data_GKS
# 
_chem_comp.id                                    GKS 
_chem_comp.name                                  "1-[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]-2,5-anhydro-1,3-dideoxy-6-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-ribo-hexitol" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H19 N4 O14 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2018-05-25 
_chem_comp.pdbx_modified_date                    2019-01-25 
_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                        524.208 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     GKS 
_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        6DIC 
_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 
GKS PG    P1  P 0 1 N N N -13.075 0.630  69.374 -5.601 1.955  -0.518 PG    GKS 1  
GKS O1G   O1  O 0 1 N N N -13.996 -0.568 69.422 -6.880 1.229  -0.686 O1G   GKS 2  
GKS O2G   O2  O 0 1 N N N -13.707 1.822  70.068 -5.472 3.087  -1.656 O2G   GKS 3  
GKS O3G   O3  O 0 1 N N N -11.731 0.392  70.026 -5.564 2.648  0.935  O3G   GKS 4  
GKS O3B   O4  O 0 1 N N N -12.794 0.945  67.866 -4.375 0.919  -0.650 O3B   GKS 5  
GKS PB    P2  P 0 1 N N N -13.319 2.228  66.974 -4.124 -0.587 -0.141 PB    GKS 6  
GKS O1B   O5  O 0 1 N N N -13.185 1.814  65.505 -4.668 -0.743 1.226  O1B   GKS 7  
GKS O2B   O6  O 0 1 N N N -14.746 2.609  67.312 -4.862 -1.619 -1.133 O2B   GKS 8  
GKS O3A   O7  O 0 1 N N N -12.184 3.370  67.199 -2.543 -0.893 -0.128 O3A   GKS 9  
GKS PA    P3  P 0 1 N N N -12.179 4.843  67.916 -1.632 -2.042 0.535  PA    GKS 10 
GKS O1A   O8  O 0 1 N N N -13.332 4.943  68.895 -1.502 -1.777 2.118  O1A   GKS 11 
GKS O2A   O9  O 0 1 N N N -10.807 5.033  68.558 -2.259 -3.363 0.306  O2A   GKS 12 
GKS "O5'" O10 O 0 1 N N N -12.308 5.942  66.774 -0.168 -2.020 -0.134 "O5'" GKS 13 
GKS "C5'" C1  C 0 1 N N N -13.589 6.232  66.258 0.841  -2.986 0.167  "C5'" GKS 14 
GKS "C4'" C2  C 0 1 N N R -13.477 6.316  64.712 2.103  -2.674 -0.639 "C4'" GKS 15 
GKS "O4'" O11 O 0 1 N N N -12.775 7.542  64.362 2.675  -1.433 -0.190 "O4'" GKS 16 
GKS "C3'" C3  C 0 1 N N S -12.635 5.198  64.077 3.156  -3.776 -0.412 "C3'" GKS 17 
GKS "O3'" O12 O 0 1 N N N -13.466 4.085  63.665 3.488  -4.412 -1.647 "O3'" GKS 18 
GKS "C2'" C4  C 0 1 N N N -12.070 5.887  62.816 4.381  -3.019 0.158  "C2'" GKS 19 
GKS "C1'" C5  C 0 1 N N S -11.814 7.278  63.335 4.108  -1.562 -0.309 "C1'" GKS 20 
GKS C9    C6  C 0 1 N N N -10.415 7.422  63.972 4.818  -0.562 0.605  C9    GKS 21 
GKS C4    C7  C 0 1 N N N -9.258  7.615  63.021 4.639  0.832  0.060  C4    GKS 22 
GKS N3    N1  N 0 1 N N N -9.435  8.212  61.733 5.464  1.291  -0.880 N3    GKS 23 
GKS C2    C8  C 0 1 N N N -8.353  8.367  60.908 5.331  2.501  -1.380 C2    GKS 24 
