data_2LJ
# 
_chem_comp.id                                    2LJ 
_chem_comp.name                                  "1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C12 H20 N4 O6" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "5-(2-oxopropylideneamino)-6-D-ribitylaminouracil" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2013-11-27 
_chem_comp.pdbx_modified_date                    2021-03-01 
_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                        316.310 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     2LJ 
_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        6MWR 
_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 
2LJ C4    C1  C 0 1 N N N 9.157  14.141 37.680 -3.914 0.723  -0.181 C4    2LJ 1  
2LJ C6    C2  C 0 1 N N N 7.755  11.559 37.330 -3.476 -2.142 -0.047 C6    2LJ 2  
2LJ C7    C3  C 0 1 N N N 7.107  10.252 37.184 -3.564 -3.577 -0.501 C7    2LJ 3  
2LJ C8    C4  C 0 1 N N N 5.677  10.201 36.720 -3.255 -4.504 0.676  C8    2LJ 4  
2LJ N1    N1  N 0 1 N N N 8.152  16.030 35.833 -1.537 2.014  0.241  N1    2LJ 5  
2LJ N3    N2  N 0 1 N N N 9.533  15.473 37.631 -3.882 2.025  0.163  N3    2LJ 6  
2LJ N5    N3  N 0 1 N N N 7.530  12.517 36.503 -2.700 -1.316 -0.666 N5    2LJ 7  
2LJ C4A   C5  C 0 1 N N N 8.154  13.755 36.656 -2.698 0.010  -0.321 C4A   2LJ 8  
2LJ O4    O1  O 0 1 N N N 9.643  13.407 38.540 -4.980 0.162  -0.365 O4    2LJ 9  
2LJ C2    C6  C 0 1 N N N 9.077  16.433 36.763 -2.712 2.655  0.369  C2    2LJ 10 
2LJ O2    O2  O 0 1 N N N 9.448  17.600 36.838 -2.716 3.832  0.674  O2    2LJ 11 
2LJ C8A   C7  C 0 1 N N N 7.683  14.753 35.753 -1.501 0.686  -0.102 C8A   2LJ 12 
2LJ N8    N4  N 0 1 N N N 6.698  14.493 34.893 -0.303 0.035  -0.232 N8    2LJ 13 
2LJ "C1'" C8  C 0 1 N N N 5.929  15.411 34.067 0.951  0.757  -0.005 "C1'" 2LJ 14 
2LJ "C2'" C9  C 0 1 N N S 6.351  15.503 32.601 2.132  -0.193 -0.213 "C2'" 2LJ 15 
2LJ "O2'" O3  O 0 1 N N N 6.466  14.201 32.024 2.035  -1.282 0.708  "O2'" 2LJ 16 
2LJ "C3'" C10 C 0 1 N N S 7.653  16.287 32.415 3.441  0.560  0.024  "C3'" 2LJ 17 
2LJ "O3'" O4  O 0 1 N N N 7.668  17.438 33.253 3.538  1.649  -0.896 "O3'" 2LJ 18 
2LJ "C4'" C11 C 0 1 N N R 7.970  16.699 30.975 4.622  -0.390 -0.184 "C4'" 2LJ 19 
2LJ "O4'" O5  O 0 1 N N N 9.341  17.091 30.897 4.525  -1.479 0.737  "O4'" 2LJ 20 
2LJ "C5'" C12 C 0 1 N N N 7.092  17.823 30.413 5.932  0.363  0.054  "C5'" 2LJ 21 
2LJ "O5'" O6  O 0 1 N N N 7.483  18.170 29.091 7.036  -0.491 -0.253 "O5'" 2LJ 22 
2LJ H1    H1  H 0 1 N N N 8.437  11.721 38.151 -4.062 -1.806 0.795  H1    2LJ 23 
2LJ H2    H2  H 0 1 N N N 7.146  9.760  38.167 -4.570 -3.780 -0.870 H2    2LJ 24 
2LJ H3    H3  H 0 1 N N N 7.702  9.675  36.461 -2.843 -3.750 -1.300 H3    2LJ 25 
2LJ H4    H4  H 0 1 N N N 5.346  9.153  36.664 -3.977 -4.331 1.474  H4    2LJ 26 
2LJ H5    H5  H 0 1 N N N 5.041  10.749 37.431 -3.319 -5.542 0.347  H5    2LJ 27 
2LJ H6    H6  H 0 1 N N N 5.598  10.664 35.725 -2.250 -4.301 1.044  H6    2LJ 28 
2LJ H7    H7  H 0 1 N N N 10.212 15.768 38.303 -4.713 2.515  0.262  H7    2LJ 29 
2LJ H9    H9  H 0 1 N N N 6.010  14.019 35.442 -0.285 -0.904 -0.475 H9    2LJ 30 
2LJ H10   H10 H 0 1 N N N 6.018  16.415 34.507 1.025  1.587  -0.707 H10   2LJ 31 
2LJ H11   H11 H 0 1 N N N 4.877  15.090 34.095 0.969  1.141  1.015  H11   2LJ 32 
2LJ H12   H12 H 0 1 N N N 5.561  16.052 32.068 2.113  -0.578 -1.233 H12   2LJ 33 
2LJ H13   H13 H 0 1 N N N 5.652  13.727 32.147 2.045  -1.014 1.637  H13   2LJ 34 
2LJ H14   H14 H 0 1 N N N 8.468  15.623 32.738 3.460  0.944  1.044  H14   2LJ 35 
2LJ H15   H15 H 0 1 N N N 7.471  17.182 34.147 3.528  1.380  -1.825 H15   2LJ 36 
2LJ H16   H16 H 0 1 N N N 7.819  15.815 30.339 4.604  -0.774 -1.204 H16   2LJ 37 
2LJ H17   H17 H 0 1 N N N 9.889  16.397 31.244 4.535  -1.211 1.666  H17   2LJ 38 
