data_WMJ # _chem_comp.id WMJ _chem_comp.name "1-[[(2R,3S,5S)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl]-3-(4-nitrophenyl)urea" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H19 N5 O7" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-10-24 _chem_comp.pdbx_modified_date 2014-09-05 _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 405.362 _chem_comp.one_letter_code ? _chem_comp.three_letter_code WMJ _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 2YOH _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 WMJ OAD OAD O 0 1 N N N 12.426 3.708 30.018 6.206 -1.109 1.162 OAD WMJ 1 WMJ CAX CAX C 0 1 N N N 13.636 3.973 29.986 5.780 -0.077 0.680 CAX WMJ 2 WMJ NAQ NAQ N 0 1 N N N 14.412 3.517 28.924 6.641 0.892 0.319 NAQ WMJ 3 WMJ CAW CAW C 0 1 N N N 15.773 3.810 28.822 6.183 2.042 -0.217 CAW WMJ 4 WMJ OAC OAC O 0 1 N N N 16.411 3.366 27.864 6.962 2.920 -0.544 OAC WMJ 5 WMJ CAT CAT C 0 1 N N N 16.378 4.589 29.810 4.791 2.219 -0.398 CAT WMJ 6 WMJ CAA CAA C 0 1 N N N 17.860 4.933 29.714 4.254 3.494 -0.995 CAA WMJ 7 WMJ CAL CAL C 0 1 N N N 15.606 5.052 30.882 3.949 1.230 -0.028 CAL WMJ 8 WMJ NBC NBC N 0 1 N N N 14.232 4.740 30.976 4.454 0.076 0.509 NBC WMJ 9 WMJ CBA CBA C 0 1 N N S 13.407 5.188 32.140 3.542 -0.999 0.906 CBA WMJ 10 WMJ OAR OAR O 0 1 N N N 14.312 5.511 33.234 2.192 -0.629 0.601 OAR WMJ 11 WMJ CAN CAN C 0 1 N N N 12.532 6.382 31.848 3.865 -2.281 0.108 CAN WMJ 12 WMJ CAY CAY C 0 1 N N S 13.334 7.504 32.439 2.451 -2.851 -0.186 CAY WMJ 13 WMJ OAE OAE O 0 1 N N N 14.295 7.947 31.483 2.446 -3.621 -1.390 OAE WMJ 14 WMJ CAZ CAZ C 0 1 N N R 14.042 6.866 33.629 1.636 -1.544 -0.356 CAZ WMJ 15 WMJ CAM CAM C 0 1 N N N 13.089 6.803 34.853 0.158 -1.797 -0.054 CAM WMJ 16 WMJ NAO NAO N 0 1 N N N 12.949 8.153 35.433 -0.603 -0.563 -0.269 NAO WMJ 17 WMJ CAS CAS C 0 1 N N N 11.963 9.017 35.134 -1.934 -0.547 -0.063 CAS WMJ 18 WMJ OAB OAB O 0 1 N N N 11.091 8.792 34.320 -2.505 -1.557 0.303 OAB WMJ 19 WMJ NAP NAP N 0 1 N N N 12.009 10.154 35.794 -2.634 0.587 -0.262 NAP WMJ 20 WMJ CAU CAU C 0 1 Y N N 11.193 11.162 35.581 -4.029 0.577 -0.155 CAU WMJ 21 WMJ CAI CAI C 0 1 Y N N 11.188 12.160 36.540 -4.699 1.696 0.322 CAI WMJ 22 WMJ CAK CAK C 0 1 Y N N 10.378 13.268 36.378 -6.076 1.683 0.425 CAK WMJ 23 WMJ CAH CAH C 0 1 Y N N 10.440 11.280 34.410 -4.747 -0.550 -0.533 CAH WMJ 24 WMJ CAJ CAJ C 0 1 Y N N 9.621 12.409 34.240 -6.124 -0.557 -0.427 CAJ WMJ 25 WMJ CAV CAV C 0 1 Y N N 9.601 13.408 35.231 -6.788 0.557 0.054 CAV WMJ 26 WMJ NBB NBB N 1 1 N N N 8.853 14.508 35.141 -8.264 0.546 0.166 NBB WMJ 27 WMJ OAG OAG O -1 1 N N N 8.213 14.855 34.010 -8.850 1.528 0.585 OAG WMJ 28 WMJ OAF OAF O 0 1 N N N 8.735 15.278 36.250 -8.892 -0.445 -0.161 OAF WMJ 29 WMJ HAQ HAQ H 0 1 N N N 13.981 2.962 28.212 7.594 0.764 0.446 HAQ WMJ 30 WMJ HAA1 HAA1 H 0 0 N N N 18.151 5.549 30.578 5.082 4.163 -1.227 HAA1 WMJ 31 WMJ HAA2 HAA2 H 0 0 N N N 18.452 4.006 29.709 3.706 3.264 -1.909 HAA2 WMJ 32 WMJ HAA3 HAA3 H 0 0 N N N 18.047 5.492 28.785 3.585 3.976 -0.282 HAA3 WMJ 33 WMJ HAL HAL H 0 1 N N N 16.068 5.657 31.648 2.884 1.347 -0.158 HAL WMJ 34 WMJ HBA HBA H 0 1 N N N 12.759 4.354 32.448 3.640 -1.192 1.974 HBA WMJ 35 WMJ HAN1 HAN1 H 0 0 N N N 12.389 6.519 30.766 4.387 -2.041 -0.818 HAN1 WMJ 36 WMJ HAN2 HAN2 H 0 0 N N N 11.552 6.289 32.338 4.446 -2.978 0.713 HAN2 WMJ 37 WMJ HAZ HAZ H 0 1 N N N 14.960 7.417 33.882 1.755 -1.153 -1.367 HAZ WMJ 38 