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 
# 
