data_V12 # _chem_comp.id V12 _chem_comp.name "5'-[(1H-BENZIMIDAZOL-2-YLACETYL)AMINO]-5'-DEOXYCYTIDINE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H20 N6 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-06-07 _chem_comp.pdbx_modified_date 2011-06-04 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 400.389 _chem_comp.one_letter_code ? _chem_comp.three_letter_code V12 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details "Corina V3.40" _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code ? _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 V12 OAC OAC O 0 1 N N N 12.876 -10.068 14.898 3.253 0.810 1.507 OAC V12 1 V12 CAV CAV C 0 1 N N N 12.982 -9.133 15.695 4.131 1.165 0.739 CAV V12 2 V12 NAO NAO N 0 1 N N N 12.262 -8.019 15.475 4.836 2.261 1.012 NAO V12 3 V12 CAT CAT C 0 1 N N N 12.307 -6.953 16.293 5.798 2.669 0.194 CAT V12 4 V12 NAA NAA N 0 1 N N N 11.575 -5.873 16.034 6.519 3.803 0.486 NAA V12 5 V12 CAF CAF C 0 1 N N N 13.117 -6.955 17.421 6.075 1.934 -0.977 CAF V12 6 V12 CAG CAG C 0 1 N N N 13.880 -8.078 17.699 5.350 0.821 -1.240 CAG V12 7 V12 NBD NBD N 0 1 N N N 13.828 -9.190 16.831 4.376 0.439 -0.367 NBD V12 8 V12 CBC CBC C 0 1 N N R 14.677 -10.372 17.184 3.588 -0.766 -0.638 CBC V12 9 V12 OAS OAS O 0 1 N N N 15.195 -10.090 18.538 2.176 -0.468 -0.571 OAS V12 10 V12 CBA CBA C 0 1 N N R 15.903 -10.550 16.268 3.824 -1.822 0.465 CBA V12 11 V12 OAE OAE O 0 1 N N N 15.937 -11.889 15.727 4.784 -2.789 0.035 OAE V12 12 V12 CAZ CAZ C 0 1 N N S 17.097 -10.290 17.189 2.439 -2.479 0.659 CAZ V12 13 V12 OAD OAD O 0 1 N N N 18.113 -11.263 16.949 2.500 -3.874 0.356 OAD V12 14 V12 CB0 CB0 C 0 1 N N R 16.559 -10.490 18.594 1.529 -1.741 -0.352 CB0 V12 15 V12 CAN CAN C 0 1 N N N 17.290 -9.475 19.479 0.132 -1.534 0.237 CAN V12 16 V12 NAQ NAQ N 0 1 N N N 16.970 -9.662 20.905 -0.723 -0.875 -0.752 NAQ V12 17 V12 CAU CAU C 0 1 N N N 17.777 -10.289 21.765 -2.006 -0.590 -0.452 CAU V12 18 V12 OAB OAB O 0 1 N N N 18.866 -10.783 21.470 -2.452 -0.879 0.638 OAB V12 19 V12 CAL CAL C 0 1 N N N 17.243 -10.349 23.202 -2.886 0.088 -1.470 CAL V12 20 V12 CA0 CA0 C 0 1 Y N N 17.597 -11.665 23.910 -4.261 0.292 -0.889 CA0 V12 21 V12 NAR NAR N 0 1 Y N N 17.345 -11.920 25.194 -5.005 -0.650 -0.387 NAR V12 22 V12 CAY CAY C 0 1 Y N N 17.779 -13.143 25.477 -6.179 -0.122 0.046 CAY V12 23 V12 CAK CAK C 0 1 Y N N 17.770 -13.900 26.648 -7.314 -0.666 0.653 CAK V12 24 V12 CAI CAI C 0 1 Y N N 18.310 -15.186 26.642 -8.365 0.144 0.981 CAI V12 25 V12 CAH CAH C 0 1 Y N N 18.857 -15.709 25.469 -8.318 1.505 0.717 CAH V12 26 V12 CAJ CAJ C 0 1 Y N N 18.864 -14.948 24.300 -7.208 2.064 0.119 CAJ V12 27 V12 CAX CAX C 0 1 Y N N 18.322 -13.663 24.308 -6.131 1.257 -0.221 CAX V12 28 V12 NAP NAP N 0 1 Y N N 18.193 -12.730 23.368 -4.903 1.489 -0.808 NAP V12 29 V12 HAA1 1HAA H 0 0 N N N 11.391 -5.382 16.886 6.326 4.307 1.292 HAA1 V12 30 V12 HAA2 2HAA H 0 0 N N N 12.073 -5.275 15.406 7.222 4.099 -0.114 HAA2 V12 31 V12 HAF HAF H 0 1 N N N 13.152 -6.094 18.072 6.854 2.253 -1.653 HAF V12 32 V12 HAG HAG H 0 1 N N N 14.511 -8.102 18.575 5.544 0.241 -2.130 HAG V12 33 V12 HBC HBC H 0 1 N N N 14.067 -11.283 17.093 3.843 -1.175 -1.615 HBC V12 34 V12 HBA HBA H 0 1 N N N 15.894 -9.873 15.401 4.152 -1.344 1.388 HBA V12 35 V12 HB0 HB0 H 0 1 N N N 16.681 -11.519 18.965 1.468 -2.301 -1.286 HB0 V12 36 V12 HAE HAE H 0 1 N N N 15.944 -11.847 14.778 4.970 -3.476 0.689 HAE V12 37 V12 HAZ HAZ H 0 1 N N N 17.527 -9.290 17.031 2.082 -2.325 