GKS N2    N2  N 0 1 N N N -8.576  8.949  59.729 6.204  2.930  -2.347 N2    GKS 25 
GKS N1    N3  N 0 1 N N N -7.068  8.016  61.187 4.342  3.335  -0.957 N1    GKS 26 
GKS C6    C9  C 0 1 N N N -6.774  7.391  62.478 3.476  2.922  -0.007 C6    GKS 27 
GKS O6    O13 O 0 1 N N N -5.624  7.045  62.754 2.584  3.657  0.384  O6    GKS 28 
GKS C5    C10 C 0 1 N N N -7.894  7.183  63.409 3.625  1.623  0.526  C5    GKS 29 
GKS N7    N4  N 0 1 N N N -7.611  6.545  64.679 2.744  1.150  1.513  N7    GKS 30 
GKS C8    C11 C 0 1 N N N -6.989  5.371  64.740 2.640  1.797  2.691  C8    GKS 31 
GKS O8    O14 O 0 1 N N N -6.637  4.795  63.779 3.242  2.835  2.867  O8    GKS 32 
GKS H1    H1  H 0 1 N N N -14.564 1.579  70.399 -6.179 3.747  -1.636 H1    GKS 33 
GKS H2    H2  H 0 1 N N N -11.695 -0.495 70.364 -4.752 3.142  1.115  H2    GKS 34 
GKS H3    H3  H 0 1 N N N -15.290 2.517  66.539 -4.554 -1.572 -2.049 H3    GKS 35 
GKS H4    H4  H 0 1 N N N -12.994 5.112  69.767 -1.098 -0.927 2.343  H4    GKS 36 
GKS H5    H5  H 0 1 N N N -13.944 7.193  66.659 1.071  -2.951 1.232  H5    GKS 37 
GKS H6    H6  H 0 1 N N N -14.293 5.435  66.538 0.480  -3.981 -0.095 H6    GKS 38 
GKS H7    H7  H 0 1 N N N -14.486 6.309  64.274 1.859  -2.607 -1.699 H7    GKS 39 
GKS H8    H8  H 0 1 N N N -11.823 4.886  64.750 2.792  -4.509 0.308  H8    GKS 40 
GKS H9    H9  H 0 1 N N N -13.357 3.365  64.275 4.147  -5.115 -1.562 H9    GKS 41 
GKS H10   H10 H 0 1 N N N -12.803 5.891  61.996 4.404  -3.081 1.246  H10   GKS 42 
GKS H11   H11 H 0 1 N N N -11.141 5.406  62.475 5.308  -3.398 -0.272 H11   GKS 43 
GKS H12   H12 H 0 1 N N N -11.913 8.003  62.514 4.423  -1.425 -1.344 H12   GKS 44 
GKS H13   H13 H 0 1 N N N -10.219 6.511  64.557 4.391  -0.618 1.606  H13   GKS 45 
GKS H14   H14 H 0 1 N N N -10.442 8.291  64.646 5.881  -0.800 0.649  H14   GKS 46 
GKS H15   H15 H 0 1 N N N -9.499  9.248  59.485 6.114  3.820  -2.722 H15   GKS 47 
GKS H16   H16 H 0 1 N N N -7.821  9.087  59.088 6.912  2.343  -2.655 H16   GKS 48 
GKS H18   H18 H 0 1 N N N -7.889  6.997  65.527 2.210  0.357  1.347  H18   GKS 49 
GKS H19   H19 H 0 1 N N N -6.801  4.931  65.708 2.021  1.391  3.477  H19   GKS 50 
GKS H20   H20 H 0 1 N N N -6.339  8.182  60.523 4.259  4.224  -1.337 H20   GKS 51 
# 
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 
GKS N2    C2    SING N N 1  
GKS C2    N1    SING N N 2  
GKS C2    N3    DOUB N N 3  
GKS N1    C6    SING N N 4  
GKS N3    C4    SING N N 5  
GKS C6    O6    DOUB N N 6  
GKS C6    C5    SING N N 7  
GKS "C2'" "C1'" SING N N 8  
GKS "C2'" "C3'" SING N N 9  
GKS C4    C5    DOUB N N 10 
GKS C4    C9    SING N N 11 
GKS "C1'" C9    SING N N 12 
GKS "C1'" "O4'" SING N N 13 
GKS C5    N7    SING N N 14 
GKS "O3'" "C3'" SING N N 15 
GKS O8    C8    DOUB N N 16 
GKS "C3'" "C4'" SING N N 17 
