data_T5K
#
_chem_comp.id T5K
_chem_comp.name
;[[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4S,5R,6R)-6-methyl-5-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3,4-bis(oxidanyl)oxan-2-yl] hydrogen phosphate
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C24 H35 N4 O19 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2014-09-17
_chem_comp.pdbx_modified_date 2015-04-15
_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 776.471
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code T5K
_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 4ZAH
_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
T5K C01 C1 C 0 1 N N N -180.913 368.368 65.096 -2.760 -0.416 2.214 C01 T5K 1
T5K C02 C2 C 0 1 N N R -182.181 367.986 64.393 -2.122 -0.940 0.926 C02 T5K 2
T5K O03 O1 O 0 1 N N N -182.107 366.496 64.119 -2.157 -2.368 0.923 O03 T5K 3
T5K C04 C3 C 0 1 N N R -183.342 366.034 63.483 -1.560 -2.964 -0.230 C04 T5K 4
T5K O12 O2 O 0 1 N N N -185.583 368.496 69.038 -6.052 -2.658 -0.027 O12 T5K 5
T5K C14 C4 C 0 1 N N N -185.850 367.967 71.814 -8.748 -3.482 0.174 C14 T5K 6
T5K C17 C5 C 0 1 Y N N -182.000 368.357 69.933 -7.674 0.617 0.035 C17 T5K 7
T5K C18 C6 C 0 1 N N N -180.571 368.471 69.299 -7.353 2.089 -0.004 C18 T5K 8
T5K O26 O3 O 0 1 N N N -183.465 366.736 62.296 -0.194 -2.556 -0.325 O26 T5K 9
T5K O29 O4 O 0 1 N N N -183.462 366.530 59.628 2.389 -2.557 0.161 O29 T5K 10
T5K O31 O5 O 0 1 N N N -185.723 366.862 58.382 4.269 -4.064 0.914 O31 T5K 11
T5K C34 C7 C 0 1 N N R -184.982 362.521 58.303 7.016 -0.928 -0.825 C34 T5K 12
T5K C36 C8 C 0 1 N N R -185.564 360.790 59.870 7.646 1.249 -1.298 C36 T5K 13
T5K C38 C9 C 0 1 N N N -185.438 361.810 62.151 7.729 3.697 -1.254 C38 T5K 14
T5K C39 C10 C 0 1 N N N -185.269 361.646 63.597 7.867 4.862 -0.585 C39 T5K 15
T5K O43 O6 O 0 1 N N N -185.187 358.289 61.075 8.054 1.433 1.343 O43 T5K 16
T5K O44 O7 O 0 1 N N N -184.952 360.102 65.297 8.211 5.869 1.439 O44 T5K 17
T5K C45 C11 C 0 1 N N N -185.294 362.849 64.487 7.790 6.177 -1.317 C45 T5K 18
T5K C47 C12 C 0 1 N N S -186.335 362.460 58.299 8.542 -0.894 -0.558 C47 T5K 19
T5K O50 O8 O 0 1 N N N -181.257 367.083 60.869 0.743 -3.534 1.805 O50 T5K 20
T5K C05 C13 C 0 1 N N R -184.539 366.330 64.334 -2.316 -2.516 -1.484 C05 T5K 21
T5K C06 C14 C 0 1 N N S -184.687 367.802 64.592 -2.293 -0.986 -1.564 C06 T5K 22
T5K C07 C15 C 0 1 N N R -183.439 368.402 65.149 -2.900 -0.409 -0.281 C07 T5K 23
T5K N08 N1 N 0 1 N N N -183.508 368.047 66.664 -4.303 -0.818 -0.177 N08 T5K 24
T5K C09 C16 C 0 1 N N N -183.035 368.795 67.597 -5.235 0.077 -0.126 C09 T5K 25
T5K C10 C17 C 0 1 Y N N -183.142 368.490 69.146 -6.649 -0.335 -0.022 C10 T5K 26
T5K C11 C18 C 0 1 Y N N -184.396 368.378 69.764 -7.004 -1.692 0.024 C11 T5K 27
T5K C13 C19 C 0 1 Y N N -184.456 368.111 71.136 -8.347 -2.030 0.123 C13 T5K 28
