data_8ML
# 
_chem_comp.id                                    8ML 
_chem_comp.name                                  "2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methylidene-2-[(2S,3S,4R,5R)-1,2,3,4,5-pentakis(oxidanyl)-6-phosphonooxy-hexan-2-yl]-1,3-thiazolidin-5-yl]ethyl phosphono hydrogen phosphate" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C18 H33 N4 O16 P3 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2017-08-04 
_chem_comp.pdbx_modified_date                    2018-06-22 
_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                        686.458 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     8ML 
_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        5XTX 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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 
8ML O2A   O1  O 0 1 N N N -15.159 40.926 -23.934 -4.945 -1.742 -1.560 O2A 8ML 1  
8ML PA    P1  P 0 1 N N N -16.139 41.288 -22.914 -5.585 -0.842 -0.574 PA  8ML 2  
8ML O1A   O2  O 0 1 N N N -16.042 42.641 -22.370 -6.475 0.254  -1.347 O1A 8ML 3  
8ML O3A   O3  O 0 1 N N N -17.611 41.018 -23.498 -6.526 -1.704 0.407  O3A 8ML 4  
8ML PB    P2  P 0 1 N N N -19.018 41.685 -23.165 -7.531 -2.942 0.191  PB  8ML 5  
8ML O3B   O4  O 0 1 N N N -20.021 40.876 -23.799 -6.890 -3.952 -0.682 O3B 8ML 6  
8ML O2B   O5  O 0 1 N N N -18.973 43.089 -23.437 -7.879 -3.607 1.615  O2B 8ML 7  
8ML O1B   O6  O 0 1 N N N -19.214 41.547 -21.614 -8.887 -2.418 -0.502 O1B 8ML 8  
8ML O7    O7  O 0 1 N N N -16.066 40.291 -21.716 -4.448 -0.098 0.289  O7  8ML 9  
8ML C7    C1  C 0 1 N N N -15.899 38.920 -22.206 -3.392 0.661  -0.304 C7  8ML 10 
8ML C6    C2  C 0 1 N N N -15.802 37.996 -21.155 -2.493 1.230  0.795  C6  8ML 11 
8ML C5    C3  C 0 1 N N R -15.635 36.614 -21.595 -1.363 2.043  0.160  C5  8ML 12 
8ML S1    S1  S 0 1 N N N -16.795 35.886 -22.732 -0.128 0.943  -0.639 S1  8ML 13 
8ML C2    C4  C 0 1 N N S -16.282 34.282 -22.348 1.324  1.947  -0.144 C2  8ML 14 
8ML CF2   C5  C 0 1 N N S -17.224 33.056 -22.559 2.416  1.054  0.447  CF2 8ML 15 
8ML OF2   O8  O 0 1 N N N -16.467 31.887 -22.540 2.093  0.741  1.804  OF2 8ML 16 
8ML CF1   C6  C 0 1 N N N -17.912 33.245 -23.870 3.758  1.788  0.398  CF1 8ML 17 
8ML OF1   O9  O 0 1 N N N -17.004 33.145 -24.967 3.984  2.279  -0.924 OF1 8ML 18 
8ML CF3   C7  C 0 1 N N S -18.217 33.049 -21.399 2.512  -0.240 -0.365 CF3 8ML 19 
8ML OF3   O10 O 0 1 N N N -19.200 34.043 -21.522 2.819  0.074  -1.725 OF3 8ML 20 
8ML CF4   C8  C 0 1 N N R -18.901 31.742 -21.095 3.616  -1.125 0.216  CF4 8ML 21 
8ML OF4   O11 O 0 1 N N N -19.840 31.477 -22.161 4.893  -0.590 -0.140 OF4 8ML 22 
8ML CF5   C9  C 0 1 N N R -19.630 31.714 -19.764 3.483  -2.542 -0.347 CF5 8ML 23 
