data_LKC
# 
_chem_comp.id                                    LKC 
_chem_comp.name                                  "4-AMINO-1-[(1S,3R,4R,7S)-7-HYDROXY-1-(HYDROXYMETHYL)-2,5-DIOXABICYCLO[2.2.1]HEPT-3-YL]-5-METHYLPYRIMIDIN-2(1H)-ONE" 
_chem_comp.type                                  "RNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C11 H15 N3 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2002-06-27 
_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                        269.254 
_chem_comp.one_letter_code                       N 
_chem_comp.three_letter_code                     LKC 
_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        1H0Q 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
# 
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 
LKC N1     N1   N 0 1 N N N -7.188  -9.451  1.189  -0.418 -0.393 0.957  N1     LKC 1  
LKC C2     C2   C 0 1 N N N -5.874  -9.822  1.509  -1.336 -0.443 1.940  C2     LKC 2  
LKC N3     N3   N 0 1 N N N -4.915  -9.757  0.542  -1.000 -0.210 3.207  N3     LKC 3  
LKC C4     C4   C 0 1 N N N -5.203  -9.332  -0.696 0.253  0.073  3.534  C4     LKC 4  
LKC C5     C5   C 0 1 N N N -6.543  -8.915  -1.044 1.238  0.139  2.528  C5     LKC 5  
LKC C6     C6   C 0 1 N N N -7.492  -8.991  -0.075 0.881  -0.100 1.244  C6     LKC 6  
LKC O2     O2   O 0 1 N N N -5.576  -10.206 2.640  -2.495 -0.707 1.665  O2     LKC 7  
LKC N4     N4   N 0 1 N N N -4.207  -9.303  -1.587 0.588  0.313  4.847  N4     LKC 8  
LKC "C1'"  C1*  C 0 1 N N R -8.237  -9.624  2.236  -0.817 -0.655 -0.427 "C1'"  LKC 9  
LKC "C2'"  C2*  C 0 1 N N R -8.223  -8.502  3.283  -1.350 0.651  -1.093 "C2'"  LKC 10 
LKC "C3'"  C3*  C 0 1 N N S -9.157  -7.474  2.661  0.017  1.240  -1.604 "C3'"  LKC 11 
LKC "C4'"  C4*  C 0 1 N N S -10.221 -8.558  2.553  0.429  -0.100 -2.314 "C4'"  LKC 12 
LKC "O4'"  O4*  O 0 1 N N N -9.576  -9.546  1.751  0.326  -1.046 -1.212 "O4'"  LKC 13 
LKC "O3'"  O3*  O 0 1 N N N -9.495  -6.396  3.522  -0.160 2.305  -2.540 "O3'"  LKC 14 
LKC "C5'"  C5*  C 0 1 N N N -11.549 -8.078  1.953  1.753  -0.093 -3.081 "C5'"  LKC 15 
LKC "O5'"  O5*  O 0 1 N N N -12.524 -9.100  1.995  1.969  -1.378 -3.668 "O5'"  LKC 16 
LKC C5A    C5A  C 0 1 N N N -6.890  -8.410  -2.435 2.667  0.465  2.876  C5A    LKC 17 
LKC "O2'"  O2*  O 0 1 N N N -8.929  -8.988  4.419  -1.944 0.162  -2.365 "O2'"  LKC 18 
LKC "C6'"  C6*  C 0 1 N N N -10.288 -9.062  4.005  -0.859 -0.366 -3.154 "C6'"  LKC 19 
LKC H6     H6   H 0 1 N N N -8.504  -8.690  -0.303 1.618  -0.060 0.456  H6     LKC 20 
LKC H41    1H4  H 0 1 N N N -3.280  -9.600  -1.308 -0.093 0.274  5.536  H41    LKC 21 
LKC H42    2H4  H 0 1 N N N -4.374  -8.976  -2.526 1.505  0.520  5.083  H42    LKC 22 
LKC "H1'"  H1*  H 0 1 N N N -8.087  -10.580 2.739  -1.580 -1.433 -0.458 "H1'"  LKC 23 
LKC "H2'1" 1H2* H 0 0 N N N -7.226  -8.129  3.507  -1.978 1.302  -0.485 "H2'1" LKC 24 
LKC "H3'"  H3*  H 0 1 N N N -8.824  -7.132  1.679  0.684  1.518  -0.788 "H3'"  LKC 25 
LKC H3T    H3T  H 0 1 N Y N -10.078 -5.754  3.134  -0.636 3.007  -2.077 H3T    LKC 26 
LKC "H5'1" 1H5* H 0 0 N N N -11.911 -7.221  2.522  1.715  0.662  -3.864 "H5'1" LKC 27 
LKC "H5'2" 2H5* H 0 0 N N N -11.386 -7.771  0.918  2.568  0.134  -2.395 "H5'2" LKC 28 
LKC H5T    H5T  H 0 1 N N N -13.337 -8.766  1.609  2.812  -1.330 -4.141 H5T    LKC 29 
