data_RBD # _chem_comp.id RBD _chem_comp.name "(R,R)-N6,N6-(2,3-dihydroxy-1,4-butadiyl)-2'-deoxyadenosine-5'-monophosphate" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C14 H22 N5 O8 P" _chem_comp.mon_nstd_parent_comp_id DA _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-01-07 _chem_comp.pdbx_modified_date 2014-05-23 _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 419.327 _chem_comp.one_letter_code ? _chem_comp.three_letter_code RBD _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 2MHX _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 RBD P P P 0 1 N N N 5.883 -6.485 20.015 -6.057 1.692 -0.509 P RBD 1 RBD O1P O1P O 0 1 N N N 6.417 -7.762 20.553 -4.878 2.915 -0.238 O1P RBD 2 RBD O2P O2P O 0 1 N N N 6.686 -5.751 19.006 -6.639 1.898 1.097 O2P RBD 3 RBD "O5'" "O5'" O 0 1 N N N 4.417 -6.763 19.390 -4.806 0.557 -0.831 "O5'" RBD 4 RBD "C5'" "C5'" C 0 1 N N N 3.381 -7.378 20.151 -4.345 -0.144 0.325 "C5'" RBD 5 RBD "C4'" "C4'" C 0 1 N N R 2.014 -7.347 19.444 -3.322 -1.202 -0.094 "C4'" RBD 6 RBD "O4'" "O4'" O 0 1 N N N 1.626 -5.992 19.220 -2.108 -0.577 -0.564 "O4'" RBD 7 RBD "C1'" "C1'" C 0 1 N N R 1.525 -5.776 17.821 -1.061 -1.555 -0.451 "C1'" RBD 8 RBD N9 N9 N 0 1 Y N N 2.061 -4.440 17.472 0.203 -0.895 -0.115 N9 RBD 9 RBD C8 C8 C 0 1 Y N N 3.328 -4.084 17.071 0.344 0.315 0.497 C8 RBD 10 RBD N7 N7 N 0 1 Y N N 3.443 -2.842 16.689 1.606 0.595 0.642 N7 RBD 11 RBD C5 C5 C 0 1 Y N N 2.154 -2.333 16.878 2.354 -0.414 0.134 C5 RBD 12 RBD C6 C6 C 0 1 Y N N 1.550 -1.081 16.630 3.732 -0.659 0.013 C6 RBD 13 RBD N6 N6 N 0 1 N N N 2.172 -0.064 16.014 4.658 0.259 0.479 N6 RBD 14 RBD CA CA C 0 1 N N N 2.833 1.035 16.721 6.045 -0.217 0.242 CA RBD 15 RBD CB CB C 0 1 N N R 3.802 1.575 15.663 6.909 1.062 0.292 CB RBD 16 RBD OB OB O 0 1 N N N 5.002 2.131 16.193 7.958 0.990 -0.676 OB RBD 17 RBD CG CG C 0 1 N N R 4.088 0.327 14.810 5.941 2.213 -0.052 CG RBD 18 RBD OG OG O 0 1 N N N 4.635 0.641 13.533 5.862 3.136 1.036 OG RBD 19 RBD CD CD C 0 1 N N N 2.693 -0.253 14.657 4.574 1.533 -0.280 CD RBD 20 RBD N1 N1 N 0 1 Y N N 0.257 -0.893 16.954 4.127 -1.792 -0.559 N1 RBD 21 RBD C2 C2 C 0 1 Y N N -0.428 -1.913 17.458 3.251 -2.673 -1.006 C2 RBD 22 RBD N3 N3 N 0 1 Y N N -0.005 -3.148 17.691 1.951 -2.486 -0.915 N3 RBD 23 RBD C4 C4 C 0 1 Y N N 1.313 -3.291 17.384 1.462 -1.385 -0.353 C4 RBD 24 RBD "C3'" "C3'" C 0 1 N N S 2.008 -8.088 18.096 -2.856 -2.027 1.133 "C3'" RBD 25 RBD "C2'" "C2'" C 0 1 N N N 2.238 -6.939 17.122 -1.463 -2.528 0.675 "C2'" RBD 26 RBD "O3'" "O3'" O 0 1 N N N 0.750 -8.715 17.886 -3.741 -3.122 1.377 "O3'" RBD 27 RBD H1 H1 H 0 1 N N N 5.805 -8.121 21.185 -4.514 3.297 -1.048 H1 RBD 28 RBD H3 H3 H 0 1 N N N 7.552 -5.578 19.355 -7.378 1.316 1.324 H3 RBD 29 RBD "H5'2" "H5'2" H 0 0 N N N 3.657 -8.427 20.335 -3.879 0.559 1.015 "H5'2" RBD 30 RBD "H5'1" "H5'1" H 0 0 N N N 3.291 -6.849 21.111 -5.189 -0.629 0.816 "H5'1" RBD 31 RBD "H4'" "H4'" H 0 1 N N N 1.280 -7.834 20.103 -3.739 -1.855 -0.860 "H4'" RBD 32 RBD "H1'" "H1'" H 0 1 N N N 0.465 -5.810 17.527 -0.958 -2.098 -1.390 "H1'" RBD 33 RBD H8 H8 H 0 1 N N N 4.158 -4.775 17.072 -0.472 0.947 0.814 H8 RBD 34 RBD HA2 HA2 H 0 1 N N N 3.374 0.670 17.606 6.348 -0.911 1.026 HA2 RBD 35 RBD HA1 HA1 H 0 1 N N N 2.108 1.804 17.026 6.122 -0.692 -0.736 HA1 RBD 36 RBD HB HB H 0 1 N N N 3.276 2.316 15.043 7.324 1.199 1.290 HB RBD 37 RBD HOB HOB H 0 1 N N N 4.793 2.898 16.713 8.572 0.256 -0.536 HOB RBD 38 RBD HG HG H 0 1 N N N 4.731 -0.370 15.367 6.266 2.723 -0.958 HG RBD 39 RBD HOG HOG H 0 1 N N N 5.507 1.003 13.642 5.268 3.882 0.877 HOG RBD 40 RBD HD1 HD1 H 0 1 N N N 2.102 0.303 13.914 4.421 1.334 -1.341 HD1 RBD 41 RBD HD2 HD2 H 0 1 N N N 2.724 -1.317 14.379 3.769 2.156 0.111 HD2 RBD 42 RBD H2 H2 H 0 1 N N N -1.459 -1.711 17.710 3.614 -3.581 -1.464 H2 RBD 43 RBD "H3'" "H3'" H 0 1 N N N 2.841 -8.805 18.050 -2.769 -1.395 2.017 "H3'" RBD 44 RBD "H2'1" "H2'1" H 0 0 N N N 1.788 -7.151 16.141 -1.534 -3.546 0.292 "H2'1" RBD 45 RBD "H2'2" "H2'2" H 0 0 N N N 3.311 -6.731 16.996 -0.748 -2.477 1.496 "H2'2" RBD 46 RBD H4 H4 H 0 1 N N N 0.641 -9.424 18.509 -3.492 -3.668 2.135 H4 RBD 47 RBD O3P O3P O 0 1 N Y N ? ? ? -7.236 0.470 -0.780 O3P RBD 48 RBD H5 H5 H 0 1 N N N ? ? ? -6.629 2.487 -1.605 H5 RBD 49 RBD H6 H6 H 0 1 N N N ? ? ? -8.149 0.773 -0.676 H6 RBD 50 # 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 RBD OG CG SING N N 1 RBD CD CG SING N N 2 RBD CD N6 SING N N 3 RBD CG CB SING N N 4 RBD CB OB SING N N 5 RBD CB CA SING N N 6 RBD N6 C6 SING N N 7 RBD N6 CA SING N N 8 RBD C6 C5 DOUB Y N 9 RBD C6 N1 SING Y N 10 RBD N7 C5 SING Y N 11 RBD N7 C8 DOUB Y N 12 RBD C5 C4 SING Y N 13 RBD N1 C2 DOUB Y N 14 RBD C8 N9 SING Y N 15 RBD "C2'" "C1'" SING