T5K N15 N2 N 0 1 Y N N -183.360 367.994 71.856 -9.275 -1.097 0.174 N15 T5K 29
T5K C16 C20 C 0 1 Y N N -182.156 368.117 71.277 -8.981 0.189 0.133 C16 T5K 30
T5K O19 O9 O 0 1 N N N -180.257 369.847 69.260 -8.565 2.843 0.074 O19 T5K 31
T5K P20 P1 P 0 1 N N N -178.938 370.318 68.457 -8.599 4.452 0.058 P20 T5K 32
T5K O21 O10 O 0 1 N N N -179.197 371.870 68.398 -10.127 4.957 0.029 O21 T5K 33
T5K O22 O11 O 0 1 N N N -177.677 369.787 69.118 -7.872 5.017 1.379 O22 T5K 34
T5K O23 O12 O 0 1 N N N -178.869 369.724 67.078 -7.892 4.949 -1.144 O23 T5K 35
T5K O24 O13 O 0 1 N N N -185.768 367.904 65.546 -3.058 -0.555 -2.691 O24 T5K 36
T5K O25 O14 O 0 1 N N N -185.702 365.915 63.597 -1.686 -3.064 -2.643 O25 T5K 37
T5K P27 P2 P 0 1 N N N -182.533 366.267 60.972 1.014 -3.370 0.359 P27 T5K 38
T5K O28 O15 O 0 1 N N N -182.191 364.801 61.068 1.143 -4.819 -0.330 O28 T5K 39
T5K P30 P3 P 0 1 N N N -185.118 366.226 59.625 3.849 -2.647 0.834 P30 T5K 40
T5K O32 O16 O 0 1 N N N -185.296 364.534 59.561 4.905 -1.825 -0.062 O32 T5K 41
T5K C33 C21 C 0 1 N N N -184.473 363.846 58.615 6.307 -1.800 0.214 C33 T5K 42
T5K O35 O17 O 0 1 N N N -184.505 361.411 59.447 6.618 0.453 -0.686 O35 T5K 43
T5K N37 N3 N 0 1 N N N -185.414 360.625 61.275 7.796 2.513 -0.572 N37 T5K 44
T5K C40 C22 C 0 1 N N N -185.089 360.297 64.138 8.084 4.831 0.814 C40 T5K 45
T5K N41 N4 N 0 1 N N N -185.050 359.155 63.296 8.149 3.643 1.448 N41 T5K 46
T5K C42 C23 C 0 1 N N N -185.217 359.221 61.777 7.998 2.497 0.758 C42 T5K 47
T5K C46 C24 C 0 1 N N N -186.798 361.793 59.609 8.957 0.442 -1.222 C46 T5K 48
T5K O48 O18 O 0 1 N N N -186.853 361.644 57.185 9.195 -1.999 -1.185 O48 T5K 49
T5K O49 O19 O 0 1 N N N -185.821 366.779 60.863 3.797 -2.019 2.315 O49 T5K 50
T5K H1 H1 H 0 1 N N N -180.925 369.446 65.315 -3.795 -0.755 2.272 H1 T5K 51
T5K H2 H2 H 0 1 N N N -180.831 367.804 66.037 -2.206 -0.794 3.074 H2 T5K 52
T5K H3 H3 H 0 1 N N N -180.052 368.134 64.452 -2.734 0.674 2.216 H3 T5K 53
T5K H4 H4 H 0 1 N N N -182.194 368.502 63.421 -1.088 -0.601 0.869 H4 T5K 54
T5K H5 H5 H 0 1 N N N -183.284 364.951 63.298 -1.610 -4.050 -0.145 H5 T5K 55
T5K H6 H6 H 0 1 N N N -186.324 368.392 69.623 -5.714 -2.924 0.839 H6 T5K 56
T5K H7 H7 H 0 1 N N N -185.717 367.771 72.888 -8.773 -3.816 1.211 H7 T5K 57
T5K H8 H8 H 0 1 N N N -186.421 368.897 71.679 -9.736 -3.602 -0.271 H8 T5K 58
T5K H9 H9 H 0 1 N N N -186.397 367.131 71.354 -8.024 -4.078 -0.383 H9 T5K 59
T5K H10 H10 H 0 1 N N N -180.572 368.053 68.282 -6.712 2.344 0.839 H10 T5K 60
T5K H11 H11 H 0 1 N N N -179.838 367.931 69.916 -6.839 2.324 -0.936 H11 T5K 61
T5K H12 H12 H 0 1 N N N -184.569 362.186 57.340 6.808 -1.289 -1.832 H12 T5K 62
T5K H13 H13 H 0 1 N N N -185.759 359.834 59.362 7.391 1.447 -2.339 H13 T5K 63
