data_WVQ
# 
_chem_comp.id                                    WVQ 
_chem_comp.name                                  "N-[(5E)-2-amino-5-(formylimino)-6-oxo-5,6-dihydropyrimidin-4-yl]-2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosylamine" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H14 N5 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-10-16 
_chem_comp.pdbx_modified_date                    2024-04-19 
_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                        363.221 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     WVQ 
_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        8UKQ 
_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.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 
WVQ C5    C1  C 0 1 N N N N N N 14.808 1.898  49.374 -3.774 -0.155 0.687  C5    WVQ 1  
WVQ C4    C2  C 0 1 N N N N N N 16.080 1.459  49.114 -2.549 -0.042 -0.155 C4    WVQ 2  
WVQ N2    N1  N 0 1 N N N N N N 15.420 -1.641 47.300 -2.965 -2.809 -2.330 N2    WVQ 3  
WVQ N7    N2  N 0 1 N N N N N N 14.456 3.118  50.099 -4.031 0.694  1.650  N7    WVQ 4  
WVQ C8    C3  C 0 1 N N N N N N 15.351 4.201  50.477 -3.094 1.586  2.028  C8    WVQ 5  
WVQ "C1'" C4  C 0 1 N N R N N N 18.557 1.567  49.278 -0.492 1.101  -0.846 "C1'" WVQ 6  
WVQ C2    C5  C 0 1 N N N N N N 15.202 -0.403 48.027 -3.241 -1.925 -1.321 C2    WVQ 7  
WVQ "C2'" C6  C 0 1 N N N N N N 19.237 2.219  48.094 -0.093 2.587  -0.978 "C2'" WVQ 8  
WVQ "C3'" C7  C 0 1 N N S N N N 20.661 2.336  48.499 1.450  2.557  -1.046 "C3'" WVQ 9  
WVQ "C4'" C8  C 0 1 N N R N N N 20.754 2.006  49.948 1.801  1.056  -0.948 "C4'" WVQ 10 
WVQ "C5'" C9  C 0 1 N N N N N N 21.377 3.186  50.681 3.073  0.860  -0.120 "C5'" WVQ 11 
WVQ C6    C10 C 0 1 N N N N N N 13.758 1.149  48.948 -4.699 -1.288 0.368  C6    WVQ 12 
WVQ N1    N3  N 0 1 N N N N N N 13.947 0.022  48.285 -4.354 -2.104 -0.634 N1    WVQ 13 
WVQ N3    N4  N 0 1 N N N N N N 16.254 0.328  48.448 -2.369 -0.940 -1.103 N3    WVQ 14 
WVQ N9    N5  N 0 1 N N N N N N 17.286 2.165  49.515 -1.642 0.959  0.050  N9    WVQ 15 
WVQ "O3'" O1  O 0 1 N N N N N N 21.470 1.420  47.765 1.907  3.098  -2.288 "O3'" WVQ 16 
WVQ "O4'" O2  O 0 1 N N N N N N 19.430 1.770  50.405 0.670  0.456  -0.281 "O4'" WVQ 17 
WVQ "O5'" O3  O 0 1 N N N N N N 21.981 4.026  49.740 3.445  -0.520 -0.139 "O5'" WVQ 18 
WVQ O6    O4  O 0 1 N N N N N N 12.654 1.516  49.170 -5.727 -1.460 0.997  O6    WVQ 19 
WVQ O8    O5  O 0 1 N N N N N N 14.925 5.136  51.069 -3.360 2.769  2.055  O8    WVQ 20 
WVQ OP1   O6  O 0 1 N N N N N N 24.105 4.919  48.296 5.940  -0.343 0.194  OP1   WVQ 21 
WVQ OP2   O7  O 0 1 N N N N N N 23.765 2.244  48.679 4.543  -0.909 2.219  OP2   WVQ 22 
WVQ P     P1  P 0 1 N N N N N N 23.550 3.749  49.314 4.739  -1.089 0.631  P     WVQ 23 
WVQ O1    O8  O 0 1 N Y N N N N 24.351 3.824  50.699 4.924  -2.651 0.287  O1    WVQ 24 
WVQ H1    H1  H 0 1 N N N N N N 14.639 -2.182 46.988 -3.579 -3.536 -2.520 H1    WVQ 25 
WVQ H2    H2  H 0 1 N N N N N N 16.351 -1.952 47.111 -2.156 -2.708 -2.856 H2    WVQ 26 
WVQ H3    H3  H 0 1 N N N N N N 16.399 4.154  50.220 -2.107 1.248  2.307  H3    WVQ 27 
WVQ H4    H4  H 0 1 N N N N N N 18.442 0.491  49.079 -0.721 0.679  -1.825 H4    WVQ 28 
WVQ H5    H5  H 0 1 N N N N N N 18.806 3.212  47.897 -0.508 3.014  -1.891 H5    WVQ 29 
WVQ H6    H6  H 0 1 N N N N N N 19.139 1.592  47.196 -0.426 3.151  -0.107 H6    WVQ 30 
WVQ H7    H7  H 0 1 N N N N N N 21.006 3.368  48.335 1.880  3.106  -0.209 H7    WVQ 31 
WVQ H8    H8  H 0 1 N N N N N N 21.382 1.114  50.089 1.925  0.629  -1.943 H8    WVQ 32 
WVQ H9    H9  H 0 1 N N N N N N 22.133 2.823  51.393 3.879  1.459  -0.545 H9    WVQ 33 
