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 #