data_MDV # _chem_comp.id MDV _chem_comp.name "(7S,8S)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-7,8-dihydro-3H-imidazo[2,1-i]purine-7,8-diol" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H16 N5 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-07-23 _chem_comp.pdbx_modified_date 2011-06-04 _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 389.258 _chem_comp.one_letter_code ? _chem_comp.three_letter_code MDV _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 3O1U _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 MDV P P P 0 1 N N N 0.146 0.104 -1.105 5.881 1.114 0.212 P MDV 1 MDV N1 N1 N 0 1 N N N -0.264 -3.457 6.054 -4.747 -0.241 0.539 N1 MDV 2 MDV C2 C2 C 0 1 N N N 1.044 -3.822 5.886 -3.991 -1.171 1.183 C2 MDV 3 MDV N3 N3 N 0 1 N N N 1.794 -3.179 4.949 -2.699 -1.235 1.064 N3 MDV 4 MDV C4 C4 C 0 1 Y N N 1.233 -2.180 4.215 -2.010 -0.382 0.290 C4 MDV 5 MDV C5 C5 C 0 1 Y N N -0.091 -1.804 4.407 -2.684 0.612 -0.416 C5 MDV 6 MDV C6 C6 C 0 1 N N N -0.836 -2.512 5.319 -4.150 0.688 -0.284 C6 MDV 7 MDV N6 N6 N 0 1 N N N -2.087 -2.412 5.543 -5.001 1.515 -0.833 N6 MDV 8 MDV N7 N7 N 0 1 Y N N -0.384 -0.785 3.589 -1.764 1.320 -1.104 N7 MDV 9 MDV C8 C8 C 0 1 Y N N 0.750 -0.552 2.897 -0.580 0.829 -0.868 C8 MDV 10 MDV N9 N9 N 0 1 Y N N 1.740 -1.413 3.236 -0.683 -0.225 -0.011 N9 MDV 11 MDV "C1'" "C1'" C 0 1 N N R 3.065 -1.525 2.682 0.423 -1.041 0.497 "C1'" MDV 12 MDV O1P O1P O 0 1 N N N 0.119 -0.241 -2.541 5.615 2.036 -0.915 O1P MDV 13 MDV "C2'" "C2'" C 0 1 N N N 3.397 -2.958 2.187 0.589 -2.300 -0.376 "C2'" MDV 14 MDV C22 C22 C 0 1 N N S -1.196 -4.018 6.961 -6.200 -0.006 0.537 C22 MDV 15 MDV C23 C23 C 0 1 N N S -2.502 -3.317 6.508 -6.369 1.202 -0.403 C23 MDV 16 MDV H1 H1 H 0 1 N N N -1.258 -5.116 6.949 -6.728 -0.875 0.144 H1 MDV 17 MDV O26 O26 O 0 1 N N N -3.417 -4.239 5.918 -7.179 0.849 -1.526 O26 MDV 18 MDV O2P O2P O 0 1 N N N -0.039 1.595 -0.937 6.266 1.965 1.523 O2P MDV 19 MDV "C3'" "C3'" C 0 1 N N S 4.003 -2.740 0.797 2.043 -2.209 -0.900 "C3'" MDV 20 MDV "O3'" "O3'" O 0 1 N N N 5.424 -2.651 0.893 2.674 -3.491 -0.878 "O3'" MDV 21 MDV "C4'" "C4'" C 0 1 N N R 3.382 -1.392 0.370 2.700 -1.252 0.127 "C4'" MDV 22 MDV "O4'" "O4'" O 0 1 N N N 3.297 -0.626 1.582 1.653 -0.301 0.417 "O4'" MDV 23 MDV "C5'" "C5'" C 0 1 N N N 1.987 -1.511 -0.314 3.911 -0.549 -0.489 "C5'" MDV 24 MDV "O5'" "O5'" O 0 1 N N N 1.485 -0.283 -0.493 4.565 0.236 0.510 "O5'" MDV 25 MDV H2 H2 H 0 1 N N N 1.475 -4.608 6.488 -4.487 -1.886 1.822 H2 MDV 26 MDV H8 H8 H 0 1 N N N 0.857 0.229 2.159 0.343 1.201 -1.288 H8 MDV 27 MDV "H1'" "H1'" H 0 1 N N N 3.721 -1.259 3.524 0.228 -1.329 1.530 "H1'" MDV 28 MDV "H2'" "H2'" H 0 1 N N N 4.109 -3.459 2.860 0.456 -3.200 0.223 "H2'" MDV 29 MDV "H2'A" "H2'A" H 0 0 N N N 2.493 -3.583 2.136 -0.117 -2.284 -1.206 "H2'A" MDV 30 MDV "H3'" "H3'" H 0 1 N N N 3.800 -3.551 0.083 2.069 -1.782 -1.903 "H3'" MDV 31 MDV "HO3'" "HO3'" H 0 0 N N N 5.792 -2.516 0.028 2.243 -4.151 -1.438 "HO3'" MDV 32 MDV "H4'" "H4'" H 0 1 N N N 4.008 -0.921 -0.402 2.987 -1.794 1.028 "H4'" MDV 33 MDV "H5'" "H5'" H 