T5K H14 H14 H 0 1 N N N -185.579 362.794 61.729 7.562 3.701 -2.321 H14 T5K 64
T5K H15 H15 H 0 1 N N N -185.153 362.536 65.532 6.756 6.523 -1.334 H15 T5K 65
T5K H16 H16 H 0 1 N N N -184.485 363.536 64.198 8.411 6.914 -0.807 H16 T5K 66
T5K H17 H17 H 0 1 N N N -186.263 363.360 64.385 8.146 6.046 -2.338 H17 T5K 67
T5K H18 H18 H 0 1 N N N -186.776 363.466 58.247 8.750 -0.877 0.512 H18 T5K 68
T5K H19 H19 H 0 1 N N N -184.466 365.787 65.288 -3.348 -2.862 -1.431 H19 T5K 69
T5K H20 H20 H 0 1 N N N -184.956 368.313 63.656 -1.264 -0.642 -1.666 H20 T5K 70
T5K H21 H21 H 0 1 N N N -183.526 369.496 65.069 -2.838 0.678 -0.305 H21 T5K 71
T5K H22 H22 H 0 1 N N N -182.526 369.700 67.301 -4.980 1.126 -0.161 H22 T5K 72
T5K H23 H23 H 0 1 N N N -181.273 368.024 71.892 -9.777 0.917 0.181 H23 T5K 73
T5K H24 H24 H 0 1 N N N -179.262 372.146 67.491 -10.224 5.919 0.019 H24 T5K 74
T5K H25 H25 H 0 1 N N N -177.202 369.242 68.502 -8.283 4.731 2.207 H25 T5K 75
T5K H26 H26 H 0 1 N N N -185.919 368.818 65.758 -2.733 -0.889 -3.538 H26 T5K 76
T5K H27 H27 H 0 1 N N N -186.482 366.090 64.111 -1.660 -4.030 -2.657 H27 T5K 77
T5K H28 H28 H 0 1 N N N -181.247 364.693 61.044 1.322 -4.788 -1.280 H28 T5K 78
T5K H29 H29 H 0 1 N N N -183.460 363.747 59.033 6.704 -2.814 0.170 H29 T5K 79
T5K H30 H30 H 0 1 N N N -184.431 364.436 57.688 6.474 -1.388 1.209 H30 T5K 80
T5K H31 H31 H 0 1 N N N -184.906 358.260 63.718 8.298 3.614 2.406 H31 T5K 81
T5K H32 H32 H 0 1 N N N -186.907 362.525 60.423 9.354 0.264 -2.221 H32 T5K 82
T5K H33 H33 H 0 1 N N N -187.745 361.249 59.477 9.690 0.963 -0.605 H33 T5K 83
T5K H34 H34 H 0 1 N N N -187.802 361.627 57.219 10.151 -2.021 -1.046 H34 T5K 84
T5K H35 H35 H 0 1 N N N -186.487 367.402 60.598 3.529 -1.090 2.339 H35 T5K 85
#
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
T5K O48 C47 SING N N 1
T5K C47 C34 SING N N 2
T5K C47 C46 SING N N 3
T5K C34 C33 SING N N 4
T5K C34 O35 SING N N 5
T5K O31 P30 DOUB N N 6
T5K C33 O32 SING N N 7
T5K O35 C36 SING N N 8
T5K O32 P30 SING N N 9
T5K C46 C36 SING N N 10
T5K P30 O29 SING N N 11
T5K P30 O49 SING N N 12
T5K O29 P27 SING N N 13
T5K C36 N37 SING N N 14
T5K O50 P27 DOUB N N 15
T5K P27 O28 SING N N 16
T5K P27 O26 SING N N 17
T5K O43 C42 DOUB N N 18
T5K N37 C42 SING N N 19
T5K N37 C38 SING N N 20
T5K C42 N41 SING N N 21
T5K C38 C39 DOUB N N 22
T5K O26 C04 SING N N 23
T5K N41 C40 SING N N 24
T5K C04 O03 SING N N 25
T5K C04 C05 SING N N 26
T5K C39 C40 SING N N 27
T5K C39 C45 SING N N 28
T5K O25 C05 SING N N 29
T5K O03 C02 SING N N 30
T5K C40 O44 DOUB N N 31
T5K C05 C06 SING N N 32
T5K C02 C01 SING N N 33
T5K C02 C07 SING N N 34
T5K C06 C07 SING N N 35
T5K C06 O24 SING N N 36
T5K C07 N08 SING N N 37
T5K N08 C09 DOUB N N 38
T5K O23 P20 DOUB N N 39
T5K C09 C10 SING N N 40
T5K O21 P20 SING N N 41
T5K P20 O22 SING N N 42
T5K P20 O19 SING N N 43