WMJ HAY HAY H 0 1 N N N 12.678 8.321 32.773 2.081 -3.439 0.654 HAY WMJ 39 WMJ HAE HAE H 0 1 N N N 14.806 8.658 31.853 3.029 -4.392 -1.366 HAE WMJ 40 WMJ HAM1 HAM1 H 0 0 N N N 12.103 6.437 34.532 -0.220 -2.577 -0.714 HAM1 WMJ 41 WMJ HAM2 HAM2 H 0 0 N N N 13.506 6.120 35.608 0.048 -2.114 0.984 HAM2 WMJ 42 WMJ HAO HAO H 0 1 N N N 13.637 8.446 36.096 -0.147 0.242 -0.561 HAO WMJ 43 WMJ HAP HAP H 0 1 N N N 12.708 10.258 36.502 -2.170 1.411 -0.478 HAP WMJ 44 WMJ HAI HAI H 0 1 N N N 11.816 12.073 37.414 -4.143 2.575 0.613 HAI WMJ 45 WMJ HAH HAH H 0 1 N N N 10.487 10.516 33.648 -4.229 -1.420 -0.909 HAH WMJ 46 WMJ HAK HAK H 0 1 N N N 10.348 14.028 37.144 -6.598 2.552 0.797 HAK WMJ 47 WMJ HAJ HAJ H 0 1 N N N 9.011 12.509 33.355 -6.683 -1.433 -0.721 HAJ WMJ 48 # 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 WMJ OAD CAX DOUB N N 1 WMJ CAX NAQ SING N N 2 WMJ CAX NBC SING N N 3 WMJ NAQ CAW SING N N 4 WMJ CAW OAC DOUB N N 5 WMJ CAW CAT SING N N 6 WMJ CAT CAA SING N N 7 WMJ CAT CAL DOUB N N 8 WMJ CAL NBC SING N N 9 WMJ NBC CBA SING N N 10 WMJ CBA OAR SING N N 11 WMJ CBA CAN SING N N 12 WMJ OAR CAZ SING N N 13 WMJ CAN CAY SING N N 14 WMJ CAY OAE SING N N 15 WMJ CAY CAZ SING N N 16 WMJ CAZ CAM SING N N 17 WMJ CAM NAO SING N N 18 WMJ NAO CAS SING N N 19 WMJ CAS OAB DOUB N N 20 WMJ CAS NAP SING N N 21 WMJ NAP CAU SING N N 22 WMJ CAU CAI SING Y N 23 WMJ CAU CAH DOUB Y N 24 WMJ CAI CAK DOUB Y N 25 WMJ CAK CAV SING Y N 26 WMJ CAH CAJ SING Y N 27 WMJ CAJ CAV DOUB Y N 28 WMJ CAV NBB SING N N 29 WMJ NBB OAG SING N N 30 WMJ NBB OAF DOUB N N 31 WMJ NAQ HAQ SING N N 32 WMJ CAA HAA1 SING N N 33 WMJ CAA HAA2 SING N N 34 WMJ CAA HAA3 SING N N 35 WMJ CAL HAL SING N N 36 WMJ CBA HBA SING N N 37 WMJ CAN HAN1 SING N N 38 WMJ CAN HAN2 SING N N 39 WMJ CAZ HAZ SING N N 40 WMJ CAY HAY SING N N 41 WMJ OAE HAE SING N N 42 WMJ CAM HAM1 SING N N 43 WMJ CAM HAM2 SING N N 44 WMJ NAO HAO SING N N 45 WMJ NAP HAP SING N N 46 WMJ CAI HAI SING N N 47 WMJ CAH HAH SING N N 48 WMJ CAK HAK SING N N 49 WMJ CAJ HAJ SING N N 50 # 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 WMJ SMILES ACDLabs 12.01 "[O-][N+](=O)c1ccc(cc1)NC(=O)NCC3OC(N2C(=O)NC(=O)C(=C2)C)CC3O" WMJ InChI InChI 1.03 "InChI=1S/C17H19N5O7/c1-9-8-21(17(26)20-15(9)24)14-6-12(23)13(29-14)7-18-16(25)19-10-2-4-11(5-3-10)22(27)28/h2-5,8,12-14,23H,6-7H2,1H3,(H2,18,19,25)(H,20,24,26)/t12-,13+,14-/m0/s1" WMJ InChIKey InChI 1.03 GGXGAHUHZPSFRR-MJBXVCDLSA-N WMJ SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@@H]2C[C@H](O)[C@@H](CNC(=O)Nc3ccc(cc3)[N+]([O-])=O)O2)C(=O)NC1=O" WMJ SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](CNC(=O)Nc3ccc(cc3)[N+]([O-])=O)O2)C(=O)NC1=O" WMJ SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "CC1=CN(C(=O)NC1=O)[C@@H]2C[C@@H]([C@H](O2)CNC(=O)Nc3ccc(cc3)[N+](=O)[O-])O" WMJ SMILES "OpenEye OEToolkits" 1.9.2 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)CNC(=O)Nc3ccc(cc3)[N+](=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 WMJ "SYSTEMATIC NAME" ACDLabs 12.01 "2',5'-dideoxy-5'-{[(4-nitrophenyl)carbamoyl]amino}-3,4-dihydrothymidine" WMJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "1-[[(2R,3S,5S)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl]-3-(4-nitrophenyl)urea" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site WMJ "Create component" 2012-10-24 EBI WMJ "Initial release" 2013-07-24 RCSB WMJ "Modify descriptor" 2014-09-05 RCSB #