data_2KH # _chem_comp.id 2KH _chem_comp.name "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H16 N3 O14 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-11-19 _chem_comp.pdbx_modified_date 2013-12-13 _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 483.156 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 2KH _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 4NKT _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 2KH PA PA P 0 1 N N N 63.667 19.290 93.655 1.254 0.834 0.500 PA 2KH 1 2KH O1A O1A O 0 1 N N N 65.099 18.844 94.192 1.094 1.502 -0.811 O1A 2KH 2 2KH O2A O2A O 0 1 N N N 62.844 19.789 94.805 1.534 1.940 1.635 O2A 2KH 3 2KH N3A N3A N 0 1 N N N 62.931 18.002 92.908 2.550 -0.238 0.429 N3A 2KH 4 2KH "O5'" "O5'" O 0 1 N N N 63.907 20.489 92.632 -0.091 0.026 0.858 "O5'" 2KH 5 2KH PB PB P 0 1 N N N 61.538 17.475 93.613 3.980 0.568 0.056 PB 2KH 6 2KH O1B O1B O 0 1 N N N 60.627 18.688 94.067 3.830 1.293 -1.374 O1B 2KH 7 2KH O2B O2B O 0 1 N N N 60.836 16.737 92.527 4.259 1.583 1.096 O2B 2KH 8 2KH O3B O3B O 0 1 N N N 61.711 16.391 94.796 5.192 -0.489 -0.002 O3B 2KH 9 2KH PG PG P 0 1 N N N 61.605 16.682 96.340 6.770 -0.366 -0.300 PG 2KH 10 2KH O1G O1G O 0 1 N N N 60.374 16.109 96.802 7.350 -1.807 -0.722 O1G 2KH 11 2KH O2G O2G O 0 1 N N N 61.617 18.141 96.662 6.990 0.597 -1.402 O2G 2KH 12 2KH O3G O3G O 0 1 N N N 62.743 16.042 97.082 7.527 0.151 1.023 O3G 2KH 13 2KH "C5'" "C5'" C 0 1 N N N 62.867 20.949 91.779 -0.723 -0.877 -0.052 "C5'" 2KH 14 2KH "C4'" "C4'" C 0 1 N N R 63.262 21.867 90.704 -1.972 -1.471 0.603 "C4'" 2KH 15 2KH "O4'" "O4'" O 0 1 N N N 63.889 23.050 91.224 -2.954 -0.440 0.806 "O4'" 2KH 16 2KH "C1'" "C1'" C 0 1 N N R 64.953 23.387 90.361 -4.249 -1.052 0.628 "C1'" 2KH 17 2KH "C2'" "C2'" C 0 1 N N R 64.873 22.423 89.254 -4.037 -2.005 -0.576 "C2'" 2KH 18 2KH "O2'" "O2'" O 0 1 N N N 64.045 22.876 88.214 -4.980 -3.079 -0.548 "O2'" 2KH 19 2KH "C3'" "C3'" C 0 1 N N S 64.273 21.257 89.876 -2.600 -2.525 -0.328 "C3'" 2KH 20 2KH "O3'" "O3'" O 0 1 N N N 63.710 20.341 88.953 -2.634 -3.802 0.313 "O3'" 2KH 21 2KH N1 N1 N 0 1 N N N 66.218 23.313 91.030 -5.259 -0.039 0.312 N1 2KH 22 2KH C6 C6 C 0 1 N N N 66.367 22.572 92.172 -6.401 0.037 1.063 C6 2KH 23 2KH C2 C2 C 0 1 N N N 67.299 23.978 90.508 -5.054 0.811 -0.710 C2 2KH 24 2KH O2 O2 O 0 1 N N N 67.158 24.673 89.430 -4.030 0.729 -1.361 O2 2KH 25 2KH N3 N3 N 0 1 N N N 68.502 23.920 91.102 -5.965 1.751 -1.022 N3 2KH 26 2KH C4 C4 C 0 1 N N N 68.698 23.205 92.223 -7.105 1.855 -0.309 C4 2KH 27 2KH O4 O4 O 0 1 N N N 69.942 23.139 92.821 -7.930 2.706 -0.591 O4 2KH 28 2KH C5 C5 C 0 1 N N N 67.605 22.493 92.807 -7.332 0.970 0.772 C5 2KH 29 2KH H1 H1 H 0 1 N N N 63.351 19.733 95.606 1.650 1.573 2.523 H1 2KH 30 2KH H2 H2 H 0 1 N N N 63.579 17.240 92.898 2.370 -0.979 -0.231 H2 2KH 31 2KH H3 H3 H 0 1 N N N 59.827 18.693 93.555 3.645 0.687 -2.104 H3 2KH 32 2KH H4 H4 H 0 1 N N N 59.843 16.784 97.208 8.297 -1.808 -0.916 H4 2KH 33 2KH H5 H5 H 0 1 N N N 63.207 16.703 97.582 7.426 -0.433 1.788 