data_UD7 # _chem_comp.id UD7 _chem_comp.name "[(2R,3R,4R,6R)-3-acetamido-6-methyl-4-oxidanyl-5-oxidanylidene-oxan-2-yl] [[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H25 N3 O16 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-08-02 _chem_comp.pdbx_modified_date 2013-08-23 _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 589.338 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UD7 _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 4G5H _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 UD7 N1 N1 N 0 1 N N N -58.753 -9.051 12.452 5.450 1.393 0.092 N1 UD7 1 UD7 C2 C2 C 0 1 N N N -59.368 -8.111 13.348 5.985 2.498 -0.458 C2 UD7 2 UD7 O2 O2 O 0 1 N N N -58.641 -7.346 14.037 6.269 2.501 -1.640 O2 UD7 3 UD7 N3 N3 N 0 1 N N N -60.690 -8.066 13.460 6.210 3.599 0.282 N3 UD7 4 UD7 C4 C4 C 0 1 N N N -61.511 -8.862 12.749 5.901 3.612 1.594 C4 UD7 5 UD7 O4 O4 O 0 1 N N N -62.729 -8.696 12.917 6.104 4.609 2.264 O4 UD7 6 UD7 C5 C5 C 0 1 N N N -60.957 -9.819 11.868 5.337 2.456 2.186 C5 UD7 7 UD7 C6 C6 C 0 1 N N N -59.553 -9.881 11.731 5.116 1.367 1.419 C6 UD7 8 UD7 PA PA P 0 1 N N N -58.479 -13.032 9.697 0.287 -2.688 0.386 PA UD7 9 UD7 PB PB P 0 1 N N N -56.606 -14.000 7.682 -2.512 -1.731 0.573 PB UD7 10 UD7 "C1'" "C1'" C 0 1 N N R -57.724 -13.385 5.302 -4.553 -0.031 0.285 "C1'" UD7 11 UD7 "O1'" "O1'" O 0 1 N N N -57.672 -13.266 6.723 -3.266 -0.494 -0.128 "O1'" UD7 12 UD7 O1A O1A O 0 1 N N N -59.673 -13.723 10.336 0.144 -4.238 -0.027 O1A UD7 13 UD7 C1B C1B C 0 1 N N R -57.275 -9.025 12.487 5.216 0.208 -0.738 C1B UD7 14 UD7 O1B O1B O 0 1 N N N -56.456 -15.419 7.172 -2.402 -1.481 2.028 O1B UD7 15 UD7 "C2'" "C2'" C 0 1 N N R -57.113 -12.089 4.706 -5.292 0.559 -0.919 "C2'" UD7 16 UD7 "O2'" "O2'" O 0 1 N N N -55.525 -9.225 14.174 7.395 -0.911 -0.892 "O2'" UD7 17 UD7 O2A O2A O 0 1 N N N -58.726 -11.908 8.696 0.460 -2.582 1.852 O2A UD7 18 UD7 C2B C2B C 0 1 N N R -56.784 -9.760 13.771 6.109 -0.970 -0.272 C2B UD7 19 UD7 O2B O2B O 0 1 N N N -55.404 -13.068 7.843 -3.351 -3.082 0.323 O2B UD7 20 UD7 "C3'" "C3'" C 0 1 N N R -57.952 -10.917 5.247 -6.686 1.020 -0.473 "C3'" UD7 21 UD7 "O3'" "O3'" O 0 1 N N N -57.558 -9.754 4.518 -7.483 -0.115 -0.128 "O3'" UD7 22 UD7 O3A O3A O 0 1 N N N -57.446 -14.129 9.074 -1.039 -1.890 -0.057 O3A UD7 23 UD7 C3B C3B C 0 1 N N S -56.525 -11.170 13.243 5.311 -2.199 -0.771 C3B UD7 24 UD7 O3B O3B O 0 1 N N N -55.720 -12.012 14.111 5.837 -2.664 -2.016 O3B UD7 25 UD7 "C4'" "C4'" C 0 1 N N N -59.452 -11.252 5.172 -6.518 1.915 0.738 "C4'" UD7 26 UD7 "O4'" "O4'" O 0 1 N N N -60.246 -10.462 4.685 -7.073 2.986 0.804 "O4'" UD7 27 UD7 C4B C4B C 0 1 N N R -55.948 -10.893 11.835 3.876 -1.668 -0.956 C4B UD7 28 UD7 O4B O4B O 0 1 N N N -56.588 -9.664 11.382 3.875 -0.290 -0.547 O4B UD7 29 UD7 "C5'" "C5'" C 0 1 N N R -59.938 -12.610 5.686 -5.630 1.423 1.861 "C5'" UD7 30 UD7 "O5'" "O5'" O 0 1 N N N -59.129 -13.586 5.008 -4.397 0.969 1.294 "O5'" UD7 31 UD7 C5B C5B C 0 1 N N N -56.211 -12.041 10.827 2.908 -2.473 -0.088 C5B UD7 32 UD7 O5B O5B O 0 1 N N N -57.570 -12.501 10.934 1.568 -2.052 -0.353 O5B UD7 33 UD7 "C6'" "C6'" C 0 1 N N N -61.440 -12.933 5.555 -6.319 0.270 2.594 "C6'" UD7 34 UD7 "C7'" "C7'" C 0 1 N N N -54.744 -11.080 4.547 -4.689 2.074 -2.729 "C7'" UD7 35 UD7 "O7'" "O7'" O 0 1 N N N -54.500 -10.873 3.353 -5.442 1.460 -3.455 "O7'" UD7 36 UD7 "C8'" "C8'" C 0 1 N N N -54.004 -10.346 5.654 -3.917 3.251 -3.267 "C8'" UD7 37 UD7 "N2'" "N2'" N 0 1 N N N -55.654 -11.985 4.970 -4.542 1.704 -1.442 "N2'" UD7 38 UD7 H1 H1 H 0 1 N N N -61.094 -7.413 14.100 6.597 4.387 -0.131 H1 UD7 39 UD7 H2 H2 H 0 1 N N N -61.595 -10.489 11.311 5.083 2.447 3.235 H2 UD7 40 UD7 H3 H3 H 0 1 N N N -59.112 -10.593 11.049 4.687 0.476 1.853 H3 UD7 41 UD7 H4 H4 H 0 1 N N N -57.134 -14.249 4.962 -5.126 -0.866 0.688 H4 UD7 42 UD7 H5 H5 H 0 1 N N N -60.476 -13.338 10.006 0.027 -4.383 -0.976 H5 UD7 43 UD7 H6 H6 H 0 1 N N N -56.944 -7.978 12.556 5.398 0.436 -1.788 H6 UD7 44 UD7 H7 H7 H 0 1 N N N -57.262 -12.127 3.617 -5.389 -0.199 -1.695 H7 UD7 45 UD7 H8 H8 H 0 1 N N N -55.226 -9.673 14.957 7.990 -1.627 -0.632 H8 UD7 46 UD7 H9 H9 H 0 1 N N N -57.547 -9.747 14.564 6.203 -0.981 0.814 H9 UD7 47 UD7 H10 H10 H 0 1 N N N -54.613 -13.523 7.580 -3.463 -3.309 -0.611 H10 UD7 48 UD7 H11 H11 H 0 1 N N N -57.692 -10.782 6.307 -7.166 1.576 -1.279 H11 UD7 49 UD7 H12 H12 H 0 1 N N N -58.327 -9.334 4.152 -8.378 0.106 0.162 H12 UD7 50 UD7 H13 H13 H 0 1 N N N -57.503 -11.653 13.103 5.332 -2.995 -0.028 H13 UD7 51 UD7 H14 H14 H 0 1 N N N -56.160 -12.119 14.946 6.757 -2.956 -1.970 H14 UD7 52 UD7 H15 H15 H 0 1 N N N -54.862 -10.741 11.921 3.585 -1.743 -2.004 H15 UD7 53 UD7 H16 H16 H 0 1 N N N -59.696 -12.652 6.758 -5.436 2.238 2.559 H16 UD7 54 UD7 H17 H17 H 0 1 N N N -55.528 -12.876 11.042 3.008 -3.533 -0.320 H17 UD7 55 UD7 H18 H18 H 0 1 N N N -56.032 -11.674 9.805 3.139 -2.307 0.964 H18 UD7 56 UD7 H19 H19 H 0 1 N N N -62.028 -12.168 6.084 -6.504 -0.546 1.896 H19 UD7 57 UD7 H20 H20 H 0 1 N N N -61.722 -12.941 4.492 -5.677 -0.082 3.402 H20 UD7 58 UD7 H21 H21 H 0 1 N N N -61.642 -13.920 5.996 -7.266 0.616 3.007 H21 UD7 59 UD7 H22 H22 H 0 1 N N N -53.272 -9.655 5.211 -3.298 3.672 -2.475 H22 UD7 60 UD7 H23 H23 H 0 1 N N N -54.724 -9.778 6.262 -3.281 2.923 -4.090 H23 UD7 61 UD7 H24 H24 H 0 1 N N N -53.481 -11.075 6.291 -4.613 4.009 -3.626 H24 UD7 62 UD7 H25 H25 H 0 1 N N N -55.284 -12.704 5.558 -3.940 2.195 -0.861 H25 UD7 63 # 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 UD7 "O7'" "C7'" DOUB N N 1 UD7 "O3'" "C3'" SING N N 2 UD7 "C7'" "N2'" SING N N 3 UD7 "C7'" "C8'" SING N N 4 UD7 "O4'" "C4'" DOUB N N 5 UD7 "C2'" "N2'" SING N N 6 UD7 "C2'" "C3'" SING N N 7 UD7 "C2'" "C1'" SING N N 8 UD7 "O5'" "C1'" SING N N 9 