data_7SG
#
_chem_comp.id 7SG
_chem_comp.name
"(2R,3R,4S,5R,6R)-3,5-dihydroxy-4-[(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)"
_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 2016-12-03
_chem_comp.pdbx_modified_date 2017-01-06
_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 7SG
_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 5U24
_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.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_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
7SG O2P O1 O 0 1 N N N N N N 20.538 0.135 6.649 2.893 5.155 1.089 O2P 7SG 1
7SG P P1 P 0 1 N N N N N N 20.153 1.307 7.539 4.060 4.896 1.960 P 7SG 2
7SG O3P O2 O 0 1 N N N N N N 21.336 2.172 7.886 4.805 6.286 2.288 O3P 7SG 3
7SG O1P O3 O 0 1 N N N N N N 19.016 2.166 7.039 3.565 4.216 3.333 O1P 7SG 4
7SG O4P O4 O 0 1 N N N N N N 19.613 0.757 8.945 5.082 3.904 1.209 O4P 7SG 5
7SG "C5'" C1 C 0 1 N N N N N N 18.724 -0.355 9.052 4.692 2.630 0.693 "C5'" 7SG 6
7SG C5P C2 C 0 1 Y N N N N N 17.943 -0.432 10.330 5.881 1.961 0.053 C5P 7SG 7
7SG C4P C3 C 0 1 Y N N N N N 16.977 0.635 10.635 5.756 0.695 -0.529 C4P 7SG 8
7SG "C4'" C4 C 0 1 N N N N N N 16.641 1.747 9.739 4.462 -0.015 -0.531 "C4'" 7SG 9
7SG C3P C5 C 0 1 Y N N N N N 16.243 0.422 11.890 6.897 0.119 -1.111 C3P 7SG 10
7SG "O3'" O5 O 0 1 N N N N N N 15.318 1.322 12.277 6.832 -1.107 -1.691 "O3'" 7SG 11
7SG C2P C6 C 0 1 Y N N N N N 16.536 -0.742 12.753 8.091 0.825 -1.085 C2P 7SG 12
7SG "C2'" C7 C 0 1 N N N N N N 15.741 -0.841 14.029 9.326 0.223 -1.705 "C2'" 7SG 13
7SG N1P N1 N 0 1 Y N N N N N 17.500 -1.632 12.393 8.158 2.015 -0.524 N1P 7SG 14
7SG C6P C8 C 0 1 Y N N N N N 18.136 -1.489 11.231 7.109 2.592 0.028 C6P 7SG 15
7SG O4 O6 O 0 1 N N N N N N 18.133 13.092 3.343 -6.997 2.820 -4.762 O4 7SG 16
7SG C4 C9 C 0 1 N N N N N N 17.113 13.145 4.075 -6.697 2.664 -3.592 C4 7SG 17
7SG N3 N2 N 0 1 N N N N N N 16.561 14.317 4.463 -7.036 1.529 -2.948 N3 7SG 18
7SG C2 C10 C 0 1 N N N N N N 15.473 14.387 5.235 -6.705 1.357 -1.655 C2 7SG 19
7SG O2 O7 O 0 1 N N N N N N 15.017 15.524 5.553 -7.017 0.328 -1.088 O2 7SG 20
7SG C5 C11 C 0 1 N N N N N N 16.506 11.878 4.523 -5.985 3.671 -2.896 C5 7SG 21
7SG C5M C12 C 0 1 N N N N N N 17.106 10.537 4.157 -5.589 4.947 -3.594 C5M 7SG 22
7SG C6 C13 C 0 1 N N N N N N 15.393 11.982 5.357 -5.666 3.473 -1.599 C6 7SG 23
7SG N1 N3 N 0 1 N N N N N N 14.879 13.190 5.687 -6.033 2.308 -0.981 N1 7SG 24
7SG "C1'" C14 C 0 1 N N R N N N 13.693 13.225 6.545 -5.686 2.093 0.426 "C1'" 7SG 25
