data_DUP
#
_chem_comp.id DUP
_chem_comp.name
;2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H16 N3 O13 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2003-12-17
_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 467.157
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code DUP
_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 1RN8
_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
DUP O4 O4 O 0 1 N N N -4.608 33.070 2.415 -2.207 -0.898 8.166 O4 DUP 1
DUP C4 C4 C 0 1 Y N N -5.557 32.595 3.067 -1.444 -0.540 7.287 C4 DUP 2
DUP C5 C5 C 0 1 Y N N -6.573 33.399 3.592 -0.684 0.644 7.441 C5 DUP 3
DUP C6 C6 C 0 1 Y N N -7.586 32.789 4.301 0.154 1.019 6.451 C6 DUP 4
DUP N3 N3 N 0 1 Y N N -5.596 31.268 3.283 -1.314 -1.267 6.160 N3 DUP 5
DUP C2 C2 C 0 1 Y N N -6.575 30.671 3.981 -0.474 -0.867 5.187 C2 DUP 6
DUP O2 O2 O 0 1 N N N -6.536 29.438 4.169 -0.368 -1.534 4.175 O2 DUP 7
DUP N1 N1 N 0 1 Y N N -7.610 31.446 4.498 0.256 0.253 5.322 N1 DUP 8
DUP "C1'" C1* C 0 1 N N R -8.677 30.796 5.271 1.166 0.660 4.249 "C1'" DUP 9
DUP "C2'" C2* C 0 1 N N N -8.503 31.067 6.753 2.229 -0.432 4.002 "C2'" DUP 10
DUP "C3'" C3* C 0 1 N N S -9.491 32.167 7.069 2.432 -0.420 2.470 "C3'" DUP 11
DUP "O3'" O3* O 0 1 N N N -9.921 32.128 8.439 3.782 -0.084 2.146 "O3'" DUP 12
DUP "O4'" O4* O 0 1 N N N -9.921 31.364 4.899 0.453 0.771 2.998 "O4'" DUP 13
DUP "C4'" C4* C 0 1 N N R -10.597 31.928 6.041 1.466 0.677 1.969 "C4'" DUP 14
DUP "C5'" C5* C 0 1 N N N -11.423 33.160 5.672 0.835 0.273 0.635 "C5'" DUP 15
DUP "O5'" O5* O 0 1 N N N -10.593 34.233 5.217 -0.105 1.270 0.232 "O5'" DUP 16
DUP PA PA P 0 1 N N S -11.226 35.542 4.503 -0.727 0.783 -1.170 PA DUP 17
DUP O1A O1A O 0 1 N N N -12.301 36.064 5.415 -1.394 -0.525 -0.986 O1A DUP 18
DUP O2A O2A O 0 1 N N N -10.043 36.415 4.161 -1.802 1.865 -1.685 O2A DUP 19
DUP N3A N3A N 0 1 N N N -11.874 34.943 3.064 0.504 0.630 -2.306 N3A DUP 20
DUP PB PB P 0 1 N N R -13.457 35.135 2.564 -0.219 0.121 -3.738 PB DUP 21
DUP O1B O1B O 0 1 N N N -14.032 36.396 3.198 -0.893 -1.177 -3.515 O1B DUP 22
DUP O2B O2B O 0 1 N N N -13.443 35.114 1.080 -1.302 1.214 -4.210 O2B DUP 23
DUP O3B O3B O 0 1 N N N -14.204 33.801 3.087 0.905 -0.046 -4.877 O3B DUP 24
DUP PG PG P 0 1 N N N -15.321 33.739 4.265 0.147 -0.533 -6.212 PG DUP 25
DUP O2G O2G O 0 1 N N N -15.085 34.759 5.355 -0.854 0.481 -6.608 O2G DUP 26
DUP O1G O1G O 0 1 N N N -16.672 33.993 3.614 1.218 -0.722 -7.399 O1G DUP 27
DUP O3G O3G O 0 1 N N N -15.188 32.344 4.831 -0.592 -1.934 -5.928 O3G DUP 28
DUP H5 H5 H 0 1 N N N -6.575 34.492 3.449 -0.774 1.240 8.337 H5 DUP 29
DUP H6 H6 H 0 1 N N N -8.404 33.395 4.724 0.742 1.920 6.551 H6 DUP 30
DUP HN3 HN3 H 0 1 N N N -4.849 30.688 2.900 -1.831 -2.080 6.047 HN3 DUP 31
DUP "H1'" H1* H 0 1 N N N -8.637 29.700 5.068 1.645 1.607 4.497 "H1'" DUP 32
DUP "H2'1" 1H2* H 0 0 N N N -8.615 30.161 7.393 1.862 -1.404 4.330 "H2'1" DUP 33
DUP "H2'2" 2H2* H 0 0 N N N -7.454 31.303 7.048 3.160 -0.182 4.512 "H2'2" DUP 34
DUP H1 H1 H 0 1 N N N -9.073 33.197 6.987 2.166 -1.386 2.042 H1 DUP 35
