data_RCE # _chem_comp.id RCE _chem_comp.name "1-{2,5-anhydro-6-deoxy-4-[(phosphonooxy)methyl]-beta-D-gulofuranosyl}pyrimidine-2,4(1H,3H)-dione" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H15 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-01-11 _chem_comp.pdbx_modified_date 2012-06-15 _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 350.219 _chem_comp.one_letter_code ? _chem_comp.three_letter_code RCE _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 3UKB _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 RCE P P P 0 1 N N N 3.721 -9.320 6.535 -4.224 -1.035 0.164 P RCE 1 RCE N1 N1 N 0 1 N N N -0.563 -6.318 4.714 2.534 -0.116 0.340 N1 RCE 2 RCE C2 C2 C 0 1 N N N -1.534 -5.388 4.509 3.778 0.230 0.720 C2 RCE 3 RCE O2 O2 O 0 1 N N N -2.302 -5.479 3.441 3.956 1.282 1.302 O2 RCE 4 RCE N3 N3 N 0 1 N N N -1.749 -4.430 5.371 4.827 -0.574 0.465 N3 RCE 5 RCE C4 C4 C 0 1 N N N -0.957 -4.220 6.452 4.646 -1.744 -0.179 C4 RCE 6 RCE O4 O4 O 0 1 N N N -1.160 -3.256 7.195 5.595 -2.472 -0.409 O4 RCE 7 RCE C5 C5 C 0 1 N N N 0.125 -5.145 6.691 3.343 -2.120 -0.585 C5 RCE 8 RCE C6 C6 C 0 1 N N N 0.244 -6.222 5.818 2.308 -1.295 -0.317 C6 RCE 9 RCE "C1'" "C1'" C 0 1 N N R -0.470 -7.448 3.766 1.411 0.776 0.637 "C1'" RCE 10 RCE O1P O1P O 0 1 N N N 4.709 -10.391 6.084 -3.994 -2.398 -0.364 O1P RCE 11 RCE "C2'" "C2'" C 0 1 N N R 0.381 -7.108 2.545 1.266 1.855 -0.482 "C2'" RCE 12 RCE O2A O2A O 0 1 N N N 0.191 -8.263 1.699 0.309 2.803 0.070 O2A RCE 13 RCE O2P O2P O 0 1 N N N 4.339 -8.166 7.315 -5.199 -0.231 -0.833 O2P RCE 14 RCE "C3'" "C3'" C 0 1 N N S 1.777 -7.352 3.084 0.358 1.053 -1.483 "C3'" RCE 15 RCE "O3'" "O3'" O 0 1 N N N 2.794 -7.374 2.066 -0.201 1.884 -2.503 "O3'" RCE 16 RCE O3P O3P O 0 1 N Y N 2.532 -10.077 7.360 -4.905 -1.131 1.620 O3P RCE 17 RCE "C4'" "C4'" C 0 1 N N R 1.429 -8.736 3.554 -0.687 0.678 -0.371 "C4'" RCE 18 RCE "O4'" "O4'" O 0 1 N N N 0.272 -8.510 4.389 0.171 0.041 0.619 "O4'" RCE 19 RCE "C5'" "C5'" C 0 1 N N N 2.519 -9.498 4.270 -1.922 -0.104 -0.823 "C5'" RCE 20 RCE "O5'" "O5'" O 0 1 N N N 3.007 -8.701 5.303 -2.817 -0.260 0.279 "O5'" RCE 21 RCE "C6'" "C6'" C 0 1 N N R 0.964 -9.377 2.264 -0.941 2.101 0.217 "C6'" RCE 22 RCE "C7'" "C7'" C 0 1 N N N 0.113 -10.629 2.462 -1.324 2.004 1.695 "C7'" RCE 23 RCE H5 H5 H 0 1 N N N 0.813 -5.007 7.512 3.179 -3.053 -1.102 H5 RCE 24 RCE H6 H6 H 0 1 N N N 0.979 -6.989 6.012 1.307 -1.565 -0.618 H6 RCE 25 RCE "H1'" "H1'" H 0 1 N N N -1.470 -7.782 3.453 1.554 1.253 1.606 "H1'" RCE 26 RCE "H2'" "H2'" H 0 1 N N N 0.203 -6.119 2.098 2.193 2.265 -0.884 "H2'" RCE 27 RCE HO2P HO2P H 0 0 N N N 5.275 -8.305 7.398 -5.394 0.673 -0.549 HO2P RCE 28 RCE "H3'" "H3'" H 0 1 N N N 2.017 -6.679 3.920 0.862 0.178 -1.896 "H3'" RCE 29 RCE "HO3'" "HO3'" H 0 0 N Y N 3.641 -7.530 2.467 0.458 2.311 -3.067 "HO3'" RCE 30 RCE HO3P HO3P H 0 0 N Y N 2.707 -11.011 7.383 -5.757 -1.587 1.626 HO3P