7SG "O4'" O8 O 0 1 N N N N N N 13.903 12.380 7.668 -4.978 0.844 0.583 "O4'" 7SG 26
7SG C2H C15 C 0 1 N N N N N N 12.447 12.679 5.851 -6.965 1.931 1.276 C2H 7SG 27
7SG "C3'" C16 C 0 1 N N S N N N 11.681 12.002 6.962 -6.589 0.856 2.320 "C3'" 7SG 28
7SG O3H O9 O 0 1 N N N N N N 10.761 12.984 7.452 -6.675 1.391 3.643 O3H 7SG 29
7SG C4H C17 C 0 1 N N R N N N 12.701 11.741 8.069 -5.126 0.496 1.977 C4H 7SG 30
7SG C5H C18 C 0 1 N N N N N N 13.034 10.276 8.313 -4.884 -1.001 2.181 C5H 7SG 31
7SG "O5'" O10 O 0 1 N N N N N N 13.459 9.736 7.066 -3.517 -1.305 1.899 "O5'" 7SG 32
7SG PA P2 P 0 1 N N N N N N 12.732 8.486 6.390 -2.908 -2.792 2.011 PA 7SG 33
7SG O1A O11 O 0 1 N N N N N N 11.242 8.768 6.227 -2.957 -3.278 3.545 O1A 7SG 34
7SG O2A O12 O 0 1 N N N N N N 13.481 8.142 5.160 -3.706 -3.716 1.175 O2A 7SG 35
7SG O3A O13 O 0 1 N N N N N N 12.847 7.210 7.359 -1.382 -2.787 1.498 O3A 7SG 36
7SG PB P3 P 0 1 N N N N N N 11.818 6.619 8.453 -0.374 -3.928 0.977 PB 7SG 37
7SG O1B O14 O 0 1 N N N N N N 10.520 6.065 7.911 -1.079 -4.810 0.021 O1B 7SG 38
7SG O2B O15 O 0 1 N N N N N N 11.738 7.502 9.645 0.145 -4.799 2.228 O2B 7SG 39
7SG O3B O16 O 0 1 N N N N N N 12.846 5.438 8.877 0.884 -3.240 0.245 O3B 7SG 40
7SG O4Q O17 O 0 1 N N N N N N 15.449 2.172 7.093 3.664 -2.901 -3.195 O4Q 7SG 41
7SG C4Q C19 C 0 1 N N R N N N 15.421 3.441 7.744 2.648 -2.157 -2.521 C4Q 7SG 42
7SG C5Q C20 C 0 1 N N R N N N 14.593 4.412 6.940 1.345 -2.962 -2.513 C5Q 7SG 43
7SG O5Q O18 O 0 1 N N N N N N 13.213 4.057 7.100 1.543 -4.178 -1.788 O5Q 7SG 44
7SG C6Q C21 C 0 1 N N N N N N 14.753 4.501 5.439 0.936 -3.286 -3.951 C6Q 7SG 45
7SG C3Q C22 C 0 1 N N S N N N 14.967 3.431 9.206 3.082 -1.889 -1.077 C3Q 7SG 46
7SG N3Q N4 N 0 1 N N N N N N 15.547 2.349 9.993 4.367 -1.185 -1.075 N3Q 7SG 47
7SG C2Q C23 C 0 1 N N R N N N 13.468 3.166 9.298 3.229 -3.225 -0.343 C2Q 7SG 48
7SG O2Q O19 O 0 1 N N N N N N 13.033 3.326 10.632 3.564 -2.984 1.025 O2Q 7SG 49
7SG C1Q C24 C 0 1 N N R N N N 12.689 4.116 8.401 1.904 -3.989 -0.419 C1Q 7SG 50
7SG H1 H1 H 0 1 N N N N N N 22.118 1.819 7.477 4.247 6.933 2.742 H1 7SG 51
7SG H2 H2 H 0 1 N N N N N N 18.703 1.826 6.209 4.280 4.018 3.954 H2 7SG 52
7SG H3 H3 H 0 1 N N N N N N 18.008 -0.298 8.219 4.319 2.007 1.506 H3 7SG 53
7SG H4 H4 H 0 1 N N N N N N 19.319 -1.276 8.962 3.907 2.764 -0.052 H4 7SG 54
7SG H5 H5 H 0 1 N N N N N N 17.279 2.037 8.917 3.594 0.443 -0.080 H5 7SG 55
7SG H6 H6 H 0 1 N N N N N N 14.934 1.047 13.101 6.609 -1.087 -2.631 H6 7SG 56