UD7 "O5'" "C5'" SING N N 10 UD7 "C4'" "C3'" SING N N 11 UD7 "C4'" "C5'" SING N N 12 UD7 "C1'" "O1'" SING N N 13 UD7 "C6'" "C5'" SING N N 14 UD7 "O1'" PB SING N N 15 UD7 O1B PB DOUB N N 16 UD7 PB O2B SING N N 17 UD7 PB O3A SING N N 18 UD7 O2A PA DOUB N N 19 UD7 O3A PA SING N N 20 UD7 PA O1A SING N N 21 UD7 PA O5B SING N N 22 UD7 C5B O5B SING N N 23 UD7 C5B C4B SING N N 24 UD7 O4B C4B SING N N 25 UD7 O4B C1B SING N N 26 UD7 C6 C5 DOUB N N 27 UD7 C6 N1 SING N N 28 UD7 C4B C3B SING N N 29 UD7 C5 C4 SING N N 30 UD7 N1 C1B SING N N 31 UD7 N1 C2 SING N N 32 UD7 C1B C2B SING N N 33 UD7 C4 O4 DOUB N N 34 UD7 C4 N3 SING N N 35 UD7 C3B C2B SING N N 36 UD7 C3B O3B SING N N 37 UD7 C2 N3 SING N N 38 UD7 C2 O2 DOUB N N 39 UD7 C2B "O2'" SING N N 40 UD7 N3 H1 SING N N 41 UD7 C5 H2 SING N N 42 UD7 C6 H3 SING N N 43 UD7 "C1'" H4 SING N N 44 UD7 O1A H5 SING N N 45 UD7 C1B H6 SING N N 46 UD7 "C2'" H7 SING N N 47 UD7 "O2'" H8 SING N N 48 UD7 C2B H9 SING N N 49 UD7 O2B H10 SING N N 50 UD7 "C3'" H11 SING N N 51 UD7 "O3'" H12 SING N N 52 UD7 C3B H13 SING N N 53 UD7 O3B H14 SING N N 54 UD7 C4B H15 SING N N 55 UD7 "C5'" H16 SING N N 56 UD7 C5B H17 SING N N 57 UD7 C5B H18 SING N N 58 UD7 "C6'" H19 SING N N 59 UD7 "C6'" H20 SING N N 60 UD7 "C6'" H21 SING N N 61 UD7 "C8'" H22 SING N N 62 UD7 "C8'" H23 SING N N 63 UD7 "C8'" H24 SING N N 64 UD7 "N2'" H25 SING N N 65 # 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 UD7 SMILES ACDLabs 12.01 "O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(=O)C(O)C3NC(=O)C)C)O)O" UD7 InChI InChI 1.03 "InChI=1S/C17H25N3O16P2/c1-6-11(23)13(25)10(18-7(2)21)16(33-6)35-38(30,31)36-37(28,29)32-5-8-12(24)14(26)15(34-8)20-4-3-9(22)19-17(20)27/h3-4,6,8,10,12-16,24-26H,5H2,1-2H3,(H,18,21)(H,28,29)(H,30,31)(H,19,22,27)/t6-,8-,10-,12-,13-,14-,15-,16-/m1/s1" UD7 InChIKey InChI 1.03 XBILTLYIKDPORV-HZUXRPHDSA-N UD7 SMILES_CANONICAL CACTVS 3.370 "C[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](NC(C)=O)[C@@H](O)C1=O" UD7 SMILES CACTVS 3.370 "C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](NC(C)=O)[CH](O)C1=O" UD7 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C[C@@H]1C(=O)[C@@H]([C@H]([C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C)O" UD7 SMILES "OpenEye OEToolkits" 1.7.6 "CC1C(=O)C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C)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 UD7 "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,3R,4R,6R)-3-(acetylamino)-4-hydroxy-6-methyl-5-oxotetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)" UD7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3R,4R,6R)-3-acetamido-6-methyl-4-oxidanyl-5-oxidanylidene-oxan-2-yl] [[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen 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 UD7 "Create component" 2012-08-02 PDBJ UD7 "Initial release" 2013-08-28 RCSB #