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 
# 