1.677 HAZ V12 38 V12 HAD HAD H 0 1 N N N 18.133 -11.479 16.024 3.103 -4.374 0.923 HAD V12 39 V12 HAN1 1HAN H 0 0 N N N 18.374 -9.603 19.341 -0.297 -2.500 0.502 HAN1 V12 40 V12 HAN2 2HAN H 0 0 N N N 16.966 -8.466 19.184 0.203 -0.911 1.129 HAN2 V12 41 V12 HAQ HAQ H 0 1 N N N 16.103 -9.300 21.247 -0.366 -0.643 -1.624 HAQ V12 42 V12 HAL1 1HAL H 0 0 N N N 17.684 -9.518 23.772 -2.456 1.055 -1.735 HAL1 V12 43 V12 HAL2 2HAL H 0 0 N N N 16.146 -10.279 23.155 -2.956 -0.535 -2.362 HAL2 V12 44 V12 HAP HAP H 0 1 N N N 18.492 -12.812 22.417 -4.563 2.346 -1.108 HAP V12 45 V12 HAK HAK H 0 1 N N N 17.347 -13.493 27.555 -7.361 -1.724 0.862 HAK V12 46 V12 HAI HAI H 0 1 N N N 18.305 -15.778 27.546 -9.240 -0.280 1.450 HAI V12 47 V12 HAH HAH H 0 1 N N N 19.276 -16.705 25.467 -9.157 2.132 0.982 HAH V12 48 V12 HAJ HAJ H 0 1 N N N 19.287 -15.352 23.392 -7.177 3.124 -0.084 HAJ V12 49 # 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 V12 OAC CAV DOUB N N 1 V12 CAV NAO SING N N 2 V12 CAV NBD SING N N 3 V12 NAO CAT DOUB N N 4 V12 CAT NAA SING N N 5 V12 CAT CAF SING N N 6 V12 NAA HAA1 SING N N 7 V12 NAA HAA2 SING N N 8 V12 CAF HAF SING N N 9 V12 CAF CAG DOUB N N 10 V12 CAG HAG SING N N 11 V12 CAG NBD SING N N 12 V12 NBD CBC SING N N 13 V12 CBC HBC SING N N 14 V12 CBC OAS SING N N 15 V12 CBC CBA SING N N 16 V12 OAS CB0 SING N N 17 V12 CBA HBA SING N N 18 V12 CBA OAE SING N N 19 V12 CBA CAZ SING N N 20 V12 OAE HAE SING N N 21 V12 CAZ HAZ SING N N 22 V12 CAZ OAD SING N N 23 V12 CAZ CB0 SING N N 24 V12 OAD HAD SING N N 25 V12 CB0 CAN SING N N 26 V12 CB0 HB0 SING N N 27 V12 CAN NAQ SING N N 28 V12 CAN HAN1 SING N N 29 V12 CAN HAN2 SING N N 30 V12 NAQ CAU SING N N 31 V12 NAQ HAQ SING N N 32 V12 CAU OAB DOUB N N 33 V12 CAU CAL SING N N 34 V12 CAL CA0 SING N N 35 V12 CAL HAL1 SING N N 36 V12 CAL HAL2 SING N N 37 V12 CA0 NAR DOUB Y N 38 V12 CA0 NAP SING Y N 39 V12 NAR CAY SING Y N 40 V12 CAY CAK SING Y N 41 V12 CAY CAX DOUB Y N 42 V12 CAK CAI DOUB Y N 43 V12 CAK HAK SING N N 44 V12 CAI CAH SING Y N 45 V12 CAI HAI SING N N 46 V12 CAH CAJ DOUB Y N 47 V12 CAH HAH SING N N 48 V12 CAJ CAX SING Y N 49 V12 CAJ HAJ SING N N 50 V12 CAX NAP SING Y N 51 V12 NAP HAP SING N N 52 # 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 V12 SMILES ACDLabs 10.04 "O=C1N=C(N)C=CN1C2OC(C(O)C2O)CNC(=O)Cc3nc4ccccc4n3" V12 SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CNC(=O)Cc3[nH]c4ccccc4n3)[C@@H](O)[C@H]2O" V12 SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CNC(=O)Cc3[nH]c4ccccc4n3)[CH](O)[CH]2O" V12 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1ccc2c(c1)[nH]c(n2)CC(=O)NC[C@@H]3[C@H]([C@H]([C@@H](O3)N4C=CC(=NC4=O)N)O)O" V12 SMILES "OpenEye OEToolkits" 1.5.0 "c1ccc2c(c1)[nH]c(n2)CC(=O)NCC3C(C(C(O3)N4C=CC(=NC4=O)N)O)O" V12 InChI InChI 1.03 "InChI=1S/C18H20N6O5/c19-12-5-6-24(18(28)23-12)17-16(27)15(26)11(29-17)8-20-14(25)7-13-21-9-3-1-2-4-10(9)22-13/h1-6,11,15-17,26-27H,7-8H2,(H,20,25)(H,21,22)(H2,19,23,28)/t11-,15-,16-,17-/m1/s1" V12 InChIKey InChI 1.03 MMCWRTZSCVUETH-GAEVZRCVSA-N # 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 V12 "SYSTEMATIC NAME" ACDLabs 10.04 "5'-[(1H-benzimidazol-2-ylacetyl)amino]-5'-deoxycytidine" V12 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "N-[[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-2-(1H-benzimidazol-2-yl)ethanamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site V12 "Create component" 2007-06-07 RCSB V12 "Modify descriptor" 2011-06-04 RCSB #