7SG H7 H7 H 0 1 N N N N N N 16.065 -1.726 14.596 9.385 0.515 -2.753 H7 7SG 57
7SG H8 H8 H 0 1 N N N N N N 15.905 0.063 14.634 10.209 0.582 -1.177 H8 7SG 58
7SG H9 H9 H 0 1 N N N N N N 14.671 -0.932 13.788 9.276 -0.863 -1.633 H9 7SG 59
7SG H10 H10 H 0 1 N N N N N N 18.857 -2.247 10.962 7.212 3.571 0.472 H10 7SG 60
7SG H11 H11 H 0 1 N N N N N N 16.986 15.169 4.158 -7.521 0.833 -3.419 H11 7SG 61
7SG H12 H12 H 0 1 N N N N N N 16.497 9.731 4.593 -5.935 4.918 -4.627 H12 7SG 62
7SG H13 H13 H 0 1 N N N N N N 17.126 10.431 3.062 -6.043 5.796 -3.082 H13 7SG 63
7SG H14 H14 H 0 1 N N N N N N 18.132 10.475 4.550 -4.504 5.049 -3.576 H14 7SG 64
7SG H15 H15 H 0 1 N N N N N N 14.934 11.085 5.746 -5.122 4.229 -1.053 H15 7SG 65
7SG H16 H16 H 0 1 N N N N N N 13.498 14.257 6.871 -5.083 2.921 0.798 H16 7SG 66
7SG H17 H17 H 0 1 N N N N N N 11.856 13.495 5.409 -7.218 2.870 1.769 H17 7SG 67
7SG H18 H18 H 0 1 N N N N N N 12.720 11.957 5.067 -7.795 1.588 0.657 H18 7SG 68
7SG H19 H19 H 0 1 N N N N N N 11.194 11.075 6.626 -7.233 -0.017 2.219 H19 7SG 69
7SG H20 H20 H 0 1 N N N N N N 10.247 12.612 8.159 -7.562 1.689 3.889 H20 7SG 70
7SG H21 H21 H 0 1 N N N N N N 12.328 12.182 9.005 -4.438 1.079 2.589 H21 7SG 71
7SG H22 H22 H 0 1 N N N N N N 12.143 9.740 8.673 -5.111 -1.269 3.213 H22 7SG 72
7SG H23 H23 H 0 1 N N N N N N 13.840 10.190 9.057 -5.528 -1.568 1.508 H23 7SG 73
7SG H24 H24 H 0 1 N N N N N N 11.000 8.677 5.313 -2.454 -2.717 4.152 H24 7SG 74
7SG H25 H25 H 0 1 N N N N N N 10.830 7.596 9.910 0.617 -4.284 2.897 H25 7SG 75
7SG H26 H26 H 0 1 N N N N N N 15.972 1.565 7.604 3.455 -3.108 -4.117 H26 7SG 76
7SG H27 H27 H 0 1 N N N N N N 16.449 3.834 7.744 2.488 -1.210 -3.036 H27 7SG 77
7SG H28 H28 H 0 1 N N N N N N 14.752 5.418 7.356 0.560 -2.377 -2.034 H28 7SG 78
7SG H29 H29 H 0 1 N N N N N N 15.791 4.772 5.196 0.009 -3.860 -3.945 H29 7SG 79
7SG H30 H30 H 0 1 N N N N N N 14.513 3.528 4.986 0.786 -2.359 -4.504 H30 7SG 80
7SG H31 H31 H 0 1 N N N N N N 14.071 5.268 5.043 1.722 -3.870 -4.429 H31 7SG 81
7SG H32 H32 H 0 1 N N N N N N 15.196 4.404 9.666 2.329 -1.279 -0.577 H32 7SG 82
7SG H33 H33 H 0 1 N N N N N N 13.277 2.136 8.963 4.017 -3.814 -0.812 H33 7SG 83
7SG H34 H34 H 0 1 N N N N N N 13.517 2.735 11.196 3.673 -3.789 1.551 H34 7SG 84
7SG H35 H35 H 0 1 N N N N N N 11.628 3.827 8.407 2.016 -4.959 0.065 H35 7SG 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
7SG O4 C4 DOUB N N 1
7SG C4 N3 SING N N 2
7SG C4 C5 SING N N 3