WVQ H10   H10 H 0 1 N N N N N N 20.597 3.739  51.225 2.890  1.173  0.907  H10   WVQ 34 
WVQ H11   H11 H 0 1 N N N N N N 17.224 3.062  49.953 -1.759 1.576  0.789  H11   WVQ 35 
WVQ H12   H12 H 0 1 N N N N N N 22.376 1.509  48.037 1.661  4.022  -2.429 H12   WVQ 36 
WVQ H13   H13 H 0 1 N N N N N N 24.177 2.316  47.826 3.772  -1.372 2.575  H13   WVQ 37 
WVQ H14   H14 H 0 1 N Y N N N N 24.988 4.528  50.659 5.686  -3.062 0.718  H14   WVQ 38 
# 
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 
WVQ N2    C2    SING N N 1  
WVQ "O3'" "C3'" SING N N 2  
WVQ C2    N1    DOUB N N 3  
WVQ C2    N3    SING N N 4  
WVQ "C2'" "C3'" SING N N 5  
WVQ "C2'" "C1'" SING N N 6  
WVQ N1    C6    SING N N 7  
WVQ OP1   P     DOUB N N 8  
WVQ N3    C4    DOUB N N 9  
WVQ "C3'" "C4'" SING N N 10 
WVQ OP2   P     SING N N 11 
WVQ C6    O6    DOUB N N 12 
WVQ C6    C5    SING N N 13 
WVQ C4    C5    SING N N 14 
WVQ C4    N9    SING N N 15 
WVQ "C1'" N9    SING N N 16 
WVQ "C1'" "O4'" SING N N 17 
WVQ P     "O5'" SING N N 18 
WVQ C5    N7    DOUB N N 19 
WVQ "O5'" "C5'" SING N N 20 
WVQ "C4'" "O4'" SING N N 21 
WVQ "C4'" "C5'" SING N N 22 
WVQ N7    C8    SING N N 23 
WVQ C8    O8    DOUB N N 24 
WVQ P     O1    SING N N 25 
WVQ N2    H1    SING N N 26 
WVQ N2    H2    SING N N 27 
WVQ C8    H3    SING N N 28 
WVQ "C1'" H4    SING N N 29 
WVQ "C2'" H5    SING N N 30 
WVQ "C2'" H6    SING N N 31 
WVQ "C3'" H7    SING N N 32 
WVQ "C4'" H8    SING N N 33 
WVQ "C5'" H9    SING N N 34 
WVQ "C5'" H10   SING N N 35 
WVQ N9    H11   SING N N 36 
WVQ "O3'" H12   SING N N 37 
WVQ OP2   H13   SING N N 38 
WVQ O1    H14   SING N N 39 
# 
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 
WVQ SMILES           ACDLabs              12.01 "O=P(O)(O)OCC1OC(NC\2=NC(N)=NC(=O)C/2=N\C=O)CC1O"                                                                                                                  
WVQ InChI            InChI                1.06  "InChI=1S/C10H14N5O8P/c11-10-14-8(7(12-3-16)9(18)15-10)13-6-1-4(17)5(23-6)2-22-24(19,20)21/h3-6,17H,1-2H2,(H2,19,20,21)(H3,11,13,14,15,18)/b12-7+/t4-,5+,6+/m0/s1" 
WVQ InChIKey         InChI                1.06  ZSDJBOZQMXOVIY-CTYKPTQGSA-N                                                                                                                                        
WVQ SMILES_CANONICAL CACTVS               3.385 "NC1=NC(=O)C(=NC=O)C(=N1)N[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2"                                                                                                  
WVQ SMILES           CACTVS               3.385 "NC1=NC(=O)C(=NC=O)C(=N1)N[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2"                                                                                                      
WVQ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@@H]([C@H](O[C@H]1NC\2=NC(=NC(=O)/C2=N/C=O)N)COP(=O)(O)O)O"                                                                                                   
WVQ SMILES           "OpenEye OEToolkits" 2.0.7 "C1C(C(OC1NC2=NC(=NC(=O)C2=NC=O)N)COP(=O)(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 
WVQ "SYSTEMATIC NAME" ACDLabs              12.01 "N-[(5E)-2-amino-5-(formylimino)-6-oxo-5,6-dihydropyrimidin-4-yl]-2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosylamine"                           
WVQ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},5~{R})-5-[[(5~{E})-2-azanyl-5-methanoylimino-6-oxidanylidene-pyrimidin-4-yl]amino]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen 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 
WVQ "Create component"    2023-10-16 RCSB 
WVQ "Modify linking type" 2023-10-17 RCSB 
WVQ "Initial release"     2024-04-24 RCSB 
# 
