data_YQP # _chem_comp.id YQP _chem_comp.name "(2~{S})-2-azanyl-4-[[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl-methyl-$l^{3}-sulfanyl]butanoic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H21 N3 O7 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-03-23 _chem_comp.pdbx_modified_date 2022-02-25 _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 375.397 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YQP _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 7LNH _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 YQP N N1 N 0 1 N N N 8.133 -58.580 29.945 6.213 0.667 0.997 N YQP 1 YQP CA C1 C 0 1 N N S 6.709 -58.335 30.082 5.650 -0.647 0.658 CA YQP 2 YQP C C2 C 0 1 N N N 5.953 -59.652 30.171 6.685 -1.462 -0.075 C YQP 3 YQP O O1 O 0 1 N N N 4.882 -59.720 30.825 6.568 -2.798 -0.135 O YQP 4 YQP CB C3 C 0 1 N N N 6.183 -57.501 28.884 4.421 -0.461 -0.233 CB YQP 5 YQP CG C4 C 0 1 N N N 7.389 -56.846 28.109 3.324 0.257 0.554 CG YQP 6 YQP SD S1 S 0 1 N N N 6.878 -56.558 26.389 1.866 0.477 -0.502 SD YQP 7 YQP CE C5 C 0 1 N N N 8.285 -56.799 25.312 2.311 1.598 -1.482 CE YQP 8 YQP OXT O2 O 0 1 N N N 6.395 -60.667 29.586 7.619 -0.912 -0.610 OXT YQP 9 YQP CAH C6 C 0 1 N N N 6.257 -54.833 26.210 0.696 1.332 0.589 CAH YQP 10 YQP CAK C7 C 0 1 N N S 5.711 -54.648 24.842 -0.608 1.595 -0.167 CAK YQP 11 YQP CAM C8 C 0 1 N N R 4.410 -55.666 23.155 -2.681 0.734 -0.651 CAM YQP 12 YQP CAN C9 C 0 1 N N R 3.753 -54.455 23.659 -2.969 1.852 0.376 CAN YQP 13 YQP CAO C10 C 0 1 N N S 4.343 -54.127 24.911 -1.574 2.431 0.701 CAO YQP 14 YQP CAS C11 C 0 1 N N N 3.449 -57.425 21.801 -4.493 -0.745 -1.380 CAS YQP 15 YQP CAT C12 C 0 1 N N N 2.732 -57.216 24.117 -3.478 -1.112 0.716 CAT YQP 16 YQP CAV C13 C 0 1 N N N 2.589 -58.523 21.629 -5.311 -1.800 -1.175 CAV YQP 17 YQP CAW C14 C 0 1 N N N 1.778 -58.983 22.720 -5.197 -2.537 0.028 CAW YQP 18 YQP NAR N2 N 0 1 N N N 3.526 -56.762 23.046 -3.572 -0.407 -0.426 NAR YQP 19 YQP NAU N3 N 0 1 N N N 1.844 -58.352 23.928 -4.276 -2.171 0.943 NAU YQP 20 YQP OAL O3 O 0 1 N N N 5.620 -56.005 24.093 -1.308 0.355 -0.408 OAL YQP 21 YQP OAP O4 O 0 1 N N N 4.360 -52.666 25.095 -1.507 3.811 0.337 OAP YQP 22 YQP OAQ O5 O 0 1 N N N 3.991 -53.340 22.699 -3.806 2.857 -0.200 OAQ YQP 23 YQP OAX O6 O 0 1 N N N 0.922 -60.083 22.532 -5.923 -3.492 0.235 OAX YQP 24 YQP OAY O7 O 0 1 N N N 2.771 -56.596 25.373 -2.652 -0.794 1.550 OAY YQP 25 YQP H1 H1 H 0 1 N N N 8.456 -59.118 30.724 6.489 1.168 0.166 H1 YQP 26 YQP H2 H2 H 0 1 N N N 8.305 -59.084 29.098 5.561 1.208 1.546 H2 YQP 27 YQP H4 H4 H 0 1 N N N 6.524 -57.764 31.004 5.361 -1.166 1.572 H4 YQP 28 YQP H5 H5 H 0 1 N N N 4.536 -60.603 30.776 7.256 -3.277 -0.617 H5 YQP 29 YQP H6 H6 H 0 1 N N N 5.517 -56.709 29.257 4.691 0.134 -1.105 H6 YQP 30 YQP H7 H7 H 0 1 N N N 5.625 -58.158 28.200 4.057 -1.436 -0.557 H7 YQP 31 YQP H8 H8 H 0 1 N N N 8.256 -57.523 28.131 3.053 -0.338 1.427 H8 YQP 32 YQP H9 H9 H 0 1 N N N 7.659 -55.890 28.581 3.688 1.232 0.879 H9 YQP 33 YQP H10 H10 H 0 1 N N N 9.243 -57.072 25.728 1.633 1.948 -2.246 H10 YQP 34 YQP H11 H11 H 0 1 N N N 8.177 -56.671 24.245 3.299 2.026 -1.400 H11 YQP 35 YQP H13 H13 H 0 1 N N N 7.083 -54.126 26.375 0.491 0.709 1.461 H13 YQP 36 YQP