7SG C5M C5 SING N N 4
7SG N3 C2 SING N N 5
7SG C5 C6 DOUB N N 6
7SG O2A PA DOUB N N 7
7SG C2 O2 DOUB N N 8
7SG C2 N1 SING N N 9
7SG C6 N1 SING N N 10
7SG C6Q C5Q SING N N 11
7SG N1 "C1'" SING N N 12
7SG C2H "C1'" SING N N 13
7SG C2H "C3'" SING N N 14
7SG O1A PA SING N N 15
7SG PA "O5'" SING N N 16
7SG PA O3A SING N N 17
7SG "C1'" "O4'" SING N N 18
7SG O2P P DOUB N N 19
7SG C5Q O5Q SING N N 20
7SG C5Q C4Q SING N N 21
7SG "C3'" O3H SING N N 22
7SG "C3'" C4H SING N N 23
7SG O1P P SING N N 24
7SG "O5'" C5H SING N N 25
7SG O4Q C4Q SING N N 26
7SG O5Q C1Q SING N N 27
7SG O3A PB SING N N 28
7SG P O3P SING N N 29
7SG P O4P SING N N 30
7SG "O4'" C4H SING N N 31
7SG C4Q C3Q SING N N 32
7SG O1B PB DOUB N N 33
7SG C4H C5H SING N N 34
7SG C1Q O3B SING N N 35
7SG C1Q C2Q SING N N 36
7SG PB O3B SING N N 37
7SG PB O2B SING N N 38
7SG O4P "C5'" SING N N 39
7SG "C5'" C5P SING N N 40
7SG C3Q C2Q SING N N 41
7SG C3Q N3Q SING N N 42
7SG C2Q O2Q SING N N 43
7SG "C4'" N3Q DOUB N N 44
7SG "C4'" C4P SING N N 45
7SG C5P C4P DOUB Y N 46
7SG C5P C6P SING Y N 47
7SG C4P C3P SING Y N 48
7SG C6P N1P DOUB Y N 49
7SG C3P "O3'" SING N N 50
7SG C3P C2P DOUB Y N 51
7SG N1P C2P SING Y N 52
7SG C2P "C2'" SING N N 53
7SG O3P H1 SING N N 54
7SG O1P H2 SING N N 55
7SG "C5'" H3 SING N N 56
7SG "C5'" H4 SING N N 57
7SG "C4'" H5 SING N N 58
7SG "O3'" H6 SING N N 59
7SG "C2'" H7 SING N N 60
7SG "C2'" H8 SING N N 61
7SG "C2'" H9 SING N N 62
7SG C6P H10 SING N N 63
7SG N3 H11 SING N N 64
7SG C5M H12 SING N N 65
7SG C5M H13 SING N N 66
7SG C5M H14 SING N N 67
7SG C6 H15 SING N N 68
7SG "C1'" H16 SING N N 69
7SG C2H H17 SING N N 70
7SG C2H H18 SING N N 71
7SG "C3'" H19 SING N N 72
7SG O3H H20 SING N N 73
7SG C4H H21 SING N N 74
7SG C5H H22 SING N N 75
7SG C5H H23 SING N N 76
7SG O1A H24 SING N N 77
7SG O2B H25 SING N N 78
7SG O4Q H26 SING N N 79
7SG C4Q H27 SING N N 80
7SG C5Q H28 SING N N 81
7SG C6Q H29 SING N N 82
7SG C6Q H30 SING N N 83
7SG C6Q H31 SING N N 84
7SG C3Q H32 SING N N 85
7SG C2Q H33 SING N N 86
7SG O2Q H34 SING N N 87
7SG C1Q 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
7SG SMILES ACDLabs 12.01 O=P(O)(OCc1c(c(O)c(C)nc1)\C=N\C4C(O)C(OC(OP(OP(OCC3OC(N2C(NC(=O)C(=C2)C)=O)CC3O)(O)=O)(O)=O)C4O)C)O
7SG 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)18(20(31)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
7SG InChIKey InChI 1.03 UJDWKFAFGYHSFM-QBLVGKJYSA-N
7SG 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](N=Cc4c(O)c(C)ncc4CO[P](O)(O)=O)[C@H]1O
