data_PUP
#
_chem_comp.id PUP
_chem_comp.name
"(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-hydroxy-2-({[(S)-hydroxy{[(2R,3S,4S)-4-hydroxy-2-(hydroxymethyl)tetrahydrofuran-3-yl]oxy}phosphoryl]oxy}methyl)tetrahydrofuran-3-yl dihydrogen phosphate"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H22 N2 O15 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2014-03-04
_chem_comp.pdbx_modified_date 2014-03-07
_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 520.276
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PUP
_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 4OAV
_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
PUP N01 N01 N 0 1 N N N 15.273 5.366 20.071 -3.347 -2.040 -0.224 N01 PUP 1
PUP N N N 0 1 N N N 15.767 7.525 20.976 -4.615 -3.934 -0.765 N PUP 2
PUP C01 C01 C 0 1 N N N 13.735 2.439 17.805 0.052 0.969 0.672 C01 PUP 3
PUP C02 C02 C 0 1 N N R 15.103 2.338 18.323 -1.138 0.798 -0.274 C02 PUP 4
PUP C03 C03 C 0 1 N N S 15.106 1.811 19.720 -2.382 1.486 0.321 C03 PUP 5
PUP C04 C04 C 0 1 N N R 14.860 2.975 20.483 -3.425 0.348 0.438 C04 PUP 6
PUP C05 C05 C 0 1 N N R 15.666 3.975 19.785 -2.883 -0.695 -0.572 C05 PUP 7
PUP C06 C06 C 0 1 N N N 16.119 6.232 20.703 -4.173 -2.697 -1.059 C06 PUP 8
PUP C07 C07 C 0 1 N N N 14.537 8.001 20.621 -4.234 -4.537 0.379 C07 PUP 9
PUP C08 C08 C 0 1 N N N 13.616 7.137 19.958 -3.356 -3.862 1.262 C08 PUP 10
PUP C09 C09 C 0 1 N N N 14.024 5.804 19.696 -2.933 -2.620 0.944 C09 PUP 11
PUP C10 C10 C 0 1 N N N 10.344 -1.595 15.577 6.948 0.976 0.021 C10 PUP 12
PUP C11 C11 C 0 1 N N R 9.767 -0.607 16.550 6.062 -0.040 -0.701 C11 PUP 13
PUP C12 C12 C 0 1 N N S 10.639 -0.391 17.696 5.059 -0.660 0.292 C12 PUP 14
PUP C13 C13 C 0 1 N N S 10.365 -1.529 18.533 5.355 -2.178 0.232 C13 PUP 15
PUP C C C 0 1 N N N 8.972 -1.856 18.269 6.075 -2.315 -1.134 C PUP 16
PUP O01 O01 O 0 1 N N N 12.700 1.728 18.461 1.224 0.416 0.067 O01 PUP 17
PUP O02 O02 O 0 1 N N N 15.645 3.614 18.408 -1.450 -0.597 -0.421 O02 PUP 18
PUP O03 O03 O 0 1 N N N 16.401 1.348 20.038 -2.856 2.509 -0.557 O03 PUP 19
PUP O04 O04 O 0 1 N N N 15.322 2.804 21.783 -4.723 0.803 0.053 O04 PUP 20
PUP O05 O05 O 0 1 N N N 17.239 5.855 21.046 -4.525 -2.165 -2.095 O05 PUP 21
PUP O06 O06 O 0 1 N N N 14.177 9.332 20.903 -4.633 -5.656 0.646 O06 PUP 22
PUP O07 O07 O 0 1 N N N 15.532 -1.015 19.722 -4.048 4.216 1.049 O07 PUP 23
PUP O08 O08 O 0 1 N N N 17.901 -0.549 19.205 -1.639 4.521 0.361 O08 PUP 24
PUP O09 O09 O 0 1 N N N 17.114 -0.577 21.562 -3.404 4.940 -1.394 O09 PUP 25
PUP O10 O10 O 0 1 N N N 11.059 2.635 16.796 2.558 -0.220 2.113 O10 PUP 26