H14 H14 H 0 1 N N N 5.464 -54.649 26.950 1.126 2.279 0.912 H14 YQP 37 YQP H15 H15 H 0 1 N N N 6.353 -53.962 24.269 -0.404 2.106 -1.108 H15 YQP 38 YQP H16 H16 H 0 1 N N N 4.826 -55.443 22.161 -2.796 1.112 -1.666 H16 YQP 39 YQP H17 H17 H 0 1 N N N 2.672 -54.628 23.769 -3.429 1.438 1.273 H17 YQP 40 YQP H18 H18 H 0 1 N N N 3.797 -54.605 25.737 -1.344 2.303 1.759 H18 YQP 41 YQP H19 H19 H 0 1 N N N 4.056 -57.085 20.975 -4.563 -0.174 -2.294 H19 YQP 42 YQP H20 H20 H 0 1 N N N 2.538 -59.022 20.673 -6.043 -2.078 -1.920 H20 YQP 43 YQP H21 H21 H 0 1 N N N 1.278 -58.673 24.688 -4.192 -2.671 1.770 H21 YQP 44 YQP H22 H22 H 0 1 N N N 4.755 -52.456 25.933 -2.094 4.383 0.851 H22 YQP 45 YQP H23 H23 H 0 1 N N N 3.569 -52.551 23.018 -4.019 3.583 0.401 H23 YQP 46 # # 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 YQP CAV CAS DOUB N N 1 YQP CAV CAW SING N N 2 YQP CAS NAR SING N N 3 YQP OAX CAW DOUB N N 4 YQP OAQ CAN SING N N 5 YQP CAW NAU SING N N 6 YQP NAR CAM SING N N 7 YQP NAR CAT SING N N 8 YQP CAM CAN SING N N 9 YQP CAM OAL SING N N 10 YQP CAN CAO SING N N 11 YQP NAU CAT SING N N 12 YQP OAL CAK SING N N 13 YQP CAT OAY DOUB N N 14 YQP CAK CAO SING N N 15 YQP CAK CAH SING N N 16 YQP CAO OAP SING N N 17 YQP CE SD DOUB N N 18 YQP CAH SD SING N N 19 YQP SD CG SING N N 20 YQP CG CB SING N N 21 YQP CB CA SING N N 22 YQP OXT C DOUB N N 23 YQP N CA SING N N 24 YQP CA C SING N N 25 YQP C O SING N N 26 YQP N H1 SING N N 27 YQP N H2 SING N N 28 YQP CA H4 SING N N 29 YQP O H5 SING N N 30 YQP CB H6 SING N N 31 YQP CB H7 SING N N 32 YQP CG H8 SING N N 33 YQP CG H9 SING N N 34 YQP CE H10 SING N N 35 YQP CE H11 SING N N 36 YQP CAH H13 SING N N 37 YQP CAH H14 SING N N 38 YQP CAK H15 SING N N 39 YQP CAM H16 SING N N 40 YQP CAN H17 SING N N 41 YQP CAO H18 SING N N 42 YQP CAS H19 SING N N 43 YQP CAV H20 SING N N 44 YQP NAU H21 SING N N 45 YQP OAP H22 SING N N 46 YQP OAQ H23 SING N N 47 # # 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 YQP SMILES ACDLabs 12.01 "O=C(O)C(N)CCS(=C)CC1OC(N2C=CC(=O)NC2=O)C(O)C1O" YQP InChI InChI 1.03 "InChI=1S/C14H21N3O7S/c1-25(5-3-7(15)13(21)22)6-8-10(19)11(20)12(24-8)17-4-2-9(18)16-14(17)23/h2,4,7-8,10-12,19-20H,1,3,5-6,15H2,(H,21,22)(H,16,18,23)/t7-,8+,10+,11+,12+,25-/m0/s1" YQP InChIKey InChI 1.03 HBPDMWXHIXRRKQ-GGUSWIIGSA-N YQP SMILES_CANONICAL CACTVS 3.385 "N[C@@H](CC[S](=C)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)NC2=O)C(O)=O" YQP SMILES CACTVS 3.385 "N[CH](CC[S](=C)C[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=O)NC2=O)C(O)=O" YQP SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C=S(CC[C@@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=O)NC2=O)O)O" YQP SMILES "OpenEye OEToolkits" 2.0.7 "C=S(CCC(C(=O)O)N)CC1C(C(C(O1)N2C=CC(=O)NC2=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 YQP "SYSTEMATIC NAME" ACDLabs 12.01 "5'-{[(3S)-3-amino-3-carboxypropyl](methylidene)-lambda~4~-sulfanyl}-5'-deoxyuridine" YQP "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-azanyl-4-[[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl-methylidene-$l^{4}-sulfanyl]butanoic 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 YQP "Create component" 2021-03-23 RCSB YQP "Initial release" 2022-03-02 RCSB ##