data_2JU # _chem_comp.id 2JU _chem_comp.name ;2'-deoxy-5-[(naphthalen-1-ylmethyl)carbamoyl]uridine 5'-(dihydrogen phosphate) ; _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C21 H22 N3 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-11-12 _chem_comp.pdbx_modified_date 2014-01-17 _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 491.388 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 2JU _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 4NI7 _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 2JU P P P 0 1 N N N 12.546 8.666 9.215 -7.254 1.699 0.105 P 2JU 1 2JU O1P O1P O 0 1 N N N 12.048 9.734 10.384 -8.524 0.956 0.262 O1P 2JU 2 2JU O2P O2P O 0 1 N N N 14.006 7.867 9.183 -6.818 2.325 1.523 O2P 2JU 3 2JU "O5'" "O5'" O 0 1 N N N 11.422 7.890 8.208 -6.106 0.697 -0.416 "O5'" 2JU 4 2JU "C5'" "C5'" C 0 1 N N N 11.134 6.677 8.883 -5.766 -0.514 0.261 "C5'" 2JU 5 2JU "C4'" "C4'" C 0 1 N N R 10.169 5.820 8.117 -4.641 -1.223 -0.496 "C4'" 2JU 6 2JU "C3'" "C3'" C 0 1 N N S 10.744 5.468 6.776 -4.315 -2.578 0.169 "C3'" 2JU 7 2JU "C2'" "C2'" C 0 1 N N N 9.939 6.314 5.811 -2.780 -2.701 0.038 "C2'" 2JU 8 2JU "C1'" "C1'" C 0 1 N N R 8.589 6.444 6.497 -2.361 -1.406 -0.692 "C1'" 2JU 9 2JU "O4'" "O4'" O 0 1 N N N 8.900 6.460 7.892 -3.417 -0.461 -0.407 "O4'" 2JU 10 2JU N1 N1 N 0 1 N N N 7.814 7.656 6.248 -1.083 -0.916 -0.168 N1 2JU 11 2JU C6 C6 C 0 1 N N N 8.113 8.806 6.891 0.003 -0.892 -0.983 C6 2JU 12 2JU C5 C5 C 0 1 N N N 7.333 9.939 6.682 1.208 -0.430 -0.491 C5 2JU 13 2JU C4 C4 C 0 1 N N N 6.237 9.851 5.819 1.258 0.018 0.910 C4 2JU 14 2JU O4 O4 O 0 1 N N N 5.456 10.810 5.534 2.294 0.434 1.393 O4 2JU 15 2JU N3 N3 N 0 1 N N N 6.002 8.674 5.223 0.129 -0.042 1.647 N3 2JU 16 2JU C2 C2 C 0 1 N N N 6.750 7.595 5.438 -1.014 -0.497 1.105 C2 2JU 17 2JU O2 O2 O 0 1 N N N 6.419 6.541 4.851 -2.015 -0.539 1.794 O2 2JU 18 2JU C5M C5M C 0 1 N N N 7.699 11.204 7.400 2.407 -0.389 -1.342 C5M 2JU 19 2JU N22 N22 N 0 1 N N N 6.799 12.160 7.594 3.542 0.170 -0.879 N22 2JU 20 2JU C23 C23 C 0 1 N N N 7.069 13.393 8.286 4.702 0.313 -1.764 C23 2JU 21 2JU C24 C24 C 0 1 Y N N 7.166 14.531 7.288 5.833 0.962 -1.008 C24 2JU 22 2JU C29 C29 C 0 1 Y N N 7.474 15.824 7.752 6.634 0.199 -0.142 C29 2JU 23 2JU C30 C30 C 0 1 Y N N 7.684 16.069 9.126 6.405 -1.175 0.042 C30 2JU 24 2JU C31 C31 C 0 1 Y N N 7.978 17.365 9.579 7.202 -1.883 0.890 C31 2JU 25 2JU C32 C32 C 0 1 Y N N 8.063 18.409 8.647 8.243 -1.265 1.579 C32 2JU 26 2JU C33 C33 C 0 1 Y N N 