PUP O11 O11 O 0 1 N N N 10.758 3.166 19.170 3.172 1.939 0.959 O11 PUP 27
PUP O12 O12 O 0 1 N N N 9.536 -2.029 14.538 7.806 1.617 -0.925 O12 PUP 28
PUP O13 O13 O 0 1 N N N 8.599 -1.126 17.104 6.868 -1.112 -1.219 O13 PUP 29
PUP O14 O14 O 0 1 N N N 10.301 0.798 18.367 3.717 -0.395 -0.122 O14 PUP 30
PUP O O O 0 1 N N N 10.520 -1.191 19.863 4.143 -2.935 0.247 O PUP 31
PUP P01 P01 P 0 1 N N N 16.735 -0.227 20.132 -2.958 4.057 -0.124 P01 PUP 32
PUP P P P 0 1 N N N 11.207 2.105 18.202 2.665 0.421 0.784 P PUP 33
PUP H1 H1 H 0 1 N N N 16.416 8.128 21.440 -5.210 -4.392 -1.378 H1 PUP 34
PUP H2 H2 H 0 1 N N N 13.459 3.504 17.827 0.211 2.029 0.869 H2 PUP 35
PUP H3 H3 H 0 1 N N N 13.758 2.088 16.763 -0.151 0.451 1.609 H3 PUP 36
PUP H4 H4 H 0 1 N N N 15.708 1.686 17.676 -0.903 1.230 -1.247 H4 PUP 37
PUP H5 H5 H 0 1 N N N 14.333 1.041 19.860 -2.156 1.901 1.303 H5 PUP 38
PUP H6 H6 H 0 1 N N N 13.795 3.251 20.462 -3.443 -0.061 1.449 H6 PUP 39
PUP H7 H7 H 0 1 N N N 16.700 3.858 20.140 -3.182 -0.437 -1.588 H7 PUP 40
PUP H8 H8 H 0 1 N N N 12.637 7.487 19.664 -3.034 -4.332 2.179 H8 PUP 41
PUP H9 H9 H 0 1 N N N 13.347 5.126 19.197 -2.269 -2.086 1.609 H9 PUP 42
PUP H10 H10 H 0 1 N N N 10.644 -2.484 16.152 6.322 1.724 0.508 H10 PUP 43
PUP H11 H11 H 0 1 N N N 11.234 -1.131 15.128 7.552 0.464 0.770 H11 PUP 44
PUP H12 H12 H 0 1 N N N 9.573 0.346 16.036 5.527 0.448 -1.516 H12 PUP 45
PUP H13 H13 H 0 1 N N N 11.693 -0.384 17.381 5.231 -0.275 1.297 H13 PUP 46
PUP H14 H14 H 0 1 N N N 11.013 -2.374 18.257 6.010 -2.480 1.049 H14 PUP 47
PUP H15 H15 H 0 1 N N N 8.344 -1.558 19.121 6.715 -3.198 -1.144 H15 PUP 48
PUP H16 H16 H 0 1 N N N 8.862 -2.936 18.092 5.351 -2.358 -1.947 H16 PUP 49
PUP H17 H17 H 0 1 N N N 15.152 3.592 22.286 -5.411 0.126 0.110 H17 PUP 50
PUP H18 H18 H 0 1 N N N 15.747 -1.552 18.968 -4.938 3.930 0.801 H18 PUP 51
PUP H19 H19 H 0 1 N N N 17.998 -0.923 21.580 -3.485 5.886 -1.207 H19 PUP 52
PUP H20 H20 H 0 1 N N N 10.480 3.937 18.689 3.266 2.421 0.126 H20 PUP 53
PUP H21 H21 H 0 1 N N N 10.017 -2.646 13.999 8.398 2.276 -0.536 H21 PUP 54
PUP H22 H22 H 0 1 N N N 10.337 -1.949 20.406 4.277 -3.892 0.211 H22 PUP 55
#
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
PUP O12 C10 SING N N 1
PUP C10 C11 SING N N 2
PUP C11 O13 SING N N 3
PUP C11 C12 SING N N 4
PUP O10 P DOUB N N 5
PUP O13 C SING N N 6
PUP C12 O14 SING N N 7
PUP C12 C13 SING N N 8
PUP C01 C02 SING N N 9
PUP C01 O01 SING N N 10
PUP P O14 SING N N 11
PUP P O01 SING N N 12
PUP P O11 SING N N 13
PUP C C13 SING N N 14
PUP C02 O02 SING N N 15
