data_XPB # _chem_comp.id XPB _chem_comp.name "O6-[4-oxo-4-(3-pyridyl)butyl]-2'-deoxyguanosine-5'-monophosphate" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C19 H23 N6 O8 P" _chem_comp.mon_nstd_parent_comp_id DG _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-07-30 _chem_comp.pdbx_modified_date 2014-08-01 _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 494.395 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XPB _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 1PYJ _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 XPB C4 C4 C 0 1 Y N N -7.100 -2.166 -9.671 -0.754 1.481 0.303 C4 XPB 1 XPB C5 C5 C 0 1 Y N N -7.420 -2.499 -8.340 0.233 0.529 -0.004 C5 XPB 2 XPB C6 C6 C 0 1 Y N N -6.300 -2.735 -7.512 1.578 0.873 0.201 C6 XPB 3 XPB N1 N1 N 0 1 Y N N -5.073 -2.627 -8.015 1.859 2.080 0.674 N1 XPB 4 XPB C8 C8 C 0 1 Y N N -9.289 -2.218 -9.332 -1.692 -0.370 -0.444 C8 XPB 5 XPB N2 N2 N 0 1 N N N -3.629 -2.144 -9.742 1.244 4.197 1.445 N2 XPB 6 XPB C10 C10 C 0 1 N N N -6.382 -2.055 -5.205 3.908 0.425 0.160 C10 XPB 7 XPB O6 O6 O 0 1 N N N -6.331 -3.080 -6.216 2.568 -0.008 -0.079 O6 XPB 8 XPB C11 C11 C 0 1 N N N -4.962 -1.870 -4.694 4.880 -0.696 -0.212 C11 XPB 9 XPB C12 C12 C 0 1 N N N -4.911 -1.914 -3.166 6.316 -0.233 0.043 C12 XPB 10 XPB N3 N3 N 0 1 Y N N -5.891 -2.049 -10.217 -0.384 2.667 0.775 N3 XPB 11 XPB C13 C13 C 0 1 N N N -3.525 -2.245 -2.625 7.273 -1.337 -0.323 C13 XPB 12 XPB C14 C14 C 0 1 Y N N -3.327 -2.310 -1.139 8.723 -1.137 -0.167 C14 XPB 13 XPB C15 C15 C 0 1 Y N N -2.057 -2.638 -0.641 9.625 -2.156 -0.504 C15 XPB 14 XPB P P P 0 1 N N N -13.284 0.168 -10.864 -7.869 -2.117 0.464 P XPB 15 XPB OP1 OP1 O 0 1 N N N -14.469 0.386 -11.722 -9.073 -1.785 -0.330 OP1 XPB 16 XPB OP2 OP2 O 0 1 N N N -13.672 -0.646 -9.690 -7.118 -3.376 -0.201 OP2 XPB 17 XPB "O5'" "O5'" O 0 1 N N N -12.029 -0.427 -11.658 -6.875 -0.850 0.487 "O5'" XPB 18 XPB "C5'" "C5'" C 0 1 N N N -11.301 0.373 -12.609 -6.395 -0.216 -0.701 "C5'" XPB 19 XPB "C4'" "C4'" C 0 1 N N R -9.988 -0.292 -12.945 -5.477 0.948 -0.322 "C4'" XPB 20 XPB "O4'" "O4'" O 0 1 N N N -9.174 -0.390 -11.744 -4.275 0.461 0.312 "O4'" XPB 21 XPB "C3'" "C3'" C 0 1 N N S -10.082 -1.726 -13.457 -4.951 1.664 -1.592 "C3'" XPB 22 XPB "O3'" "O3'" O 0 1 N N N -9.345 -1.804 -14.682 -5.873 2.663 -2.033 "O3'" XPB 23 XPB "C2'" "C2'" C 0 1 N N N -9.389 -2.622 -12.437 -3.639 2.308 -1.082 "C2'" XPB 24 XPB "C1'" "C1'" C 0 1 N N R -8.499 -1.638 -11.694 -3.282 1.491 0.175 "C1'" XPB 25 XPB N9 N9 N 0 1 Y N N -8.316 -1.991 -10.289 -1.957 0.887 0.016 N9 XPB 26 XPB N7 N7 N 0 1 Y N N -8.802 -2.523 -8.160 -0.408 -0.576 -0.459 N7 XPB 27 XPB C2 C2 C 0 1 Y N N -4.923 -2.288 -9.312 0.896 2.950 0.952 C2 XPB 28 XPB C16 C16 C 0 1 Y N N -1.867 -2.701 0.733 10.977 -1.916 -0.338 C16 XPB 29 XPB C17 C17 C 0 1 Y N N -2.955 -2.433 1.568 11.393 -0.690 0.149 C17 XPB 30 XPB "N1'" "N1'" N 0 1 Y N N -4.177 -2.117 1.119 10.522 0.253 0.459 "N1'" XPB 31 XPB C18 C18 C 0 1 Y N N -4.344 -2.061 -0.207 9.226 0.076 0.315 C18 XPB 32 XPB O13 O13 O 0 1 N N N -2.586 -2.454 -3.377 6.849 -2.391 -0.746 O13 XPB 33 XPB H8 H8 H 0 1 N N N -10.348 -2.150 -9.535 -2.439 -1.086 -0.755 H8 XPB 34 XPB H22 H22 H 0 1 N N N -3.625 -1.872 -10.704 0.553 4.846 1.654 H22 XPB 35 XPB H21 H21 H 0 1 N N N -3.172 -1.442 -9.195 2.178 4.422 1.581 H21 XPB 36 XPB H10 H10 H 0 1 N N N -6.754 -1.115 -5.638 4.119 1.305 -0.448 H10 XPB 37 XPB H7 H7 H 0 1 N N N -7.043 -2.367 -4.383 4.028 0.675 1.214 H7 XPB 38 XPB H11 H11 H 0 1 N N N -4.329 -2.674 -5.097 4.669 -1.576 0.396 H11 XPB 39 XPB H9 H9 H 0 1 N N N -4.582 -0.897 -5.037 4.761 -0.946 -1.266 H9 XPB 40 XPB H12 H12 H 0 1 N N N -5.213 -0.931 -2.777 6.527 0.647 -0.564 H12 XPB 41 XPB H13 H13 H 0 1 N N N -5.617 -2.681 -2.814 6.435 0.017 1.097 H13 XPB 42 XPB H15 H15 H 0 1 N N N -1.239 -2.839 -1.317 9.273 -3.105 -0.882 H15 XPB 43 XPB H2 H2 H 0 1 N N N -14.598 -0.853 -9.740 -6.317 -3.650 0.269 H2 XPB 44 XPB "H5'" "H5'" H 0 1 N N N -11.107 1.366 -12.177 -5.839 -0.938 -1.299 "H5'" XPB 45 XPB "H5''" "H5''" H 0 0 N N N -11.899 0.483 -13.526 -7.240 0.160 -1.278 "H5''" XPB 46 XPB "H4'" "H4'" H 0 1 N N N -9.464 0.316 -13.697 -5.998 1.650 0.329 "H4'" XPB 47 XPB "H3'" "H3'" H 0 1 N N N -11.133 -2.024 -13.586 -4.748 0.946 -2.387 "H3'" XPB 48 XPB H3 H3 H 0 1 N Y N -9.388 -2.690 -15.022 -5.588 3.139 -2.825 H3 XPB 49 XPB "H2''" "H2''" H 0 0 N N N -10.117 -3.091 -11.759 -2.853 2.218 -1.832 "H2''" XPB 50 XPB "H2'" "H2'" H 0 1 N N N -8.793 -3.403 -12.932 -3.804 3.354 -0.823 "H2'" XPB 51 XPB "H1'" "H1'" H 0 1 N N N -7.524 -1.575 -12.200 -3.294 2.137 1.053 "H1'" XPB 52 XPB H16 H16 H 0 1 N N N -0.901 -2.951 1.147 11.701 -2.678 -0.587 H16 XPB 53 XPB H17 H17 H 0 1 N N N -2.802 -2.483 2.636 12.448 -0.500 0.279 H17 XPB 54 XPB H18 H18 H 0 1 N N N -5.324 -1.808 -0.583 8.544 0.873 0.575 H18 XPB 55 XPB OP3 OP3 O 0 1 N Y N ? ? ? -8.303 -2.485 1.970 OP3 XPB 56 XPB H1 H1 H 0 1 N Y N ? ? ? -8.903 -3.241 2.033 H1 XPB 57 # 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 XPB "O3'" "C3'" SING N N 1 XPB "C3'" "C4'" SING N N 2 XPB "C3'" "C2'" SING N N 3 XPB "C4'" "C5'" SING N N 4 XPB "C4'" "O4'" SING N N 5 XPB "C5'" "O5'" SING N N 6 XPB "C2'" "C1'" SING N N 7 XPB "O4'" "C1'" SING N N 8 XPB OP1 P DOUB