2LJ H18   H18 H 0 1 N N N 7.186  18.708 31.059 5.965  1.245  -0.587 H18   2LJ 39 
2LJ H19   H19 H 0 1 N N N 6.044  17.488 30.401 5.990  0.671  1.098  H19   2LJ 40 
2LJ H20   H20 H 0 1 N N N 6.924  18.867 28.768 7.900  -0.078 -0.125 H20   2LJ 41 
2LJ H8    H8  H 0 1 N N N 7.805  16.706 35.183 -0.708 2.494  0.391  H8    2LJ 42 
# 
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 
2LJ "O5'" "C5'" SING N N 1  
2LJ "C5'" "C4'" SING N N 2  
2LJ "O4'" "C4'" SING N N 3  
2LJ "C4'" "C3'" SING N N 4  
2LJ "O2'" "C2'" SING N N 5  
2LJ "C3'" "C2'" SING N N 6  
2LJ "C3'" "O3'" SING N N 7  
2LJ "C2'" "C1'" SING N N 8  
2LJ "C1'" N8    SING N N 9  
2LJ N8    C8A   SING N N 10 
2LJ C8A   N1    SING N N 11 
2LJ C8A   C4A   DOUB N N 12 
2LJ N1    C2    SING N N 13 
2LJ N5    C4A   SING N N 14 
2LJ N5    C6    DOUB N N 15 
2LJ C4A   C4    SING N N 16 
2LJ C8    C7    SING N N 17 
2LJ C2    O2    DOUB N N 18 
2LJ C2    N3    SING N N 19 
2LJ C7    C6    SING N N 20 
2LJ N3    C4    SING N N 21 
2LJ C4    O4    DOUB N N 22 
2LJ C6    H1    SING N N 23 
2LJ C7    H2    SING N N 24 
2LJ C7    H3    SING N N 25 
2LJ C8    H4    SING N N 26 
2LJ C8    H5    SING N N 27 
2LJ C8    H6    SING N N 28 
2LJ N3    H7    SING N N 29 
2LJ N8    H9    SING N N 30 
2LJ "C1'" H10   SING N N 31 
2LJ "C1'" H11   SING N N 32 
2LJ "C2'" H12   SING N N 33 
2LJ "O2'" H13   SING N N 34 
2LJ "C3'" H14   SING N N 35 
2LJ "O3'" H15   SING N N 36 
2LJ "C4'" H16   SING N N 37 
2LJ "O4'" H17   SING N N 38 
2LJ "C5'" H18   SING N N 39 
2LJ "C5'" H19   SING N N 40 
2LJ "O5'" H20   SING N N 41 
2LJ N1    H8    SING N N 42 
# 
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 
2LJ SMILES           ACDLabs              12.01 "C1(=O)NC(NC(=C1\N=C\CC)NCC(O)C(O)C(O)CO)=O"                                                                                                             
2LJ InChI            InChI                1.03  "InChI=1S/C12H20N4O6/c1-2-3-13-8-10(15-12(22)16-11(8)21)14-4-6(18)9(20)7(19)5-17/h3,6-7,9,17-20H,2,4-5H2,1H3,(H3,14,15,16,21,22)/b13-3+/t6-,7+,9-/m0/s1" 
2LJ InChIKey         InChI                1.03  YCMPUNANLDFPQG-FHZGFTDOSA-N                                                                                                                              
2LJ SMILES_CANONICAL CACTVS               3.385 "CCC=NC1=C(NC[C@H](O)[C@H](O)[C@H](O)CO)NC(=O)NC1=O"                                                                                                     
2LJ SMILES           CACTVS               3.385 "CCC=NC1=C(NC[CH](O)[CH](O)[CH](O)CO)NC(=O)NC1=O"                                                                                                        
2LJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC/C=N/C1=C(NC(=O)NC1=O)NC[C@@H]([C@@H]([C@@H](CO)O)O)O"                                                                                                
2LJ SMILES           "OpenEye OEToolkits" 2.0.6 "CCC=NC1=C(NC(=O)NC1=O)NCC(C(C(CO)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 
2LJ "SYSTEMATIC NAME" ACDLabs              12.01 "1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol"                       
2LJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "5-[(~{E})-propylideneamino]-6-[[(2~{S},3~{S},4~{R})-2,3,4,5-tetrakis(oxidanyl)pentyl]amino]-1~{H}-pyrimidine-2,4-dione" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      2LJ 
_pdbx_chem_comp_synonyms.name         "5-(2-oxopropylideneamino)-6-D-ribitylaminouracil" 
_pdbx_chem_comp_synonyms.provenance   ? 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
2LJ "Create component"         2013-11-27 RCSB 
2LJ "Initial release"          2014-04-16 RCSB 
2LJ "Modify leaving atom flag" 2018-11-02 RCSB 
2LJ "Modify value order"       2019-01-09 RCSB 
2LJ "Modify synonyms"          2021-03-01 PDBE 
# 