0 1 N N N 2.094 -2.013 -1.287 4.605 -1.294 -0.878 "H5'" MDV 34 MDV "H5'A" "H5'A" H 0 0 N N N 1.311 -2.098 0.325 3.581 0.098 -1.302 "H5'A" MDV 35 MDV O8 O8 O 0 1 N N N -0.976 -0.613 -0.388 7.102 0.137 -0.171 O8 MDV 36 MDV H13 H13 H 0 1 N N N -0.134 2.001 -1.791 7.052 2.519 1.416 H13 MDV 37 MDV H14 H14 H 0 1 N N N -1.466 -1.137 -1.010 7.332 -0.496 0.523 H14 MDV 38 MDV O24 O24 O 0 1 N N N -0.847 -3.704 8.308 -6.660 0.312 1.851 O24 MDV 39 MDV H141 H141 H 0 0 N N N -3.023 -2.853 7.358 -6.803 2.047 0.132 H141 MDV 40 MDV H15 H15 H 0 1 N N N -3.706 -4.863 6.574 -7.270 1.554 -2.182 H15 MDV 41 MDV H16 H16 H 0 1 N N N -1.484 -4.089 8.899 -7.611 0.476 1.906 H16 MDV 42 # 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 MDV P O1P DOUB N N 1 MDV P O2P SING N N 2 MDV P "O5'" SING N N 3 MDV N1 C2 SING N N 4 MDV N1 C6 SING N N 5 MDV N1 C22 SING N N 6 MDV C2 N3 DOUB N N 7 MDV C2 H2 SING N N 8 MDV N3 C4 SING N N 9 MDV C4 C5 DOUB Y N 10 MDV C4 N9 SING Y N 11 MDV C5 C6 SING N N 12 MDV C5 N7 SING Y N 13 MDV C6 N6 DOUB N N 14 MDV N6 C23 SING N N 15 MDV N7 C8 DOUB Y N 16 MDV C8 N9 SING Y N 17 MDV C8 H8 SING N N 18 MDV N9 "C1'" SING N N 19 MDV "C1'" "C2'" SING N N 20 MDV "C1'" "O4'" SING N N 21 MDV "C1'" "H1'" SING N N 22 MDV "C2'" "C3'" SING N N 23 MDV "C2'" "H2'" SING N N 24 MDV "C2'" "H2'A" SING N N 25 MDV C22 C23 SING N N 26 MDV C22 H1 SING N N 27 MDV C23 O26 SING N N 28 MDV O2P H13 SING N N 29 MDV "C3'" "O3'" SING N N 30 MDV "C3'" "C4'" SING N N 31 MDV "C3'" "H3'" SING N N 32 MDV "O3'" "HO3'" SING N N 33 MDV "C4'" "O4'" SING N N 34 MDV "C4'" "C5'" SING N N 35 MDV "C4'" "H4'" SING N N 36 MDV "C5'" "O5'" SING N N 37 MDV "C5'" "H5'" SING N N 38 MDV "C5'" "H5'A" SING N N 39 MDV O8 P SING N N 40 MDV O8 H14 SING N N 41 MDV C22 O24 SING N N 42 MDV C23 H141 SING N N 43 MDV O26 H15 SING N N 44 MDV O24 H16 SING N N 45 # 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 MDV SMILES ACDLabs 12.01 "O=P(O)(O)OCC4OC(n3cnc2c3N=CN1C2=NC(O)C1O)CC4O" MDV SMILES_CANONICAL CACTVS 3.370 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3c2N=CN4[C@@H](O)[C@H](O)N=C34" MDV SMILES CACTVS 3.370 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2cnc3c2N=CN4[CH](O)[CH](O)N=C34" MDV SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N=CN4C2=N[C@H]([C@@H]4O)O" MDV SMILES "OpenEye OEToolkits" 1.7.0 "c1nc2c(n1C3CC(C(O3)COP(=O)(O)O)O)N=CN4C2=NC(C4O)O" MDV InChI InChI 1.03 "InChI=1S/C12H16N5O8P/c18-5-1-7(25-6(5)2-24-26(21,22)23)16-3-13-8-9(16)14-4-17-10(8)15-11(19)12(17)20/h3-7,11-12,18-20H,1-2H2,(H2,21,22,23)/t5-,6+,7+,11-,12-/m0/s1" MDV InChIKey InChI 1.03 MMGFTCXHWADSBK-BJMSXLCZSA-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 MDV "SYSTEMATIC NAME" ACDLabs 12.01 "(7S,8S)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-7,8-dihydro-3H-imidazo[2,1-i]purine-7,8-diol" MDV "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3S,5R)-5-[(7S,8S)-7,8-dihydroxy-7,8-dihydroimidazo[2,1-f]purin-3-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 MDV "Create component" 2010-07-23 RCSB MDV "Modify descriptor" 2011-06-04 RCSB #