N N 9 XPB "C1'" N9 SING N N 10 XPB "O5'" P SING N N 11 XPB P OP2 SING N N 12 XPB N9 C4 SING Y N 13 XPB N9 C8 SING Y N 14 XPB N3 C4 SING Y N 15 XPB N3 C2 DOUB Y N 16 XPB N2 C2 SING N N 17 XPB C4 C5 DOUB Y N 18 XPB C8 N7 DOUB Y N 19 XPB C2 N1 SING Y N 20 XPB C5 N7 SING Y N 21 XPB C5 C6 SING Y N 22 XPB N1 C6 DOUB Y N 23 XPB C6 O6 SING N N 24 XPB O6 C10 SING N N 25 XPB C10 C11 SING N N 26 XPB C11 C12 SING N N 27 XPB O13 C13 DOUB N N 28 XPB C12 C13 SING N N 29 XPB C13 C14 SING N N 30 XPB C14 C15 DOUB Y N 31 XPB C14 C18 SING Y N 32 XPB C15 C16 SING Y N 33 XPB C18 "N1'" DOUB Y N 34 XPB C16 C17 DOUB Y N 35 XPB "N1'" C17 SING Y N 36 XPB C8 H8 SING N N 37 XPB N2 H22 SING N N 38 XPB N2 H21 SING N N 39 XPB C10 H10 SING N N 40 XPB C10 H7 SING N N 41 XPB C11 H11 SING N N 42 XPB C11 H9 SING N N 43 XPB C12 H12 SING N N 44 XPB C12 H13 SING N N 45 XPB C15 H15 SING N N 46 XPB OP2 H2 SING N N 47 XPB "C5'" "H5'" SING N N 48 XPB "C5'" "H5''" SING N N 49 XPB "C4'" "H4'" SING N N 50 XPB "C3'" "H3'" SING N N 51 XPB "O3'" H3 SING N N 52 XPB "C2'" "H2''" SING N N 53 XPB "C2'" "H2'" SING N N 54 XPB "C1'" "H1'" SING N N 55 XPB C16 H16 SING N N 56 XPB C17 H17 SING N N 57 XPB C18 H18 SING N N 58 XPB P OP3 SING N N 59 XPB OP3 H1 SING N N 60 # 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 XPB SMILES ACDLabs 12.01 "O=P(O)(O)OCC4OC(n3cnc2c3nc(nc2OCCCC(=O)c1cccnc1)N)CC4O" XPB InChI InChI 1.03 "InChI=1S/C19H23N6O8P/c20-19-23-17-16(18(24-19)31-6-2-4-12(26)11-3-1-5-21-8-11)22-10-25(17)15-7-13(27)14(33-15)9-32-34(28,29)30/h1,3,5,8,10,13-15,27H,2,4,6-7,9H2,(H2,20,23,24)(H2,28,29,30)/t13-,14+,15+/m0/s1" XPB InChIKey InChI 1.03 YYZAHCOFAHEYAN-RRFJBIMHSA-N XPB SMILES_CANONICAL CACTVS 3.385 "Nc1nc(OCCCC(=O)c2cccnc2)c3ncn([C@H]4C[C@H](O)[C@@H](CO[P](O)(O)=O)O4)c3n1" XPB SMILES CACTVS 3.385 "Nc1nc(OCCCC(=O)c2cccnc2)c3ncn([CH]4C[CH](O)[CH](CO[P](O)(O)=O)O4)c3n1" XPB SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1cc(cnc1)C(=O)CCCOc2c3c(nc(n2)N)n(cn3)[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)O" XPB SMILES "OpenEye OEToolkits" 1.7.6 "c1cc(cnc1)C(=O)CCCOc2c3c(nc(n2)N)n(cn3)C4CC(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 XPB "SYSTEMATIC NAME" ACDLabs 12.01 "9-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-6-[4-oxo-4-(pyridin-3-yl)butoxy]-9H-purin-2-amine" XPB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[2-azanyl-6-(4-oxidanylidene-4-pyridin-3-yl-butoxy)purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen 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 XPB "Create component" 2014-07-30 RCSB XPB "Initial release" 2014-08-06 RCSB #