data_VVC
# 
_chem_comp.id                                    VVC 
_chem_comp.name                                  "4-azanyl-1-[(2~{R},4~{S},5~{R})-5-ethynyl-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]pyrimidin-2-one" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H13 N3 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-04-05 
_chem_comp.pdbx_modified_date                    2023-12-15 
_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                        251.239 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VVC 
_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        8OOJ 
_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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
VVC C4  C1  C 0 1 N N N N N N -25.456 -50.376 -8.102  -2.935 1.585  0.179  C4  VVC 1  
VVC C5  C2  C 0 1 N N R N N N -26.978 -47.461 -8.972  -0.134 -0.716 -0.215 C5  VVC 2  
VVC C6  C3  C 0 1 N N N N N N -24.706 -46.460 -8.930  2.135  -1.203 -0.990 C6  VVC 3  
VVC C11 C4  C 0 1 N N S N N N -27.449 -49.697 -9.576  -2.002 -0.460 1.328  C11 VVC 4  
VVC C7  C5  C 0 1 N N N N N N -23.859 -45.419 -8.892  3.463  -0.937 -0.992 C7  VVC 5  
VVC C8  C6  C 0 1 N N N N N N -24.424 -44.113 -8.949  3.951  0.113  -0.187 C8  VVC 6  
VVC C9  C7  C 0 1 N N N N N N -26.595 -45.000 -8.999  1.801  0.551  0.537  C9  VVC 7  
VVC C10 C8  C 0 1 N N N N N N -26.923 -48.396 -10.183 -0.608 -1.114 1.201  C10 VVC 8  
VVC N1  N1  N 0 1 N N N N N N -26.057 -46.290 -8.990  1.306  -0.447 -0.216 N1  VVC 9  
VVC N2  N2  N 0 1 N N N N N N -23.635 -43.037 -8.897  5.295  0.405  -0.171 N2  VVC 10 
VVC C3  C9  C 0 1 N N R N N N -26.802 -49.667 -8.178  -2.206 0.256  -0.026 C3  VVC 11 
VVC N3  N3  N 0 1 N N N N N N -25.758 -43.936 -8.976  3.106  0.817  0.554  N3  VVC 12 
VVC C1  C10 C 0 1 N N N N N N -28.321 -50.639 -6.242  -3.562 -1.290 -1.690 C1  VVC 13 
VVC C2  C11 C 0 1 N N N N N N -27.683 -50.230 -7.144  -2.960 -0.604 -0.952 C2  VVC 14 
VVC O1  O1  O 0 1 N N N N N N -24.460 -49.933 -9.050  -3.217 2.175  -1.092 O1  VVC 15 
VVC O2  O2  O 0 1 N N N N N N -26.618 -48.284 -7.873  -0.870 0.487  -0.525 O2  VVC 16 
VVC O3  O3  O 0 1 N N N N N N -27.823 -44.875 -9.051  1.043  1.224  1.216  O3  VVC 17 
VVC O4  O4  O 0 1 N N N N N N -28.866 -49.789 -9.497  -3.007 -1.457 1.524  O4  VVC 18 
VVC H1  H1  H 0 1 N N N N N N -25.629 -51.449 -8.271  -3.869 1.408  0.712  H1  VVC 19 
VVC H2  H2  H 0 1 N N N N N N -25.051 -50.224 -7.091  -2.306 2.259  0.761  H2  VVC 20 
VVC H3  H3  H 0 1 N N N N N N -28.011 -47.104 -8.853  -0.374 -1.503 -0.930 H3  VVC 21 
VVC H4  H4  H 0 1 N N N N N N -24.305 -47.463 -8.912  1.737  -2.001 -1.598 H4  VVC 22 
VVC H5  H5  H 0 1 N N N N N N -27.038 -50.548 -10.140 -2.015 0.260  2.147  H5  VVC 23 
VVC H6  H6  H 0 1 N N N N N N -22.791 -45.566 -8.821  4.138  -1.520 -1.601 H6  VVC 24 
VVC H7  H7  H 0 1 N N N N N N -25.895 -48.512 -10.557 -0.685 -2.198 1.287  H7  VVC 25 