7SG 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](N=Cc4c(O)c(C)ncc4CO[P](O)(O)=O)[CH]1O
7SG SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@H]2[C@H]([C@H](O[C@@H]([C@@H]2O)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)O
7SG SMILES "OpenEye OEToolkits" 2.0.6 Cc1c(c(c(cn1)COP(=O)(O)O)C=NC2C(C(OC(C2O)OP(=O)(O)OP(=O)(O)OCC3C(CC(O3)N4C=C(C(=O)NC4=O)C)O)C)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
7SG "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,3R,4S,5R,6R)-3,5-dihydroxy-4-[(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)"
7SG "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{S},5~{R},6~{R})-6-methyl-4-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3,5-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
7SG 'Create component' 2016-12-03 RCSB
7SG 'Initial release' 2017-01-11 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
7SG O2P O 2.989 -7.555 1
7SG P P 1.689 -8.304 2
7SG O3P O 0.940 -7.004 3
7SG O1P O 2.438 -9.603 4
7SG O4P O 0.389 -9.052 5
7SG "C5'" C -0.909 -8.301 6
7SG C5P C -2.209 -9.052 7
7SG C4P C -3.507 -8.298 8
7SG "C4'" C -3.506 -6.800 9
7SG C3P C -4.807 -9.050 10
7SG "O3'" O -6.105 -8.297 11
7SG C2P C -4.808 -10.548 12
7SG "C2'" C -6.108 -11.298 13
7SG N1P N -3.509 -11.301 14
7SG C6P C -2.210 -10.550 15
7SG O4 O 5.982 13.856 16
7SG C4 C 5.098 12.642 17
7SG N3 N 5.711 11.272 18
7SG C2 C 4.826 10.060 19
7SG O2 O 5.437 8.688 20
7SG C5 C 3.607 12.802 21
7SG C5M C 2.998 14.171 22
7SG C6 C 2.728 11.586 23
7SG N1 N 3.335 10.214 24
7SG "C1'" C 2.455 9.001 25
7SG "O4'" O 2.910 7.572 26
7SG C2H C 0.951 9.007 27
7SG "C3'" C 0.487 7.584 28
7SG O3H O -0.943 7.127 29
7SG C4H C 1.694 6.693 30
7SG C5H C 1.645 5.175 31
7SG "O5'" O 0.293 4.323 32
7SG PA P 0.531 2.831 33
7SG O1A O -0.939 2.434 34
7SG O2A O 1.951 3.240 35
7SG O3A O 1.122 1.410 36
7SG PB P 0.565 -0.034 37
7SG O1B O 1.998 -0.393 38
7SG O2B O -0.913 0.333 39
7SG O3B O 0.361 -1.576 40
7SG O4Q O -4.805 -4.549 41
7SG C4Q C -3.504 -3.798 42
7SG C5Q C -3.504 -2.301 43
7SG O5Q O -2.205 -1.549 44
7SG C6Q C -4.803 -1.549 45
7SG C3Q C -2.206 -4.552 46
7SG N3Q N -2.207 -6.051 47
7SG C2Q C -0.908 -3.801 48
7SG O2Q O 0.391 -4.554 49
7SG C1Q C -0.907 -2.302 50
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
7SG O4 C4 DOUBLE NONE 1
7SG C4 N3 SINGLE NONE 2
7SG C4 C5 SINGLE NONE 3
7SG C5M C5 SINGLE NONE 4
7SG N3 C2 SINGLE NONE 5
7SG C5 C6 DOUBLE NONE 6
7SG O2A PA DOUBLE NONE 7