PUP C02 C03 SING N N 16
PUP O02 C05 SING N N 17
PUP C13 O SING N N 18
PUP O08 P01 DOUB N N 19
PUP C09 C08 DOUB N N 20
PUP C09 N01 SING N N 21
PUP C03 O03 SING N N 22
PUP C03 C04 SING N N 23
PUP O07 P01 SING N N 24
PUP C05 N01 SING N N 25
PUP C05 C04 SING N N 26
PUP C08 C07 SING N N 27
PUP O03 P01 SING N N 28
PUP N01 C06 SING N N 29
PUP P01 O09 SING N N 30
PUP C04 O04 SING N N 31
PUP C07 O06 DOUB N N 32
PUP C07 N SING N N 33
PUP C06 N SING N N 34
PUP C06 O05 DOUB N N 35
PUP N H1 SING N N 36
PUP C01 H2 SING N N 37
PUP C01 H3 SING N N 38
PUP C02 H4 SING N N 39
PUP C03 H5 SING N N 40
PUP C04 H6 SING N N 41
PUP C05 H7 SING N N 42
PUP C08 H8 SING N N 43
PUP C09 H9 SING N N 44
PUP C10 H10 SING N N 45
PUP C10 H11 SING N N 46
PUP C11 H12 SING N N 47
PUP C12 H13 SING N N 48
PUP C13 H14 SING N N 49
PUP C H15 SING N N 50
PUP C H16 SING N N 51
PUP O04 H17 SING N N 52
PUP O07 H18 SING N N 53
PUP O09 H19 SING N N 54
PUP O11 H20 SING N N 55
PUP O12 H21 SING N N 56
PUP O H22 SING N N 57
#
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
PUP SMILES ACDLabs 12.01 "O=P(OC1C(O)COC1CO)(O)OCC3OC(N2C(=O)NC(=O)C=C2)C(O)C3OP(=O)(O)O"
PUP InChI InChI 1.03
"InChI=1S/C14H22N2O15P2/c17-3-7-11(6(18)4-27-7)31-33(25,26)28-5-8-12(30-32(22,23)24)10(20)13(29-8)16-2-1-9(19)15-14(16)21/h1-2,6-8,10-13,17-18,20H,3-5H2,(H,25,26)(H,15,19,21)(H2,22,23,24)/t6-,7+,8+,10+,11-,12+,13+/m0/s1"
PUP InChIKey InChI 1.03 CTEYAHSJKMGMOL-HHUJUQMJSA-N
PUP SMILES_CANONICAL CACTVS 3.385 "OC[C@H]1OC[C@H](O)[C@@H]1O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O[P](O)(O)=O)N3C=CC(=O)NC3=O"
PUP SMILES CACTVS 3.385 "OC[CH]1OC[CH](O)[CH]1O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O[P](O)(O)=O)N3C=CC(=O)NC3=O"
PUP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1[C@@H]([C@@H]([C@H](O1)CO)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)OP(=O)(O)O)O"
PUP SMILES "OpenEye OEToolkits" 1.7.6 "C1C(C(C(O1)CO)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)OP(=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
PUP "SYSTEMATIC NAME" ACDLabs 12.01
"(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-hydroxy-2-({[(S)-hydroxy{[(2R,3S,4S)-4-hydroxy-2-(hydroxymethyl)tetrahydrofuran-3-yl]oxy}phosphoryl]oxy}methyl)tetrahydrofuran-3-yl dihydrogen phosphate (non-preferred name)"
PUP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl [(2R,3S,4S)-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] hydrogen 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
PUP "Create component" 2014-03-04 RCSB
PUP "Initial release" 2014-03-12 RCSB
#