8ML OF5   O12 O 0 1 N N N -18.750 32.105 -18.734 2.206  -3.077 0.009  OF5 8ML 24 
8ML CF6   C10 C 0 1 N N N -20.201 30.332 -19.489 4.587  -3.428 0.234  CF6 8ML 25 
8ML OF6   O13 O 0 1 N N N -21.004 30.372 -18.300 4.534  -4.718 -0.379 OF6 8ML 26 
8ML PF    P3  P 0 1 N N N -21.514 29.173 -17.487 5.552  -5.908 -0.006 PF  8ML 27 
8ML OF8   O14 O 0 1 N N N -20.994 29.396 -16.051 5.322  -6.352 1.524  OF8 8ML 28 
8ML OF7   O15 O 0 1 N N N -23.006 29.148 -17.535 5.286  -7.165 -0.976 OF7 8ML 29 
8ML OF9   O16 O 0 1 N N N -20.929 27.938 -18.112 6.945  -5.437 -0.179 OF9 8ML 30 
8ML N3    N1  N 0 1 N N N -15.209 34.342 -21.460 0.802  2.865  0.877  N3  8ML 31 
8ML C4    C11 C 0 1 N N N -14.925 35.637 -20.954 -0.519 2.725  1.223  C4  8ML 32 
8ML CM4   C12 C 0 1 N N N -13.942 35.860 -19.937 -1.011 3.145  2.374  CM4 8ML 33 
8ML "C7'" C13 C 0 1 N N N -14.283 33.236 -21.206 1.653  3.883  1.499  C7, 8ML 34 
8ML "C5'" C14 C 0 1 Y N N -13.011 33.267 -21.971 1.720  5.095  0.606  C5, 8ML 35 
8ML "C4'" C15 C 0 1 Y N N -12.919 33.116 -23.410 0.687  6.035  0.596  C4, 8ML 36 
8ML "N4'" N2  N 0 1 N N N -13.985 32.991 -24.170 -0.424 5.867  1.407  N4, 8ML 37 
8ML "N3'" N3  N 0 1 Y N N -11.706 33.118 -24.052 0.787  7.093  -0.202 N3, 8ML 38 
8ML "C2'" C16 C 0 1 Y N N -10.598 33.192 -23.340 1.843  7.255  -0.974 C2, 8ML 39 
8ML CM2   C17 C 0 1 N N N -9.287  33.094 -23.969 1.920  8.469  -1.865 CM2 8ML 40 
8ML "N1'" N4  N 0 1 Y N N -10.631 33.343 -21.991 2.834  6.387  -0.988 N1, 8ML 41 
8ML "C6'" C18 C 0 1 Y N N -11.819 33.375 -21.312 2.806  5.307  -0.220 C6, 8ML 42 
8ML H1    H1  H 0 1 N N N -15.320 43.099 -22.785 -6.925 0.879  -0.762 H1  8ML 43 
8ML H2    H2  H 0 1 N N N -19.665 43.316 -24.047 -8.481 -4.362 1.561  H2  8ML 44 
8ML H3    H3  H 0 1 N N N -19.944 40.966 -21.437 -9.361 -1.753 0.015  H3  8ML 45 
8ML H4    H4  H 0 1 N N N -16.766 38.658 -22.831 -2.804 0.018  -0.958 H4  8ML 46 
8ML H5    H5  H 0 1 N N N -14.982 38.868 -22.811 -3.816 1.480  -0.886 H5  8ML 47 
8ML H6    H6  H 0 1 N N N -14.936 38.268 -20.533 -3.081 1.874  1.449  H6  8ML 48 
8ML H7    H7  H 0 1 N N N -16.720 38.059 -20.553 -2.069 0.411  1.377  H7  8ML 49 
8ML H8    H8  H 0 1 N N N -16.044 31.797 -21.694 1.253  0.274  1.910  H8  8ML 50 
8ML H9    H9  H 0 1 N N N -18.380 34.240 -23.886 3.741  2.623  1.099  H9  8ML 51 
8ML H10   H10 H 0 1 N N N -18.688 32.473 -23.979 4.558  1.100  0.673  H10 8ML 52 
8ML H11   H11 H 0 1 N N N -17.476 33.270 -25.782 4.819  2.756  -1.029 H11 8ML 53 
8ML H12   H12 H 0 1 N N N -17.626 33.292 -20.504 1.561  -0.769 -0.319 H12 8ML 54 
8ML H13   H13 H 0 1 N N N -19.791 33.998 -20.780 3.702  0.446  -1.853 H13 8ML 55 