7SG C2 O2 DOUBLE NONE 8
7SG C2 N1 SINGLE NONE 9
7SG C6 N1 SINGLE NONE 10
7SG C5Q C6Q SINGLE BEGINWEDGE 11
7SG "C1'" N1 SINGLE BEGINDASH 12
7SG C2H "C1'" SINGLE NONE 13
7SG C2H "C3'" SINGLE NONE 14
7SG PA O1A SINGLE BEGINDASH 15
7SG PA "O5'" SINGLE NONE 16
7SG PA O3A SINGLE NONE 17
7SG "C1'" "O4'" SINGLE NONE 18
7SG O2P P DOUBLE NONE 19
7SG C5Q O5Q SINGLE NONE 20
7SG C5Q C4Q SINGLE NONE 21
7SG "C3'" O3H SINGLE BEGINWEDGE 22
7SG "C3'" C4H SINGLE NONE 23
7SG O1P P SINGLE NONE 24
7SG "O5'" C5H SINGLE NONE 25
7SG C4Q O4Q SINGLE BEGINWEDGE 26
7SG O5Q C1Q SINGLE NONE 27
7SG O3A PB SINGLE NONE 28
7SG P O3P SINGLE NONE 29
7SG P O4P SINGLE NONE 30
7SG "O4'" C4H SINGLE NONE 31
7SG C4Q C3Q SINGLE NONE 32
7SG O1B PB DOUBLE NONE 33
7SG C4H C5H SINGLE BEGINDASH 34
7SG C1Q O3B SINGLE BEGINDASH 35
7SG C1Q C2Q SINGLE NONE 36
7SG PB O3B SINGLE NONE 37
7SG PB O2B SINGLE BEGINDASH 38
7SG O4P "C5'" SINGLE NONE 39
7SG "C5'" C5P SINGLE NONE 40
7SG C3Q C2Q SINGLE NONE 41
7SG C3Q N3Q SINGLE BEGINWEDGE 42
7SG C2Q O2Q SINGLE BEGINDASH 43
7SG "C4'" N3Q DOUBLE NONE 44
7SG "C4'" C4P SINGLE ENDDOWNRIGHT 45
7SG C5P C4P DOUBLE NONE 46
7SG C5P C6P SINGLE NONE 47
7SG C4P C3P SINGLE NONE 48
7SG C6P N1P DOUBLE NONE 49
7SG C3P "O3'" SINGLE NONE 50
7SG C3P C2P DOUBLE NONE 51
7SG N1P C2P SINGLE NONE 52
7SG C2P "C2'" SINGLE NONE 53
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
7SG MurckoScaffold S1 scaffold 'O=c1ccn([C@H]2CC[C@@H](CO[PH](=O)O[PH](=O)O[C@@H]3C[C@@H](/N=C/c4ccncc4)CCO3)O2)c(=O)[nH]1' InChI=1S/C20H26N4O9P2/c25-17-5-9-24(20(26)23-17)18-2-1-16(31-18)13-30-34(27)33-35(28)32-19-11-15(6-10-29-19)22-12-14-3-7-21-8-4-14/h3-5,7-9,12,15-16,18-19,34-35H,1-2,6,10-11,13H2,(H,23,25,26)/b22-12+/t15-,16-,18+,19+/m0/s1 OBXAHNLFXPFEOH-PYAVRWBGSA-N
7SG deoxyribose F1 fragment 'OCC1OC[CH2]C1O' InChI=1S/C5H10O3/c6-3-5-4(7)1-2-8-5/h4-7H,1-3H2 NSMOSDAEGJTOIQ-UHFFFAOYSA-N
7SG phosphate F2 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
7SG pyranose F3 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N
7SG pyridine F4 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
7SG pyrimidine F5 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
7SG C5P S1 1
7SG C4P S1 1
7SG "C4'" S1 1
7SG C3P S1 1
7SG C2P S1 1
7SG N1P S1 1
7SG C6P S1 1
7SG O4 S1 1
7SG C4 S1 1
7SG N3 S1 1
7SG C2 S1 1
7SG O2 S1 1
7SG C5 S1 1
7SG C6 S1 1
7SG N1 S1 1
7SG "C1'" S1 1
7SG "O4'" S1 1
7SG C2H S1 1
7SG "C3'" S1 1
7SG C4H S1 1
7SG C5H S1 1
7SG "O5'" S1 1
7SG PA S1 1
7SG O2A S1 1
7SG O3A S1 1
