data_5YL
# 
_chem_comp.id                                    5YL 
_chem_comp.name                                  "5-(6-D-RIBITYLAMINO-2,4(1H,3H)PYRIMIDINEDIONE-5-YL) PENTYL-1-PHOSPHONIC ACID" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C14 H26 N3 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2003-02-04 
_chem_comp.pdbx_modified_date                    2011-06-04 
_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                        411.345 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     5YL 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1NQW 
_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 
5YL O3P  O3P  O 0 1 N N N 145.611 9.797  153.263 2.760  0.523  -6.974 O3P  5YL 1  
5YL P    P    P 0 1 N N N 145.139 9.436  151.869 1.858  -0.284 -5.913 P    5YL 2  
5YL O1P  O1P  O 0 1 N N N 143.678 9.112  151.830 0.815  -1.048 -6.633 O1P  5YL 3  
5YL O2P  O2P  O 0 1 N N N 146.004 8.389  151.220 2.789  -1.300 -5.081 O2P  5YL 4  
5YL C17  C17  C 0 1 N N N 145.349 10.830 151.001 1.067  0.892  -4.767 C17  5YL 5  
5YL C16  C16  C 0 1 N N N 144.956 10.949 149.524 0.210  0.124  -3.759 C16  5YL 6  
5YL C15  C15  C 0 1 N N N 145.966 11.712 148.611 -0.453 1.111  -2.797 C15  5YL 7  
5YL C14  C14  C 0 1 N N N 145.390 12.229 147.259 -1.311 0.343  -1.789 C14  5YL 8  
5YL C13  C13  C 0 1 N N N 144.414 13.409 147.441 -1.975 1.330  -0.827 C13  5YL 9  
5YL C5   C5   C 0 1 Y N N 144.156 14.108 146.129 -2.819 0.574  0.165  C5   5YL 10 
5YL C4   C4   C 0 1 Y N N 145.237 15.014 145.720 -4.168 0.301  -0.109 C4   5YL 11 
5YL O4   O4   O 0 1 N N N 146.206 15.237 146.480 -4.669 0.675  -1.156 O4   5YL 12 
5YL N3   N3   N 0 1 Y N N 145.191 15.613 144.548 -4.906 -0.376 0.790  N3   5YL 13 
5YL C2   C2   C 0 1 Y N N 144.201 15.417 143.686 -4.362 -0.792 1.948  C2   5YL 14 
5YL O2   O2   O 0 1 N N N 144.257 16.050 142.624 -5.046 -1.403 2.747  O2   5YL 15 
5YL N1   N1   N 0 1 Y N N 143.185 14.594 143.942 -3.069 -0.549 2.232  N1   5YL 16 
5YL C6   C6   C 0 1 Y N N 143.079 13.921 145.106 -2.281 0.143  1.346  C6   5YL 17 
5YL N7   N7   N 0 1 N N N 142.021 13.084 145.293 -0.966 0.396  1.640  N7   5YL 18 
5YL C8   C8   C 0 1 N N N 140.768 13.269 144.579 -0.397 -0.067 2.908  C8   5YL 19 
5YL C9   C9   C 0 1 N N S 140.743 12.468 143.266 1.075  0.341  2.986  C9   5YL 20 
5YL O9   O9   O 0 1 N N N 141.581 13.069 142.283 1.791  -0.246 1.898  O9   5YL 21 
5YL C10  C10  C 0 1 N N S 139.316 12.351 142.714 1.669  -0.143 4.309  C10  5YL 22 
5YL O10  O10  O 0 1 N N N 138.755 13.648 142.528 0.953  0.444  5.397  O10  5YL 23 
5YL C11  C11  C 0 1 N N R 138.405 11.535 143.645 3.141  0.266  4.388  C11  5YL 24 
5YL O11  O11  O 0 1 N N N 138.999 10.270 143.929 3.858  -0.321 3.300  O11  5YL 25 
5YL C12  C12  C 0 1 N N N 137.010 11.295 143.041 3.736  -0.218 5.711  C12  5YL 26 
5YL O12  O12  O 0 1 N N N 137.138 10.688 141.774 5.111  0.163  5.784  O12  5YL 27 
