data_8LK # _chem_comp.id 8LK _chem_comp.name Pyrrolo-dC _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H15 N3 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;3-[(2R,4S,5R)-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-6-methyl-7H-pyrrolo[2,3-d]pyrimidin-2-one; 6-Methyl-3-(beta-D-2-deoxyribofuranosyl)pyrrolo[2,3-d]pyrimidin-2-one; N-Pyrrolo-2'-deoxycytidine ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-10-28 _chem_comp.pdbx_modified_date 2022-08-22 _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 265.265 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 8LK _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 6YBH _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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 8LK "O5'" O1 O 0 1 N N N 52.659 -50.210 -18.964 4.400 2.224 0.864 "O5'" 8LK 1 8LK "C5'" C1 C 0 1 N N N 52.404 -49.434 -17.843 4.146 1.230 -0.131 "C5'" 8LK 2 8LK "C4'" C2 C 0 1 N N R 51.675 -48.148 -18.304 3.314 0.099 0.479 "C4'" 8LK 3 8LK "O4'" O2 O 0 1 N N N 52.627 -47.215 -18.735 1.980 0.558 0.786 "O4'" 8LK 4 8LK "C3'" C3 C 0 1 N N S 50.688 -48.400 -19.524 3.082 -1.029 -0.559 "C3'" 8LK 5 8LK "O3'" O3 O 0 1 N N N 49.464 -47.719 -19.315 4.168 -1.958 -0.553 "O3'" 8LK 6 8LK "C2'" C4 C 0 1 N N N 51.386 -47.709 -20.703 1.785 -1.691 -0.033 "C2'" 8LK 7 8LK "C1'" C5 C 0 1 N N R 52.285 -46.696 -20.012 1.141 -0.607 0.858 "C1'" 8LK 8 8LK N1 N1 N 0 1 N N N 53.534 -46.491 -20.822 -0.200 -0.287 0.363 N1 8LK 9 8LK C2 C6 C 0 1 N N N 53.627 -45.310 -21.774 -0.347 0.277 -0.848 C2 8LK 10 8LK O2 O4 O 0 1 N N N 52.664 -44.498 -21.881 0.648 0.518 -1.513 O2 8LK 11 8LK N3 N2 N 0 1 N N N 54.814 -45.124 -22.516 -1.543 0.581 -1.343 N3 8LK 12 8LK C4 C7 C 0 1 N N N 55.777 -46.114 -22.293 -2.646 0.333 -0.648 C4 8LK 13 8LK C5 C8 C 0 1 N N N 55.672 -47.246 -21.411 -2.532 -0.262 0.637 C5 8LK 14 8LK C6 C9 C 0 1 N N N 54.544 -47.412 -20.668 -1.281 -0.567 1.127 C6 8LK 15 8LK C14 C10 C 0 1 N N N 56.873 -47.987 -21.466 -3.903 -0.404 1.139 C14 8LK 16 8LK C15 C11 C 0 1 N N N 57.680 -47.367 -22.353 -4.715 0.082 0.191 C15 8LK 17 8LK C16 C12 C 0 1 N N N 59.006 -47.757 -22.772 -6.218 0.136 0.285 C16 8LK 18 8LK N17 N3 N 0 1 N N N 57.047 -46.214 -22.885 -3.976 0.525 -0.881 N17 8LK 19 8LK H1 H1 H 0 1 N N N 53.107 -51.006 -18.703 4.924 2.972 0.547 H1 8LK 20 8LK H2 H2 H 0 1 N N N 51.768 -49.992 -17.140 3.598 1.677 -0.960 H2 8LK 21 8LK H3 H3 H 0 1 N N N 53.351 -49.169 -17.349 5.092 0.829 -0.494 H3 8LK 22 8LK H4 H4 H 0 1 N N N 51.089 -47.751 -17.462 3.799 -0.294 1.372 H4 8LK 23 8LK H5 H5 H 0 1 N N N 50.562 -49.478 -19.706 2.932 -0.615 -1.556 H5 8LK 24 8LK H6 H6 H 0 1 N N N 48.999 -48.118 -18.589 4.069 -2.682 -1.185 H6 8LK 25 8LK H7 H7 H 0 1 N N N 50.657 -47.210 -21.359 1.124 -1.946 -0.862 H7 8LK 26 8LK H8 H8 H 0 1 N N N 51.976 -48.427 -21.291 2.021 -2.578 0.555 H8 