VVC H8  H8  H 0 1 N N N N N N -27.571 -48.040 -10.997 0.071  -0.717 1.956  H8  VVC 26 
VVC H9  H9  H 0 1 N N N N N N -24.038 -42.122 -8.879  5.910  -0.112 -0.714 H9  VVC 27 
VVC H10 H10 H 0 1 N N N N N N -22.641 -43.146 -8.876  5.628  1.127  0.384  H10 VVC 28 
VVC H11 H11 H 0 1 N N N N N N -28.895 -51.007 -5.430  -4.100 -1.904 -2.351 H11 VVC 29 
VVC H12 H12 H 0 1 N N N N N N -23.660 -50.431 -8.926  -3.679 3.022  -1.038 H12 VVC 30 
VVC H13 H13 H 0 1 N N N N N N -29.109 -50.622 -9.111  -2.927 -1.938 2.359  H13 VVC 31 
# 
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 
VVC C10 C11 SING N N 1  
VVC C10 C5  SING N N 2  
VVC C11 O4  SING N N 3  
VVC C11 C3  SING N N 4  
VVC O3  C9  DOUB N N 5  
VVC O1  C4  SING N N 6  
VVC C9  N1  SING N N 7  
VVC C9  N3  SING N N 8  
VVC N1  C5  SING N N 9  
VVC N1  C6  SING N N 10 
VVC N3  C8  DOUB N N 11 
VVC C5  O2  SING N N 12 
VVC C8  N2  SING N N 13 
VVC C8  C7  SING N N 14 
VVC C6  C7  DOUB N N 15 
VVC C3  C4  SING N N 16 
VVC C3  O2  SING N N 17 
VVC C3  C2  SING N N 18 
VVC C2  C1  TRIP N N 19 
VVC C4  H1  SING N N 20 
VVC C4  H2  SING N N 21 
VVC C5  H3  SING N N 22 
VVC C6  H4  SING N N 23 
VVC C11 H5  SING N N 24 
VVC C7  H6  SING N N 25 
VVC C10 H7  SING N N 26 
VVC C10 H8  SING N N 27 
VVC N2  H9  SING N N 28 
VVC N2  H10 SING N N 29 
VVC C1  H11 SING N N 30 
VVC O1  H12 SING N N 31 
VVC O4  H13 SING N N 32 
# 
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 
VVC InChI            InChI                1.06  "InChI=1S/C11H13N3O4/c1-2-11(6-15)7(16)5-9(18-11)14-4-3-8(12)13-10(14)17/h1,3-4,7,9,15-16H,5-6H2,(H2,12,13,17)/t7-,9+,11+/m0/s1" 
VVC InChIKey         InChI                1.06  MSPJPGIGNWYLAC-JVUFJMBOSA-N                                                                                                      
VVC SMILES_CANONICAL CACTVS               3.385 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@](CO)(O2)C#C"                                                                               
VVC SMILES           CACTVS               3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[C](CO)(O2)C#C"                                                                                   
VVC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C#C[C@]1([C@H](C[C@@H](O1)N2C=CC(=NC2=O)N)O)CO"                                                                                 
VVC SMILES           "OpenEye OEToolkits" 2.0.7 "C#CC1(C(CC(O1)N2C=CC(=NC2=O)N)O)CO"                                                                                             
# 
_pdbx_chem_comp_identifier.comp_id           VVC 
_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        "4-azanyl-1-[(2~{R},4~{S},5~{R})-5-ethynyl-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]pyrimidin-2-one" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VVC "Create component" 2023-04-05 PDBE 
VVC "Initial release"  2023-12-20 RCSB 
# 