DUP "H3'" H3* H 0 1 N N N -10.541 32.819 8.637 4.339 -0.786 2.508 "H3'" DUP 36
DUP "H4'" H4* H 0 1 N N N -11.371 31.249 6.469 1.992 1.626 1.867 "H4'" DUP 37
DUP "H5'1" 1H5* H 0 0 N N N -12.213 32.911 4.925 1.614 0.181 -0.121 "H5'1" DUP 38
DUP "H5'2" 2H5* H 0 0 N N N -12.076 33.480 6.516 0.325 -0.683 0.749 "H5'2" DUP 39
DUP H2A H2A H 0 1 N N N -10.414 37.182 3.742 -1.328 2.701 -1.791 H2A DUP 40
DUP H3A H3A H 0 1 N N N -11.684 33.940 3.053 0.859 1.559 -2.475 H3A DUP 41
DUP H2B H2B H 0 1 N N N -14.342 35.223 0.795 -0.822 2.043 -4.344 H2B DUP 42
DUP H1G H1G H 0 1 N N N -17.325 33.956 4.302 0.723 -1.013 -8.177 H1G DUP 43
DUP H3G H3G H 0 1 N N N -15.841 32.307 5.519 0.093 -2.566 -5.673 H3G DUP 44
#
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
DUP O4 C4 DOUB N N 1
DUP C4 C5 SING Y N 2
DUP C4 N3 SING Y N 3
DUP C5 C6 DOUB Y N 4
DUP C5 H5 SING N N 5
DUP C6 N1 SING Y N 6
DUP C6 H6 SING N N 7
DUP N3 C2 SING Y N 8
DUP N3 HN3 SING N N 9
DUP C2 O2 DOUB N N 10
DUP C2 N1 SING Y N 11
DUP N1 "C1'" SING N N 12
DUP "C1'" "C2'" SING N N 13
DUP "C1'" "O4'" SING N N 14
DUP "C1'" "H1'" SING N N 15
DUP "C2'" "C3'" SING N N 16
DUP "C2'" "H2'1" SING N N 17
DUP "C2'" "H2'2" SING N N 18
DUP "C3'" "O3'" SING N N 19
DUP "C3'" "C4'" SING N N 20
DUP "C3'" H1 SING N N 21
DUP "O3'" "H3'" SING N N 22
DUP "O4'" "C4'" SING N N 23
DUP "C4'" "C5'" SING N N 24
DUP "C4'" "H4'" SING N N 25
DUP "C5'" "O5'" SING N N 26
DUP "C5'" "H5'1" SING N N 27
DUP "C5'" "H5'2" SING N N 28
DUP "O5'" PA SING N N 29
DUP PA O1A DOUB N N 30
DUP PA O2A SING N N 31
DUP PA N3A SING N N 32
DUP O2A H2A SING N N 33
DUP N3A PB SING N N 34
DUP N3A H3A SING N N 35
DUP PB O1B DOUB N N 36
DUP PB O2B SING N N 37
DUP PB O3B SING N N 38
DUP O2B H2B SING N N 39
DUP O3B PG SING N N 40
DUP PG O2G DOUB N N 41
DUP PG O1G SING N N 42
DUP PG O3G SING N N 43
DUP O1G H1G SING N N 44
DUP O3G H3G SING N N 45
#
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
DUP SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O"
DUP SMILES_CANONICAL CACTVS 3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P@](O)(=O)N[P@](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O"
DUP SMILES CACTVS 3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O"
DUP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO[P@](=O)(N[P@@](=O)(O)OP(=O)(O)O)O)O"
DUP SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O"
DUP InChI InChI 1.03 "InChI=1S/C9H16N3O13P3/c13-5-3-8(12-2-1-7(14)10-9(12)15)24-6(5)4-23-26(16,17)11-27(18,19)25-28(20,21)22/h1-2,5-6,8,13H,3-4H2,(H,10,14,15)(H2,20,21,22)(H3,11,16,17,18,19)/t5-,6+,8+/m0/s1"
DUP InChIKey InChI 1.03 XZLLMTSKYYYJLH-SHYZEUOFSA-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
DUP "SYSTEMATIC NAME" ACDLabs 10.04 "2'-deoxy-5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine"
DUP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methoxy-N-(hydroxy-phosphonooxy-phosphoryl)phosphonamidic 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
DUP "Create component" 2003-12-17 RCSB
DUP "Modify descriptor" 2011-06-04 RCSB
#