5YL HOP3 3HOP H 0 0 N N N 146.538 10.002 153.287 3.159  -0.133 -7.560 HOP3 5YL 28 
5YL HOP2 2HOP H 0 0 N N N 145.708 8.162  150.346 3.454  -0.762 -4.628 HOP2 5YL 29 
5YL H171 1H17 H 0 0 N N N 144.834 11.650 151.553 0.436  1.579  -5.331 H171 5YL 30 
5YL H172 2H17 H 0 0 N N N 146.421 11.122 151.088 1.835  1.455  -4.237 H172 5YL 31 
5YL H161 1H16 H 0 0 N N N 144.753 9.936  149.102 0.840  -0.563 -3.195 H161 5YL 32 
5YL H162 2H16 H 0 0 N N N 143.943 11.408 149.436 -0.557 -0.438 -4.289 H162 5YL 33 
5YL H151 1H15 H 0 0 N N N 146.429 12.554 149.175 -1.084 1.799  -3.361 H151 5YL 34 
5YL H152 2H15 H 0 0 N N N 146.865 11.079 148.425 0.314  1.674  -2.267 H152 5YL 35 
5YL H141 1H14 H 0 0 N N N 146.209 12.492 146.549 -0.680 -0.344 -1.226 H141 5YL 36 
5YL H142 2H14 H 0 0 N N N 144.913 11.400 146.684 -2.079 -0.219 -2.319 H142 5YL 37 
5YL H131 1H13 H 0 0 N N N 143.464 13.085 147.927 -2.605 2.018  -1.391 H131 5YL 38 
5YL H132 2H13 H 0 0 N N N 144.771 14.120 148.221 -1.207 1.893  -0.297 H132 5YL 39 
5YL HN3  HN3  H 0 1 N N N 145.947 16.250 144.299 -5.839 -0.566 0.602  HN3  5YL 40 
5YL HN1  HN1  H 0 1 N N N 142.467 14.475 143.226 -2.694 -0.857 3.072  HN1  5YL 41 
5YL HN7  HN7  H 0 1 N N N 141.812 13.061 146.291 -0.412 0.882  1.009  HN7  5YL 42 
5YL H81  1H8  H 0 1 N N N 139.891 13.023 145.223 -0.475 -1.153 2.965  H81  5YL 43 
5YL H82  2H8  H 0 1 N N N 140.555 14.349 144.401 -0.943 0.380  3.737  H82  5YL 44 
5YL H91  1H9  H 0 1 N N N 141.126 11.446 143.497 1.154  1.427  2.928  H91  5YL 45 
5YL HO9  HO9  H 0 1 N N N 141.565 12.574 141.472 1.696  -1.204 1.986  HO9  5YL 46 
5YL H101 1H10 H 0 0 N N N 139.381 11.818 141.736 1.591  -1.229 4.367  H101 5YL 47 
5YL H10O OH10 H 0 0 N N N 137.871 13.575 142.186 1.048  1.402  5.309  H10O 5YL 48 
5YL H111 1H11 H 0 0 N N N 138.285 12.133 144.578 3.220  1.351  4.330  H111 5YL 49 
5YL H11O OH11 H 0 0 N N N 138.435 9.765  144.504 3.763  -1.280 3.388  H11O 5YL 50 
5YL H121 1H12 H 0 0 N N N 136.352 10.707 143.723 3.657  -1.304 5.769  H121 5YL 51 
5YL H122 2H12 H 0 0 N N N 136.404 12.230 142.999 3.190  0.229  6.541  H122 5YL 52 
5YL H12O OH12 H 0 0 N N N 136.276 10.539 141.401 5.447  -0.160 6.631  H12O 5YL 53 
# 
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 
5YL O3P P    SING N N 1  
5YL O3P HOP3 SING N N 2  
5YL P   O1P  DOUB N N 3  
5YL P   O2P  SING N N 4  
5YL P   C17  SING N N 5  
5YL O2P HOP2 SING N N 6  
5YL C17 C16  SING N N 7  
5YL C17 H171 SING N N 8  
5YL C17 H172 SING N N 9  
5YL C16 C15  SING N N 10 
5YL C16 H161 SING N N 11 
5YL C16 H162 SING N N 12 
5YL C15 C14  SING N N 13 
5YL C15 H151 SING N N 14 
5YL C15 H152 SING N N 15 
5YL C14 C13  SING N N 16 
5YL C14 H141 SING N N 17 
5YL C14 H142 SING N N 18 
5YL C13 C5   SING N N 19 
5YL C13 H131 SING N N 20 
5YL C13 H132 SING N N 21 
5YL C5  C4   SING Y N 22 
5YL C5  C6   DOUB Y N 23 
5YL C4  O4   DOUB N N 24 