GKS "O4'" "C4'" SING N N 18 
GKS N7    C8    SING N N 19 
GKS "C4'" "C5'" SING N N 20 
GKS O1B   PB    DOUB N N 21 
GKS "C5'" "O5'" SING N N 22 
GKS "O5'" PA    SING N N 23 
GKS PB    O3A   SING N N 24 
GKS PB    O2B   SING N N 25 
GKS PB    O3B   SING N N 26 
GKS O3A   PA    SING N N 27 
GKS O3B   PG    SING N N 28 
GKS PA    O2A   DOUB N N 29 
GKS PA    O1A   SING N N 30 
GKS PG    O1G   DOUB N N 31 
GKS PG    O3G   SING N N 32 
GKS PG    O2G   SING N N 33 
GKS O2G   H1    SING N N 34 
GKS O3G   H2    SING N N 35 
GKS O2B   H3    SING N N 36 
GKS O1A   H4    SING N N 37 
GKS "C5'" H5    SING N N 38 
GKS "C5'" H6    SING N N 39 
GKS "C4'" H7    SING N N 40 
GKS "C3'" H8    SING N N 41 
GKS "O3'" H9    SING N N 42 
GKS "C2'" H10   SING N N 43 
GKS "C2'" H11   SING N N 44 
GKS "C1'" H12   SING N N 45 
GKS C9    H13   SING N N 46 
GKS C9    H14   SING N N 47 
GKS N2    H15   SING N N 48 
GKS N2    H16   SING N N 49 
GKS N7    H18   SING N N 50 
GKS C8    H19   SING N N 51 
GKS N1    H20   SING N N 52 
# 
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 
GKS SMILES           ACDLabs              12.01 "P(=O)(O)(O)OP(OP(=O)(O)OCC1OC(CC1O)CC2=C(C(NC(=N2)N)=O)NC=O)(O)=O" 
GKS InChI            InChI                1.03  
"InChI=1S/C11H19N4O14P3/c12-11-14-6(9(13-4-16)10(18)15-11)1-5-2-7(17)8(27-5)3-26-31(22,23)29-32(24,25)28-30(19,20)21/h4-5,7-8,17H,1-3H2,(H,13,16)(H,22,23)(H,24,25)(H2,19,20,21)(H3,12,14,15,18)/t5-,7-,8+/m0/s1" 
GKS InChIKey         InChI                1.03  SEYTZONDTLWHRH-APQOSEDMSA-N 
GKS SMILES_CANONICAL CACTVS               3.385 "NC1=NC(=C(NC=O)C(=O)N1)C[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2" 
GKS SMILES           CACTVS               3.385 "NC1=NC(=C(NC=O)C(=O)N1)C[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2" 
GKS SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1[C@@H](O[C@@H]([C@H]1O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)CC2=C(C(=O)NC(=N2)N)NC=O" 
GKS SMILES           "OpenEye OEToolkits" 2.0.6 "C1C(OC(C1O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)CC2=C(C(=O)NC(=N2)N)NC=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 
GKS "SYSTEMATIC NAME" ACDLabs              12.01 "1-[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]-2,5-anhydro-1,3-dideoxy-6-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-ribo-hexitol"     
GKS "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[(2~{R},3~{S},5~{S})-5-[(2-azanyl-5-formamido-6-oxidanylidene-1~{H}-pyrimidin-4-yl)methyl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono 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 
GKS "Create component"   2018-05-25 RCSB 
GKS "Other modification" 2018-10-12 RCSB 
GKS "Initial release"    2019-01-30 RCSB 
# 