H5 2KH 34 2KH H6 H6 H 0 1 N N N 62.125 21.466 92.405 -1.007 -0.341 -0.957 H6 2KH 35 2KH H7 H7 H 0 1 N N N 62.402 20.068 91.313 -0.030 -1.679 -0.307 H7 2KH 36 2KH H8 H8 H 0 1 N N N 62.384 22.134 90.098 -1.709 -1.925 1.558 H8 2KH 37 2KH H9 H9 H 0 1 N N N 64.805 24.402 89.964 -4.535 -1.613 1.519 H9 2KH 38 2KH H10 H10 H 0 1 N N N 65.881 22.185 88.884 -4.097 -1.461 -1.518 H10 2KH 39 2KH H11 H11 H 0 1 N N N 64.437 23.639 87.806 -4.832 -3.750 -1.229 H11 2KH 40 2KH H12 H12 H 0 1 N N N 65.017 20.750 90.508 -2.049 -2.583 -1.267 H12 2KH 41 2KH H13 H13 H 0 1 N N N 63.337 19.605 89.424 -3.072 -4.491 -0.205 H13 2KH 42 2KH H14 H14 H 0 1 N N N 65.519 22.045 92.584 -6.557 -0.647 1.885 H14 2KH 43 2KH H15 H15 H 0 1 N N N 69.269 24.420 90.701 -5.801 2.356 -1.762 H15 2KH 44 2KH H16 H16 H 0 1 N N N 67.734 21.914 93.709 -8.237 1.041 1.357 H16 2KH 45 # 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 2KH "O2'" "C2'" SING N N 1 2KH "O3'" "C3'" SING N N 2 2KH "C2'" "C3'" SING N N 3 2KH "C2'" "C1'" SING N N 4 2KH O2 C2 DOUB N N 5 2KH "C3'" "C4'" SING N N 6 2KH "C1'" N1 SING N N 7 2KH "C1'" "O4'" SING N N 8 2KH C2 N1 SING N N 9 2KH C2 N3 SING N N 10 2KH "C4'" "O4'" SING N N 11 2KH "C4'" "C5'" SING N N 12 2KH N1 C6 SING N N 13 2KH N3 C4 SING N N 14 2KH "C5'" "O5'" SING N N 15 2KH C6 C5 DOUB N N 16 2KH C4 C5 SING N N 17 2KH C4 O4 DOUB N N 18 2KH O2B PB DOUB N N 19 2KH "O5'" PA SING N N 20 2KH N3A PB SING N N 21 2KH N3A PA SING N N 22 2KH PB O1B SING N N 23 2KH PB O3B SING N N 24 2KH PA O1A DOUB N N 25 2KH PA O2A SING N N 26 2KH O3B PG SING N N 27 2KH PG O2G DOUB N N 28 2KH PG O1G SING N N 29 2KH PG O3G SING N N 30 2KH O2A H1 SING N N 31 2KH N3A H2 SING N N 32 2KH O1B H3 SING N N 33 2KH O1G H4 SING N N 34 2KH O3G H5 SING N N 35 2KH "C5'" H6 SING N N 36 2KH "C5'" H7 SING N N 37 2KH "C4'" H8 SING N N 38 2KH "C1'" H9 SING N N 39 2KH "C2'" H10 SING N N 40 2KH "O2'" H11 SING N N 41 2KH "C3'" H12 SING N N 42 2KH "O3'" H13 SING N N 43 2KH C6 H14 SING N N 44 2KH N3 H15 SING N N 45 2KH C5 H16 SING N N 46 # 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 2KH SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O" 2KH InChI InChI 1.03 "InChI=1S/C9H16N3O14P3/c13-5-1-2-12(9(16)10-5)8-7(15)6(14)4(25-8)3-24-27(17,18)11-28(19,20)26-29(21,22)23/h1-2,4,6-8,14-15H,3H2,(H,10,13,16)(H2,21,22,23)(H3,11,17,18,19,20)/t4-,6-,7-,8-/m1/s1" 2KH InChIKey InChI 1.03 OZIBFYOFLVBDIY-XVFCMESISA-N 2KH SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O" 2KH SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O" 2KH SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)O" 2KH SMILES "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)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 2KH "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine" 2KH "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-N-[oxidanyl(phosphonooxy)phosphoryl]phosphonamidic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 2KH "Create component" 2013-11-19 RCSB 2KH "Initial release" 2013-12-18 RCSB #