N N 16 RBD "C2'" "C3'" SING N N 17 RBD C4 N9 SING Y N 18 RBD C4 N3 DOUB Y N 19 RBD C2 N3 SING Y N 20 RBD N9 "C1'" SING N N 21 RBD "C1'" "O4'" SING N N 22 RBD "O3'" "C3'" SING N N 23 RBD "C3'" "C4'" SING N N 24 RBD O2P P SING N N 25 RBD "O4'" "C4'" SING N N 26 RBD "O5'" P SING N N 27 RBD "O5'" "C5'" SING N N 28 RBD "C4'" "C5'" SING N N 29 RBD P O1P SING N N 30 RBD O1P H1 SING N N 31 RBD O2P H3 SING N N 32 RBD "C5'" "H5'2" SING N N 33 RBD "C5'" "H5'1" SING N N 34 RBD "C4'" "H4'" SING N N 35 RBD "C1'" "H1'" SING N N 36 RBD C8 H8 SING N N 37 RBD CA HA2 SING N N 38 RBD CA HA1 SING N N 39 RBD CB HB SING N N 40 RBD OB HOB SING N N 41 RBD CG HG SING N N 42 RBD OG HOG SING N N 43 RBD CD HD1 SING N N 44 RBD CD HD2 SING N N 45 RBD C2 H2 SING N N 46 RBD "C3'" "H3'" SING N N 47 RBD "C2'" "H2'1" SING N N 48 RBD "C2'" "H2'2" SING N N 49 RBD "O3'" H4 SING N N 50 RBD P O3P SING N N 51 RBD P H5 SING N N 52 RBD O3P H6 SING N N 53 # 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 RBD SMILES ACDLabs 12.01 "n3c1c(ncnc1N2CC(O)C(O)C2)n(c3)C4OC(C(O)C4)COP(O)(O)O" RBD InChI InChI 1.03 "InChI=1S/C14H22N5O8P/c20-7-1-11(27-10(7)4-26-28(23,24)25)19-6-17-12-13(15-5-16-14(12)19)18-2-8(21)9(22)3-18/h5-11,20-25,28H,1-4H2/t7-,8+,9+,10+,11+/m0/s1" RBD InChIKey InChI 1.03 AFIPVZHEZSDVQA-VPJKUYQRSA-N RBD SMILES_CANONICAL CACTVS 3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[PH](O)(O)O)n2cnc3c(ncnc23)N4C[C@@H](O)[C@H](O)C4" RBD SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[PH](O)(O)O)n2cnc3c(ncnc23)N4C[CH](O)[CH](O)C4" RBD SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1nc2c(c(n1)N3C[C@H]([C@@H](C3)O)O)ncn2[C@H]4C[C@@H]([C@H](O4)COP(O)(O)O)O" RBD SMILES "OpenEye OEToolkits" 1.7.6 "c1nc2c(c(n1)N3CC(C(C3)O)O)ncn2C4CC(C(O4)COP(O)(O)O)O" # 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 RBD "SYSTEMATIC NAME" ACDLabs 12.01 "(3R,4R)-1-{9-[(2R,4S,5R)-4-hydroxy-5-{[(trihydroxy-lambda~5~-phosphanyl)oxy]methyl}tetrahydrofuran-2-yl]-9H-purin-6-yl}pyrrolidine-3,4-diol (non-preferred name)" RBD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(3R,4R)-1-[9-[(2R,4S,5R)-4-oxidanyl-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]purin-6-yl]pyrrolidine-3,4-diol" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site RBD "Create component" 2014-01-07 RCSB RBD "Initial release" 2014-05-28 RCSB #