data_BVP # _chem_comp.id BVP _chem_comp.name "(E)-5-(2-BROMOVINYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H14 Br N2 O8 P" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms BVDU-MP _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-03-31 _chem_comp.pdbx_modified_date 2020-06-17 _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 413.115 _chem_comp.one_letter_code U _chem_comp.three_letter_code BVP _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1OSN _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 BVP "O3'" O3* O 0 1 N N N 84.775 22.905 52.971 -3.279 3.632 0.610 "O3'" BVP 1 BVP "C3'" C3* C 0 1 N N S 84.840 22.493 54.336 -2.776 2.504 -0.107 "C3'" BVP 2 BVP "C2'" C2* C 0 1 N N N 84.298 23.528 55.308 -1.238 2.581 -0.228 "C2'" BVP 3 BVP "C1'" C1* C 0 1 N N R 82.802 23.279 55.231 -0.739 1.317 0.507 "C1'" BVP 4 BVP "O4'" O4* O 0 1 N N N 82.642 21.899 54.864 -1.850 0.396 0.452 "O4'" BVP 5 BVP "C4'" C4* C 0 1 N N R 83.919 21.324 54.502 -3.028 1.202 0.685 "C4'" BVP 6 BVP "C5'" C5* C 0 1 N N N 84.304 20.323 55.603 -4.275 0.485 0.163 "C5'" BVP 7 BVP "O5'" O5* O 0 1 N N N 85.635 19.808 55.408 -4.510 -0.691 0.941 "O5'" BVP 8 BVP P P P 0 1 N N N 86.816 19.964 56.535 -5.829 -1.391 0.340 P BVP 9 BVP O1P O1P O 0 1 N N N 86.394 20.980 57.539 -6.944 -0.417 0.331 O1P BVP 10 BVP O2P O2P O 0 1 N N N 88.081 20.412 55.861 -5.536 -1.886 -1.164 O2P BVP 11 BVP O3P O3P O 0 1 N Y N 87.057 18.680 57.202 -6.229 -2.655 1.253 O3P BVP 12 BVP N1 N1 N 0 1 N N N 81.985 23.534 56.504 0.427 0.755 -0.179 N1 BVP 13 BVP C6 C6 C 0 1 N N N 82.142 22.736 57.644 1.635 0.741 0.459 C6 BVP 14 BVP C5 C5 C 0 1 N N N 81.364 22.995 58.842 2.724 0.218 -0.177 C5 BVP 15 BVP C5A C5A C 0 1 N N N 81.349 22.479 59.863 4.044 0.187 0.483 C5A BVP 16 BVP C5B C5B C 0 1 N N N 80.719 21.296 60.218 5.066 -0.425 -0.104 C5B BVP 17 BVP BR BR BR 0 0 N N N 80.435 20.721 62.090 6.717 -0.590 0.803 BR BVP 18 BVP C4 C4 C 0 1 N N N 80.417 24.120 58.791 2.548 -0.315 -1.536 C4 BVP 19 BVP O4 O4 O 0 1 N N N 79.675 24.474 59.745 3.489 -0.792 -2.143 O4 BVP 20 BVP N3 N3 N 0 1 N N N 80.337 24.847 57.617 1.321 -0.264 -2.097 N3 BVP 21 BVP C2 C2 C 0 1 N N N 81.078 24.592 56.498 0.285 0.259 -1.418 C2 BVP 22 BVP O2 O2 O 0 1 N N N 80.921 25.311 55.522 -0.810 0.293 -1.946 O2 BVP 23 BVP "H3'" H3* H 0 1 N N N 85.114 22.258 52.363 -3.067 4.415 0.084 "H3'" BVP 24 BVP H1 H1 H 0 1 N N N 85.915 22.293 54.554 -3.234 2.445 -1.095 H1 BVP 25 BVP "H2'1" 1H2* H 0 0 N N N 84.613 24.578 55.105 -0.935 2.558 -1.275 "H2'1" BVP 26 BVP "H2'2" 2H2* H 0 0 N N N 84.732 23.485 56.334 -0.861 3.480 0.259 "H2'2" BVP 27 BVP "H1'" H1* H 0 1 N N N 82.402 24.018 54.498 -0.493 1.553 1.542 "H1'" BVP 28 BVP "H4'" H4* H 0 1 N N N 83.938 20.740 53.553 -3.134 1.420 1.748 "H4'" BVP 29 BVP "H5'1" 1H5* H 0 0 N N N 83.556 19.500 55.685 -5.136 1.150 0.241 "H5'1" BVP 30 BVP "H5'2" 2H5* H 