RCE 31 RCE "H5'" "H5'" H 0 1 N N N 2.110 -10.432 4.683 -2.423 0.441 -1.624 "H5'" RCE 32 RCE "H5'A" "H5'A" H 0 0 N N N 3.331 -9.733 3.567 -1.618 -1.085 -1.186 "H5'A" RCE 33 RCE "H6'" "H6'" H 0 1 N N N 1.829 -9.611 1.627 -1.727 2.607 -0.345 "H6'" RCE 34 RCE "H7'" "H7'" H 0 1 N N N 0.734 -11.432 2.886 -1.453 3.006 2.104 "H7'" RCE 35 RCE "H7'A" "H7'A" H 0 0 N N N -0.715 -10.404 3.150 -2.257 1.449 1.793 "H7'A" RCE 36 RCE "H7'B" "H7'B" H 0 0 N N N -0.294 -10.953 1.493 -0.535 1.487 2.241 "H7'B" RCE 37 RCE HN3 HN3 H 0 1 N N N -2.532 -3.825 5.227 5.717 -0.310 0.747 HN3 RCE 38 # 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 RCE "O5'" P SING N N 1 RCE O1P P DOUB N N 2 RCE P O2P SING N N 3 RCE P O3P SING N N 4 RCE "C1'" N1 SING N N 5 RCE C2 N1 SING N N 6 RCE N1 C6 SING N N 7 RCE O2 C2 DOUB N N 8 RCE C2 N3 SING N N 9 RCE N3 C4 SING N N 10 RCE C4 C5 SING N N 11 RCE C4 O4 DOUB N N 12 RCE C6 C5 DOUB N N 13 RCE C5 H5 SING N N 14 RCE C6 H6 SING N N 15 RCE "C2'" "C1'" SING N N 16 RCE "C1'" "O4'" SING N N 17 RCE "C1'" "H1'" SING N N 18 RCE O2A "C2'" SING N N 19 RCE "C2'" "C3'" SING N N 20 RCE "C2'" "H2'" SING N N 21 RCE O2A "C6'" SING N N 22 RCE O2P HO2P SING N N 23 RCE "O3'" "C3'" SING N N 24 RCE "C3'" "C4'" SING N N 25 RCE "C3'" "H3'" SING N N 26 RCE "O3'" "HO3'" SING N N 27 RCE O3P HO3P SING N N 28 RCE "C6'" "C4'" SING N N 29 RCE "C4'" "C5'" SING N N 30 RCE "C4'" "O4'" SING N N 31 RCE "C5'" "O5'" SING N N 32 RCE "C5'" "H5'" SING N N 33 RCE "C5'" "H5'A" SING N N 34 RCE "C6'" "C7'" SING N N 35 RCE "C6'" "H6'" SING N N 36 RCE "C7'" "H7'" SING N N 37 RCE "C7'" "H7'A" SING N N 38 RCE "C7'" "H7'B" SING N N 39 RCE N3 HN3 SING N N 40 # 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 RCE SMILES ACDLabs 12.01 "O=P(O)(O)OCC32OC(N1C(=O)NC(=O)C=C1)C(OC2C)C3O" RCE InChI InChI 1.03 "InChI=1S/C11H15N2O9P/c1-5-11(4-20-23(17,18)19)8(15)7(21-5)9(22-11)13-3-2-6(14)12-10(13)16/h2-3,5,7-9,15H,4H2,1H3,(H,12,14,16)(H2,17,18,19)/t5-,7-,8+,9-,11+/m1/s1" RCE InChIKey InChI 1.03 YMFXFISZLBZENQ-QPLYKKBVSA-N RCE SMILES_CANONICAL CACTVS 3.370 "C[C@H]1O[C@@H]2[C@H](O)[C@@]1(CO[P](O)(O)=O)O[C@H]2N3C=CC(=O)NC3=O" RCE SMILES CACTVS 3.370 "C[CH]1O[CH]2[CH](O)[C]1(CO[P](O)(O)=O)O[CH]2N3C=CC(=O)NC3=O" RCE SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C[C@@H]1[C@]2([C@H]([C@@H](O1)[C@@H](O2)N3C=CC(=O)NC3=O)O)COP(=O)(O)O" RCE SMILES "OpenEye OEToolkits" 1.7.6 "CC1C2(C(C(O1)C(O2)N3C=CC(=O)NC3=O)O)COP(=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 RCE "SYSTEMATIC NAME" ACDLabs 12.01 "1-{2,5-anhydro-6-deoxy-4-[(phosphonooxy)methyl]-beta-D-gulofuranosyl}pyrimidine-2,4(1H,3H)-dione" RCE "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(1R,3R,4R,6R,7S)-6-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-methyl-7-oxidanyl-2,5-dioxabicyclo[2.2.1]heptan-4-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 RCE "Create component" 2012-01-11 RCSB #