8ML H14   H14 H 0 1 N N N -18.139 30.949 -21.083 3.525  -1.156 1.301  H14 8ML 56 
8ML H15   H15 H 0 1 N N N -20.287 30.655 -21.993 5.044  -0.534 -1.093 H15 8ML 57 
8ML H16   H16 H 0 1 N N N -20.468 32.424 -19.820 3.574  -2.512 -1.433 H16 8ML 58 
8ML H17   H17 H 0 1 N N N -19.208 32.087 -17.902 2.055  -3.133 0.962  H17 8ML 59 
8ML H18   H18 H 0 1 N N N -20.822 30.016 -20.340 5.558  -2.973 0.039  H18 8ML 60 
8ML H19   H19 H 0 1 N N N -19.377 29.616 -19.351 4.443  -3.530 1.309  H19 8ML 61 
8ML H20   H20 H 0 1 N N N -20.389 28.700 -15.821 4.429  -6.673 1.710  H20 8ML 62 
8ML H21   H21 H 0 1 N N N -23.296 28.347 -17.956 5.866  -7.921 -0.808 H21 8ML 63 
8ML H22   H22 H 0 1 N N N -13.388 35.027 -19.529 -2.078 3.145  2.538  H22 8ML 64 
8ML H23   H23 H 0 1 N N N -13.754 36.861 -19.578 -0.345 3.490  3.152  H23 8ML 65 
8ML H25   H25 H 0 1 N N N -14.802 32.298 -21.453 1.234  4.166  2.465  H25 8ML 66 
8ML H26   H26 H 0 1 N N N -14.033 33.245 -20.135 2.656  3.480  1.641  H26 8ML 67 
8ML H27   H27 H 0 1 N N N -13.706 32.916 -25.127 -0.390 5.253  2.156  H27 8ML 68 
8ML H28   H28 H 0 1 N N N -14.489 32.169 -23.905 -1.237 6.365  1.224  H28 8ML 69 
8ML H29   H29 H 0 1 N N N -9.409  32.959 -25.054 2.407  9.283  -1.328 H29 8ML 70 
8ML H30   H30 H 0 1 N N N -8.718  34.016 -23.776 2.495  8.227  -2.759 H30 8ML 71 
8ML H31   H31 H 0 1 N N N -8.744  32.234 -23.552 0.913  8.773  -2.151 H31 8ML 72 
8ML H32   H32 H 0 1 N N N -11.814 33.487 -20.238 3.626  4.603  -0.236 H32 8ML 73 
8ML H33   H33 H 0 1 N N N -14.877 36.830 -22.362 -1.759 2.769  -0.550 H33 8ML 74 
8ML H34   H34 H 0 1 N N N -15.690 34.136 -23.263 1.709  2.507  -0.997 H34 8ML 75 
# 
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 
8ML OF1   CF1   SING N N 1  
8ML "N4'" "C4'" SING N N 2  
8ML "N3'" "C4'" DOUB Y N 3  
8ML "N3'" "C2'" SING Y N 4  
8ML CM2   "C2'" SING N N 5  
8ML O2A   PA    DOUB N N 6  
8ML CF1   CF2   SING N N 7  
8ML O3B   PB    DOUB N N 8  
8ML O3A   PB    SING N N 9  
8ML O3A   PA    SING N N 10 
8ML O2B   PB    SING N N 11 
8ML "C4'" "C5'" SING Y N 12 
8ML "C2'" "N1'" DOUB Y N 13 
8ML PB    O1B   SING N N 14 
8ML PA    O1A   SING N N 15 
8ML PA    O7    SING N N 16 
8ML S1    C2    SING N N 17 
8ML S1    C5    SING N N 18 
8ML CF2   OF2   SING N N 19 
8ML CF2   C2    SING N N 20 
8ML CF2   CF3   SING N N 21 
8ML C2    N3    SING N N 22 
8ML C7    O7    SING N N 23 
8ML C7    C6    SING N N 24 
8ML OF4   CF4   SING N N 25 
8ML "N1'" "C6'" SING Y N 26 
8ML "C5'" "C6'" DOUB Y N 27 
8ML "C5'" "C7'" SING N N 28 
8ML C5    C6    SING N N 29 
8ML C5    C4    SING N N 30 
8ML OF3   CF3   SING N N 31 
8ML N3    "C7'" SING N N 32 
8ML N3    C4    SING N N 33 
8ML CF3   CF4   SING N N 34 
8ML CF4   CF5   SING N N 35 