0 0 N N N 84.184 20.768 56.618 -4.125 0.207 -0.880 "H5'2" BVP 31 BVP H2P H2P H 0 1 N N N 88.765 20.502 56.514 -4.806 -2.517 -1.113 H2P BVP 32 BVP H3P H3P H 0 1 N N N 87.741 18.770 57.855 -7.022 -3.045 0.859 H3P BVP 33 BVP H6 H6 H 0 1 N N N 82.872 21.911 57.599 1.728 1.141 1.458 H6 BVP 34 BVP H5A H5A H 0 1 N N N 81.952 23.133 60.516 4.179 0.661 1.444 H5A BVP 35 BVP H5B H5B H 0 1 N N N 80.491 20.895 59.216 4.954 -0.829 -1.099 H5B BVP 36 BVP HN3 HN3 H 0 1 N N N 79.683 25.629 57.573 1.185 -0.610 -2.993 HN3 BVP 37 # # 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 BVP "O3'" "C3'" SING N N 1 BVP "O3'" "H3'" SING N N 2 BVP "C3'" "C2'" SING N N 3 BVP "C3'" "C4'" SING N N 4 BVP "C3'" H1 SING N N 5 BVP "C2'" "C1'" SING N N 6 BVP "C2'" "H2'1" SING N N 7 BVP "C2'" "H2'2" SING N N 8 BVP "C1'" "O4'" SING N N 9 BVP "C1'" N1 SING N N 10 BVP "C1'" "H1'" SING N N 11 BVP "O4'" "C4'" SING N N 12 BVP "C4'" "C5'" SING N N 13 BVP "C4'" "H4'" SING N N 14 BVP "C5'" "O5'" SING N N 15 BVP "C5'" "H5'1" SING N N 16 BVP "C5'" "H5'2" SING N N 17 BVP "O5'" P SING N N 18 BVP P O1P DOUB N N 19 BVP P O2P SING N N 20 BVP P O3P SING N N 21 BVP O2P H2P SING N N 22 BVP O3P H3P SING N N 23 BVP N1 C6 SING N N 24 BVP N1 C2 SING N N 25 BVP C6 C5 DOUB N N 26 BVP C6 H6 SING N N 27 BVP C5 C5A SING N N 28 BVP C5 C4 SING N N 29 BVP C5A C5B DOUB N E 30 BVP C5A H5A SING N N 31 BVP C5B BR SING N N 32 BVP C5B H5B SING N N 33 BVP C4 O4 DOUB N N 34 BVP C4 N3 SING N N 35 BVP N3 C2 SING N N 36 BVP N3 HN3 SING N N 37 BVP C2 O2 DOUB N N 38 # # 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 BVP SMILES ACDLabs 10.04 "Br[C@H]=CC=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2)COP(=O)(O)O" BVP SMILES_CANONICAL CACTVS 3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(\C=C\Br)C(=O)NC2=O" BVP SMILES CACTVS 3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C=CBr)C(=O)NC2=O" BVP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)\C=C\Br)COP(=O)(O)O)O" BVP SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=C(C(=O)NC2=O)C=CBr)COP(=O)(O)O)O" BVP InChI InChI 1.03 "InChI=1S/C11H14BrN2O8P/c12-2-1-6-4-14(11(17)13-10(6)16)9-3-7(15)8(22-9)5-21-23(18,19)20/h1-2,4,7-9,15H,3,5H2,(H,13,16,17)(H2,18,19,20)/b2-1+/t7-,8+,9+/m0/s1" BVP InChIKey InChI 1.03 LKWCVKAHHUJPQO-PIXDULNESA-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 BVP "SYSTEMATIC NAME" ACDLabs 10.04 "5-[(E)-2-bromoethenyl]-2'-deoxyuridine 5'-(dihydrogen phosphate)" BVP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-[5-[(E)-2-bromoethenyl]-2,4-dioxo-pyrimidin-1-yl]-3-hydroxy-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 BVP "Create component" 2003-03-31 RCSB BVP "Modify descriptor" 2011-06-04 RCSB BVP "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id BVP _pdbx_chem_comp_synonyms.name BVDU-MP _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##