7.837 18.163 7.279 8.494 0.064 1.425 C33 2JU 27 2JU C28 C28 C 0 1 Y N N 7.537 16.882 6.826 7.693 0.827 0.559 C28 2JU 28 2JU C27 C27 C 0 1 Y N N 7.315 16.645 5.462 7.922 2.201 0.374 C27 2JU 29 2JU C26 C26 C 0 1 Y N N 7.022 15.354 4.992 7.127 2.908 -0.474 C26 2JU 30 2JU C25 C25 C 0 1 Y N N 6.934 14.308 5.922 6.087 2.290 -1.166 C25 2JU 31 2JU O21 O21 O 0 1 N N N 8.825 11.335 7.838 2.373 -0.858 -2.464 O21 2JU 32 2JU "O3'" "O3'" O 0 1 N N N 10.308 4.097 6.759 -4.967 -3.645 -0.522 "O3'" 2JU 33 2JU H2 H2 H 0 1 N N N 14.520 8.115 9.942 -5.993 2.827 1.494 H2 2JU 34 2JU H3 H3 H 0 1 N N N 10.697 6.912 9.865 -5.433 -0.284 1.273 H3 2JU 35 2JU H4 H4 H 0 1 N N N 12.071 6.118 9.023 -6.640 -1.164 0.306 H4 2JU 36 2JU H5 H5 H 0 1 N N N 10.009 4.889 8.681 -4.921 -1.370 -1.539 H5 2JU 37 2JU H6 H6 H 0 1 N N N 11.831 5.616 6.699 -4.609 -2.569 1.219 H6 2JU 38 2JU H7 H7 H 0 1 N N N 9.839 5.812 4.837 -2.317 -2.752 1.023 H7 2JU 39 2JU H8 H8 H 0 1 N N N 10.405 7.300 5.669 -2.516 -3.577 -0.555 H8 2JU 40 2JU H9 H9 H 0 1 N N N 7.981 5.560 6.255 -2.290 -1.581 -1.765 H9 2JU 41 2JU H10 H10 H 0 1 N N N 8.955 8.846 7.566 -0.075 -1.230 -2.006 H10 2JU 42 2JU H11 H11 H 0 1 N N N 5.231 8.604 4.590 0.140 0.253 2.571 H11 2JU 43 2JU H12 H12 H 0 1 N N N 5.876 12.015 7.237 3.592 0.478 0.039 H12 2JU 44 2JU H13 H13 H 0 1 N N N 8.019 13.305 8.833 5.015 -0.671 -2.113 H13 2JU 45 2JU H14 H14 H 0 1 N N N 6.255 13.599 8.997 4.432 0.933 -2.619 H14 2JU 46 2JU H15 H15 H 0 1 N N N 7.618 15.255 9.833 5.602 -1.668 -0.485 H15 2JU 47 2JU H16 H16 H 0 1 N N N 8.136 17.555 10.630 7.024 -2.939 1.030 H16 2JU 48 2JU H17 H17 H 0 1 N N N 8.303 19.408 8.980 8.860 -1.849 2.246 H17 2JU 49 2JU H18 H18 H 0 1 N N N 7.897 18.978 6.573 9.305 0.529 1.967 H18 2JU 50 2JU H19 H19 H 0 1 N N N 7.370 17.466 4.763 8.726 2.694 0.902 H19 2JU 51 2JU H20 H20 H 0 1 N N N 6.868 15.171 3.939 7.305 3.964 -0.614 H20 2JU 52 2JU H21 H21 H 0 1 N N N 6.684 13.314 5.581 5.471 2.874 -1.833 H21 2JU 53 2JU H22 H22 H 0 1 N N N 10.829 3.591 7.372 -4.796 -4.520 -0.146 H22 2JU 54 2JU O3P O3P O 0 1 N Y N ? ? ? -7.456 2.885 -0.965 O3P 2JU 55 2JU H1 H1 H 0 1 N N N ? ? ? -8.134 3.528 -0.717 H1 2JU 56 # 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 2JU O2 C2 DOUB N N 1 2JU C26 C27 DOUB Y N 2 2JU C26 C25 SING Y N 3 2JU N3 C2 SING N N 4 2JU N3 C4 SING N N 5 2JU C2 N1 SING N N 6 2JU C27 C28 SING Y N 7 2JU O4 C4 DOUB N N 8 2JU "C2'" "C1'" SING N N 9 2JU "C2'" "C3'" SING N N 10 2JU C4 C5 SING N N 11 2JU C25 C24 DOUB Y N 12 2JU