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
#