8ML C4    CM4   DOUB N N 36 
8ML CF5   CF6   SING N N 37 
8ML CF5   OF5   SING N N 38 
8ML CF6   OF6   SING N N 39 
8ML OF6   PF    SING N N 40 
8ML OF9   PF    DOUB N N 41 
8ML OF7   PF    SING N N 42 
8ML PF    OF8   SING N N 43 
8ML O1A   H1    SING N N 44 
8ML O2B   H2    SING N N 45 
8ML O1B   H3    SING N N 46 
8ML C7    H4    SING N N 47 
8ML C7    H5    SING N N 48 
8ML C6    H6    SING N N 49 
8ML C6    H7    SING N N 50 
8ML OF2   H8    SING N N 51 
8ML CF1   H9    SING N N 52 
8ML CF1   H10   SING N N 53 
8ML OF1   H11   SING N N 54 
8ML CF3   H12   SING N N 55 
8ML OF3   H13   SING N N 56 
8ML CF4   H14   SING N N 57 
8ML OF4   H15   SING N N 58 
8ML CF5   H16   SING N N 59 
8ML OF5   H17   SING N N 60 
8ML CF6   H18   SING N N 61 
8ML CF6   H19   SING N N 62 
8ML OF8   H20   SING N N 63 
8ML OF7   H21   SING N N 64 
8ML CM4   H22   SING N N 65 
8ML CM4   H23   SING N N 66 
8ML "C7'" H25   SING N N 67 
8ML "C7'" H26   SING N N 68 
8ML "N4'" H27   SING N N 69 
8ML "N4'" H28   SING N N 70 
8ML CM2   H29   SING N N 71 
8ML CM2   H30   SING N N 72 
8ML CM2   H31   SING N N 73 
8ML "C6'" H32   SING N N 74 
8ML C5    H33   SING N N 75 
8ML C2    H34   SING N N 76 
# 
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 
8ML InChI            InChI                1.03  
;InChI=1S/C18H33N4O16P3S/c1-9-13(3-4-36-41(34,35)38-40(31,32)33)42-17(22(9)6-11-5-20-10(2)21-16(11)19)18(27,8-23)15(26)14(25)12(24)7-37-39(28,29)30/h5,12-15,17,23-27H,1,3-4,6-8H2,2H3,(H,34,35)(H2,19,20,21)(H2,28,29,30)(H2,31,32,33)/t12-,13-,14-,15+,17?,18+/m1/s1
;
8ML InChIKey         InChI                1.03  MJHVDDPQXKRRMA-OYVLIZFGSA-N 
8ML SMILES_CANONICAL CACTVS               3.385 "Cc1ncc(CN2[C@@H](S[C@H](CCO[P](O)(=O)O[P](O)(O)=O)C2=C)[C@](O)(CO)[C@@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c(N)n1" 
8ML SMILES           CACTVS               3.385 "Cc1ncc(CN2[CH](S[CH](CCO[P](O)(=O)O[P](O)(O)=O)C2=C)[C](O)(CO)[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c(N)n1" 
8ML SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "Cc1ncc(c(n1)N)CN2C(SC(C2=C)CCOP(=O)(O)OP(=O)(O)O)[C@](CO)([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)O" 
8ML SMILES           "OpenEye OEToolkits" 2.0.6 "Cc1ncc(c(n1)N)CN2C(SC(C2=C)CCOP(=O)(O)OP(=O)(O)O)C(CO)(C(C(C(COP(=O)(O)O)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 
8ML "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methylidene-2-[(2~{S},3~{S},4~{R},5~{R})-1,2,3,4,5-pentakis(oxidanyl)-6-phosphonooxy-hexan-2-yl]-1,3-thiazolidin-5-yl]ethyl phosphono 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 
8ML "Create component" 2017-08-04 PDBJ 
8ML "Initial release"  2018-06-27 RCSB 
# 