N1 "C1'" SING N N 13 2JU N1 C6 SING N N 14 2JU "C1'" "O4'" SING N N 15 2JU C5 C6 DOUB N N 16 2JU C5 C5M SING N N 17 2JU "O3'" "C3'" SING N N 18 2JU "C3'" "C4'" SING N N 19 2JU C28 C33 DOUB Y N 20 2JU C28 C29 SING Y N 21 2JU C33 C32 SING Y N 22 2JU C24 C29 SING Y N 23 2JU C24 C23 SING N N 24 2JU C5M N22 SING N N 25 2JU C5M O21 DOUB N N 26 2JU N22 C23 SING N N 27 2JU C29 C30 DOUB Y N 28 2JU "O4'" "C4'" SING N N 29 2JU "C4'" "C5'" SING N N 30 2JU "O5'" "C5'" SING N N 31 2JU "O5'" P SING N N 32 2JU C32 C31 DOUB Y N 33 2JU C30 C31 SING Y N 34 2JU O2P P SING N N 35 2JU P O1P DOUB N N 36 2JU O2P H2 SING N N 37 2JU "C5'" H3 SING N N 38 2JU "C5'" H4 SING N N 39 2JU "C4'" H5 SING N N 40 2JU "C3'" H6 SING N N 41 2JU "C2'" H7 SING N N 42 2JU "C2'" H8 SING N N 43 2JU "C1'" H9 SING N N 44 2JU C6 H10 SING N N 45 2JU N3 H11 SING N N 46 2JU N22 H12 SING N N 47 2JU C23 H13 SING N N 48 2JU C23 H14 SING N N 49 2JU C30 H15 SING N N 50 2JU C31 H16 SING N N 51 2JU C32 H17 SING N N 52 2JU C33 H18 SING N N 53 2JU C27 H19 SING N N 54 2JU C26 H20 SING N N 55 2JU C25 H21 SING N N 56 2JU "O3'" H22 SING N N 57 2JU P O3P SING N N 58 2JU O3P H1 SING N N 59 # 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 2JU SMILES ACDLabs 12.01 "O=P(O)(O)OCC4OC(N3C(=O)NC(=O)C(C(=O)NCc2c1ccccc1ccc2)=C3)CC4O" 2JU InChI InChI 1.03 "InChI=1S/C21H22N3O9P/c25-16-8-18(33-17(16)11-32-34(29,30)31)24-10-15(20(27)23-21(24)28)19(26)22-9-13-6-3-5-12-4-1-2-7-14(12)13/h1-7,10,16-18,25H,8-9,11H2,(H,22,26)(H,23,27,28)(H2,29,30,31)/t16-,17+,18+/m0/s1" 2JU InChIKey InChI 1.03 WFMYBIOITHHLFG-RCCFBDPRSA-N 2JU SMILES_CANONICAL CACTVS 3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C(=O)NCc3cccc4ccccc34)C(=O)NC2=O" 2JU SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C(=O)NCc3cccc4ccccc34)C(=O)NC2=O" 2JU SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1ccc2c(c1)cccc2CNC(=O)C3=CN(C(=O)NC3=O)[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)O" 2JU SMILES "OpenEye OEToolkits" 1.7.6 "c1ccc2c(c1)cccc2CNC(=O)C3=CN(C(=O)NC3=O)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 2JU "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-deoxy-5-[(naphthalen-1-ylmethyl)carbamoyl]uridine 5'-(dihydrogen phosphate) ; 2JU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[5-(naphthalen-1-ylmethylcarbamoyl)-2,4-bis(oxidanylidene)pyrimidin-1-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 2JU "Create component" 2013-11-12 RCSB 2JU "Initial release" 2014-01-22 RCSB #