LKC H5M1   1H5M H 0 0 N N N -6.726  -9.205  -3.163 2.752  0.624  3.951  H5M1   LKC 30 
LKC H5M2   2H5M H 0 0 N N N -7.934  -8.100  -2.479 3.311  -0.362 2.580  H5M2   LKC 31 
LKC H5M3   3H5M H 0 0 N N N -6.260  -7.556  -2.682 2.972  1.369  2.350  H5M3   LKC 32 
LKC "H6'1" 1H6* H 0 0 N N N -10.662 -10.085 4.047  -0.800 0.152  -4.111 "H6'1" LKC 33 
LKC "H6'2" 2H6* H 0 0 N N N -10.902 -8.398  4.617  -0.993 -1.436 -3.311 "H6'2" LKC 34 
# 
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 
LKC N1    C2     SING N N 1  
LKC N1    C6     SING N N 2  
LKC N1    "C1'"  SING N N 3  
LKC C2    N3     SING N N 4  
LKC C2    O2     DOUB N N 5  
LKC N3    C4     DOUB N N 6  
LKC C4    C5     SING N N 7  
LKC C4    N4     SING N N 8  
LKC C5    C6     DOUB N N 9  
LKC C5    C5A    SING N N 10 
LKC C6    H6     SING N N 11 
LKC N4    H41    SING N N 12 
LKC N4    H42    SING N N 13 
LKC "C1'" "C2'"  SING N N 14 
LKC "C1'" "O4'"  SING N N 15 
LKC "C1'" "H1'"  SING N N 16 
LKC "C2'" "C3'"  SING N N 17 
LKC "C2'" "O2'"  SING N N 18 
LKC "C2'" "H2'1" SING N N 19 
LKC "C3'" "C4'"  SING N N 20 
LKC "C3'" "O3'"  SING N N 21 
LKC "C3'" "H3'"  SING N N 22 
LKC "C4'" "O4'"  SING N N 23 
LKC "C4'" "C5'"  SING N N 24 
LKC "C4'" "C6'"  SING N N 25 
LKC "O3'" H3T    SING N N 26 
LKC "C5'" "O5'"  SING N N 27 
LKC "C5'" "H5'1" SING N N 28 
LKC "C5'" "H5'2" SING N N 29 
LKC "O5'" H5T    SING N N 30 
LKC C5A   H5M1   SING N N 31 
LKC C5A   H5M2   SING N N 32 
LKC C5A   H5M3   SING N N 33 
LKC "O2'" "C6'"  SING N N 34 
LKC "C6'" "H6'1" SING N N 35 
LKC "C6'" "H6'2" SING N N 36 
# 
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 
LKC SMILES           ACDLabs              10.04 "O=C1N=C(N)C(=CN1C3OC2(C(O)C3OC2)CO)C"                                                                                                   
LKC SMILES_CANONICAL CACTVS               3.341 "CC1=CN([C@@H]2O[C@@]3(CO)CO[C@@H]2[C@@H]3O)C(=O)N=C1N"                                                                                  
LKC SMILES           CACTVS               3.341 "CC1=CN([CH]2O[C]3(CO)CO[CH]2[CH]3O)C(=O)N=C1N"                                                                                          
LKC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1N)[C@H]2[C@H]3[C@@H]([C@@](O2)(CO3)CO)O"                                                                                
LKC SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1N)C2C3C(C(O2)(CO3)CO)O"                                                                                                 
LKC InChI            InChI                1.03  "InChI=1S/C11H15N3O5/c1-5-2-14(10(17)13-8(5)12)9-6-7(16)11(3-15,19-9)4-18-6/h2,6-7,9,15-16H,3-4H2,1H3,(H2,12,13,17)/t6-,7+,9-,11+/m1/s1" 
LKC InChIKey         InChI                1.03  NELYIRACPIJATH-SZVQBCOZSA-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 
LKC "SYSTEMATIC NAME" ACDLabs              10.04 "4-amino-1-[2,5-anhydro-4-(hydroxymethyl)-alpha-L-lyxofuranosyl]-5-methylpyrimidin-2(1H)-one"                       
LKC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "4-amino-1-[(1R,4S,6R,7S)-7-hydroxy-4-(hydroxymethyl)-2,5-dioxabicyclo[2.2.1]heptan-6-yl]-5-methyl-pyrimidin-2-one" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
LKC "Create component"    2002-06-27 EBI  
LKC "Modify linking type" 2011-06-04 RCSB 
LKC "Modify descriptor"   2011-06-04 RCSB 
# 