5YL C4  N3   SING Y N 25 
5YL N3  C2   SING Y N 26 
5YL N3  HN3  SING N N 27 
5YL C2  O2   DOUB N N 28 
5YL C2  N1   SING Y N 29 
5YL N1  C6   SING Y N 30 
5YL N1  HN1  SING N N 31 
5YL C6  N7   SING N N 32 
5YL N7  C8   SING N N 33 
5YL N7  HN7  SING N N 34 
5YL C8  C9   SING N N 35 
5YL C8  H81  SING N N 36 
5YL C8  H82  SING N N 37 
5YL C9  O9   SING N N 38 
5YL C9  C10  SING N N 39 
5YL C9  H91  SING N N 40 
5YL O9  HO9  SING N N 41 
5YL C10 O10  SING N N 42 
5YL C10 C11  SING N N 43 
5YL C10 H101 SING N N 44 
5YL O10 H10O SING N N 45 
5YL C11 O11  SING N N 46 
5YL C11 C12  SING N N 47 
5YL C11 H111 SING N N 48 
5YL O11 H11O SING N N 49 
5YL C12 O12  SING N N 50 
5YL C12 H121 SING N N 51 
5YL C12 H122 SING N N 52 
5YL O12 H12O SING N N 53 
# 
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 
5YL SMILES           ACDLabs              10.04 "O=C1NC(NCC(O)C(O)C(O)CO)=C(C(=O)N1)CCCCCP(=O)(O)O"                                                                                                                      
5YL SMILES_CANONICAL CACTVS               3.341 "OC[C@@H](O)[C@@H](O)[C@@H](O)CNC1=C(CCCCC[P](O)(O)=O)C(=O)NC(=O)N1"                                                                                                     
5YL SMILES           CACTVS               3.341 "OC[CH](O)[CH](O)[CH](O)CNC1=C(CCCCC[P](O)(O)=O)C(=O)NC(=O)N1"                                                                                                           
5YL SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C(CCC1=C(NC(=O)NC1=O)NC[C@@H]([C@@H]([C@@H](CO)O)O)O)CCP(=O)(O)O"                                                                                                       
5YL SMILES           "OpenEye OEToolkits" 1.5.0 "C(CCC1=C(NC(=O)NC1=O)NCC(C(C(CO)O)O)O)CCP(=O)(O)O"                                                                                                                      
5YL InChI            InChI                1.03  "InChI=1S/C14H26N3O9P/c18-7-10(20)11(21)9(19)6-15-12-8(13(22)17-14(23)16-12)4-2-1-3-5-27(24,25)26/h9-11,18-21H,1-7H2,(H2,24,25,26)(H3,15,16,17,22,23)/t9-,10+,11-/m0/s1" 
5YL InChIKey         InChI                1.03  BMATWAHJJFXMFA-AXFHLTTASA-N                                                                                                                                              
# 
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 
5YL "SYSTEMATIC NAME" ACDLabs              10.04 "1-deoxy-1-{[2,6-dioxo-5-(5-phosphonopentyl)-1,2,3,6-tetrahydropyrimidin-4-yl]amino}-D-ribitol"         
5YL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "5-[2,4-dioxo-6-[[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]amino]-1H-pyrimidin-5-yl]pentylphosphonic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
5YL "Create component"  2003-02-04 RCSB 
5YL "Modify descriptor" 2011-06-04 RCSB 
# 