T5K O12 C11 SING N N 44
T5K C10 C11 DOUB Y N 45
T5K C10 C17 SING Y N 46
T5K O19 C18 SING N N 47
T5K C18 C17 SING N N 48
T5K C11 C13 SING Y N 49
T5K C17 C16 DOUB Y N 50
T5K C13 C14 SING N N 51
T5K C13 N15 DOUB Y N 52
T5K C16 N15 SING Y N 53
T5K C01 H1 SING N N 54
T5K C01 H2 SING N N 55
T5K C01 H3 SING N N 56
T5K C02 H4 SING N N 57
T5K C04 H5 SING N N 58
T5K O12 H6 SING N N 59
T5K C14 H7 SING N N 60
T5K C14 H8 SING N N 61
T5K C14 H9 SING N N 62
T5K C18 H10 SING N N 63
T5K C18 H11 SING N N 64
T5K C34 H12 SING N N 65
T5K C36 H13 SING N N 66
T5K C38 H14 SING N N 67
T5K C45 H15 SING N N 68
T5K C45 H16 SING N N 69
T5K C45 H17 SING N N 70
T5K C47 H18 SING N N 71
T5K C05 H19 SING N N 72
T5K C06 H20 SING N N 73
T5K C07 H21 SING N N 74
T5K C09 H22 SING N N 75
T5K C16 H23 SING N N 76
T5K O21 H24 SING N N 77
T5K O22 H25 SING N N 78
T5K O24 H26 SING N N 79
T5K O25 H27 SING N N 80
T5K O28 H28 SING N N 81
T5K C33 H29 SING N N 82
T5K C33 H30 SING N N 83
T5K N41 H31 SING N N 84
T5K C46 H32 SING N N 85
T5K C46 H33 SING N N 86
T5K O48 H34 SING N N 87
T5K O49 H35 SING N N 88
#
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
T5K SMILES ACDLabs 12.01 "CC1C(C(C(C(O1)OP(OP(=O)(O)OCC3OC(N2C=C(C(=O)NC2=O)C)CC3O)(=O)O)O)O)\N=C\c4c(cnc(C)c4O)COP(O)(O)=O"
T5K InChI InChI 1.03
;InChI=1S/C24H35N4O19P3/c1-10-7-28(24(34)27-22(10)33)17-4-15(29)16(45-17)9-43-49(38,39)47-50(40,41)46-23-21(32)20(31)18(12(3)44-23)26-6-14-13(8-42-48(35,36)37)5-25-11(2)19(14)30/h5-7,12,15-18,20-21,23,29-32H,4,8-9H2,1-3H3,(H,38,39)(H,40,41)(H,27,33,34)(H2,35,36,37)/b26-6+/t12-,15+,16-,17-,18+,20+,21-,23-/m1/s1
;
T5K InChIKey InChI 1.03 LEIRFGMKEVPNBT-QBLVGKJYSA-N
T5K SMILES_CANONICAL CACTVS 3.385 "C[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@@H](O)[C@H]1N=Cc4c(O)c(C)ncc4CO[P](O)(O)=O"
T5K SMILES CACTVS 3.385 "C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH](O)[CH]1N=Cc4c(O)c(C)ncc4CO[P](O)(O)=O"
T5K SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)O)OP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H](C[C@@H](O3)N4C=C(C(=O)NC4=O)C)O)C)O"
T5K SMILES "OpenEye OEToolkits" 1.9.2 "Cc1c(c(c(cn1)COP(=O)(O)O)C=NC2C(OC(C(C2O)O)OP(=O)(O)OP(=O)(O)OCC3C(CC(O3)N4C=C(C(=O)NC4=O)C)O)C)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
T5K "SYSTEMATIC NAME" ACDLabs 12.01
;(2R,3R,4S,5R,6R)-3,4-dihydroxy-5-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
;
T5K "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2
;[[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4S,5R,6R)-6-methyl-5-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3,4-bis(oxidanyl)oxan-2-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
T5K "Create component" 2014-09-17 RCSB
T5K "Initial release" 2014-09-24 RCSB
T5K "Other modification" 2015-04-15 RCSB
T5K "Modify name" 2015-04-15 RCSB
#