUB Y N 49 9BG N36 C37 DOUB Y N 50 9BG N38 C37 SING Y N 51 9BG C10 H1 SING N N 52 9BG C17 H2 SING N N 53 9BG C24 H3 SING N N 54 9BG C12 H4 SING N N 55 9BG C14 H5 SING N N 56 9BG C19 H6 SING N N 57 9BG C23 H7 SING N N 58 9BG C23 H8 SING N N 59 9BG C25 H9 SING N N 60 9BG N05 H10 SING N N 61 9BG N05 H11 SING N N 62 9BG N06 H12 SING N N 63 9BG C15 H13 SING N N 64 9BG C15 H14 SING N N 65 9BG O16 H15 SING N N 66 9BG O18 H16 SING N N 67 9BG O29 H17 SING N N 68 9BG O30 H18 SING N N 69 9BG C31 H19 SING N N 70 9BG O32 H20 SING N N 71 9BG C33 H21 SING N N 72 9BG C37 H22 SING N N 73 9BG N40 H23 SING N N 74 9BG N40 H24 SING N N 75 9BG C43 H25 SING N N 76 9BG O46 H26 SING N N 77 # # 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 9BG SMILES ACDLabs 12.01 "c2nc1C(=O)N=C(N)Nc1n2C3C(C(C(O3)CO)O)OP(O)(OCC6OC(n5c4ncnc(N)c4nc5)C(C6OP(O)(=O)O)O)=O" 9BG InChI InChI 1.03 "InChI=1S/C20H26N10O14P2/c21-14-8-15(24-3-23-14)29(4-25-8)18-11(33)12(43-45(35,36)37)7(42-18)2-40-46(38,39)44-13-10(32)6(1-31)41-19(13)30-5-26-9-16(30)27-20(22)28-17(9)34/h3-7,10-13,18-19,31-33H,1-2H2,(H,38,39)(H2,21,23,24)(H2,35,36,37)(H3,22,27,28,34)/t6-,7-,10-,11-,12-,13-,18-,19-/m1/s1" 9BG InChIKey InChI 1.03 OVXKSNAROFCXFB-INFSMZHSSA-N 9BG SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)c2ncn([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O[P](O)(O)=O)n5cnc6c(N)ncnc56)c2N1" 9BG SMILES CACTVS 3.385 "NC1=NC(=O)c2ncn([CH]3O[CH](CO)[CH](O)[CH]3O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O[P](O)(O)=O)n5cnc6c(N)ncnc56)c2N1" 9BG SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O[C@@H]4[C@@H]([C@H](O[C@H]4n5cnc6c5NC(=NC6=O)N)CO)O)OP(=O)(O)O)O)N" 9BG SMILES "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OC4C(C(OC4n5cnc6c5NC(=NC6=O)N)CO)O)OP(=O)(O)O)O)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 9BG "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,3S,4R,5R)-2-({[(R)-{[(2R,3R,4R,5R)-2-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-3-yl]oxy}(hydroxy)phosphoryl]oxy}methyl)-5-(6-amino-9H-purin-9-yl)-4-hydroxytetrahydrofuran-3-yl dihydrogen phosphate (non-preferred name)" 9BG "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl [(2~{R},3~{R},4~{R},5~{R})-2-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-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 9BG "Create component" 2017-04-17 RCSB 9BG "Initial release" 2017-09-27 RCSB 9BG "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 9BG _pdbx_chem_comp_synonyms.name "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl [(2~{R},3~{R},4~{R},5~{R})-2-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##