8LK 27 8LK H9 H9 H 0 1 N N N 51.749 -45.741 -19.914 1.084 -0.959 1.888 H9 8LK 28 8LK H13 H13 H 0 1 N N N 57.102 -48.881 -20.905 -4.201 -0.820 2.091 H13 8LK 29 8LK H14 H14 H 0 1 N N N 59.305 -48.672 -22.240 -6.520 1.082 0.734 H14 8LK 30 8LK H15 H15 H 0 1 N N N 59.007 -47.946 -23.856 -6.648 0.054 -0.713 H15 8LK 31 8LK H16 H16 H 0 1 N N N 59.716 -46.950 -22.540 -6.573 -0.689 0.902 H16 8LK 32 8LK H17 H17 H 0 1 N N N 57.435 -45.586 -23.560 -4.347 0.918 -1.686 H17 8LK 33 8LK H10 H10 H 0 1 N N N 54.445 -48.239 -19.981 -1.166 -1.025 2.099 H10 8LK 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 8LK N17 C15 SING N N 1 8LK N17 C4 SING N N 2 8LK C16 C15 SING N N 3 8LK N3 C4 DOUB N N 4 8LK N3 C2 SING N N 5 8LK C15 C14 DOUB N N 6 8LK C4 C5 SING N N 7 8LK O2 C2 DOUB N N 8 8LK C2 N1 SING N N 9 8LK C14 C5 SING N N 10 8LK C5 C6 DOUB N N 11 8LK N1 C6 SING N N 12 8LK N1 "C1'" SING N N 13 8LK "C2'" "C1'" SING N N 14 8LK "C2'" "C3'" SING N N 15 8LK "C1'" "O4'" SING N N 16 8LK "C3'" "O3'" SING N N 17 8LK "C3'" "C4'" SING N N 18 8LK "O5'" "C5'" SING N N 19 8LK "O4'" "C4'" SING N N 20 8LK "C4'" "C5'" SING N N 21 8LK "O5'" H1 SING N N 22 8LK "C5'" H2 SING N N 23 8LK "C5'" H3 SING N N 24 8LK "C4'" H4 SING N N 25 8LK "C3'" H5 SING N N 26 8LK "O3'" H6 SING N N 27 8LK "C2'" H7 SING N N 28 8LK "C2'" H8 SING N N 29 8LK "C1'" H9 SING N N 30 8LK C14 H13 SING N N 31 8LK C16 H14 SING N N 32 8LK C16 H15 SING N N 33 8LK C16 H16 SING N N 34 8LK N17 H17 SING N N 35 8LK C6 H10 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 8LK InChI InChI 1.06 "InChI=1S/C12H15N3O4/c1-6-2-7-4-15(12(18)14-11(7)13-6)10-3-8(17)9(5-16)19-10/h2,4,8-10,16-17H,3,5H2,1H3,(H,13,14,18)/t8-,9+,10+/m0/s1" 8LK InChIKey InChI 1.06 NMRPZKUERWKZCL-IVZWLZJFSA-N 8LK SMILES_CANONICAL CACTVS 3.385 "CC1=CC2=CN([C@H]3C[C@H](O)[C@@H](CO)O3)C(=O)N=C2N1" 8LK SMILES CACTVS 3.385 "CC1=CC2=CN([CH]3C[CH](O)[CH](CO)O3)C(=O)N=C2N1" 8LK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CC2=CN(C(=O)N=C2N1)[C@H]3C[C@@H]([C@H](O3)CO)O" 8LK SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CC2=CN(C(=O)N=C2N1)C3CC(C(O3)CO)O" # _pdbx_chem_comp_identifier.comp_id 8LK _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "3-[(2~{R},4~{S},5~{R})-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-6-methyl-7~{H}-pyrrolo[2,3-d]pyrimidin-2-one" # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 8LK "3-[(2R,4S,5R)-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-6-methyl-7H-pyrrolo[2,3-d]pyrimidin-2-one" PDB ? 2 8LK "6-Methyl-3-(beta-D-2-deoxyribofuranosyl)pyrrolo[2,3-d]pyrimidin-2-one" AUTHOR ? 3 8LK "N-Pyrrolo-2'-deoxycytidine" PUBCHEM ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 8LK "Create component" 2021-10-28 PDBE 8LK "Modify charge" 2021-11-03 PDBE 8LK "Initial release" 2021-11-17 RCSB 8LK "Modify descriptor" 2022-08-22 RCSB #