7SG PB S1 1
7SG O1B S1 1
7SG O3B S1 1
7SG C4Q S1 1
7SG C5Q S1 1
7SG O5Q S1 1
7SG C3Q S1 1
7SG N3Q S1 1
7SG C2Q S1 1
7SG C1Q S1 1
7SG "C1'" F1 1
7SG C2H F1 1
7SG "C3'" F1 1
7SG O3H F1 1
7SG C4H F1 1
7SG "O4'" F1 1
7SG C5H F1 1
7SG "O5'" F1 1
7SG O3P F2 1
7SG P F2 1
7SG O2P F2 1
7SG O1P F2 1
7SG O4P F2 1
7SG "O5'" F2 2
7SG PA F2 2
7SG O2A F2 2
7SG O1A F2 2
7SG O3A F2 2
7SG O3A F2 3
7SG PB F2 3
7SG O1B F2 3
7SG O3B F2 3
7SG O2B F2 3
7SG C4Q F3 1
7SG C5Q F3 1
7SG O5Q F3 1
7SG C1Q F3 1
7SG C2Q F3 1
7SG C3Q F3 1
7SG O3B F3 1
7SG C2P F4 1
7SG C3P F4 1
7SG C4P F4 1
7SG C5P F4 1
7SG C6P F4 1
7SG N1P F4 1
7SG C5 F5 1
7SG C4 F5 1
7SG N3 F5 1
7SG C2 F5 1
7SG N1 F5 1
7SG C6 F5 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 7SG
_pdbe_chem_comp_rdkit_properties.exactmw 776.111
_pdbe_chem_comp_rdkit_properties.amw 776.475
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 23
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 9
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 24
_pdbe_chem_comp_rdkit_properties.NumHBD 9
_pdbe_chem_comp_rdkit_properties.NumHBA 22
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 50
_pdbe_chem_comp_rdkit_properties.NumAtoms 85
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 26
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.583
_pdbe_chem_comp_rdkit_properties.NumRings 4
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 4
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 10
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 330.648
_pdbe_chem_comp_rdkit_properties.tpsa 348.540
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.165
_pdbe_chem_comp_rdkit_properties.CrippenMR 162.111
_pdbe_chem_comp_rdkit_properties.chi0v 25.570
_pdbe_chem_comp_rdkit_properties.chi1v 15.989
_pdbe_chem_comp_rdkit_properties.chi2v 7.446
_pdbe_chem_comp_rdkit_properties.chi3v 7.446
_pdbe_chem_comp_rdkit_properties.chi4v 4.850
_pdbe_chem_comp_rdkit_properties.chi0n 57.887
_pdbe_chem_comp_rdkit_properties.chi1n 28.320
_pdbe_chem_comp_rdkit_properties.chi2n 4.827
_pdbe_chem_comp_rdkit_properties.chi3n 4.827
_pdbe_chem_comp_rdkit_properties.chi4n 2.882
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.530
_pdbe_chem_comp_rdkit_properties.kappa1 14.033
_pdbe_chem_comp_rdkit_properties.kappa2 15.603
_pdbe_chem_comp_rdkit_properties.kappa3 10.076
_pdbe_chem_comp_rdkit_properties.Phi 4.379
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
7SG UniChem PDBe 7SG
7SG UniChem ZINC ZINC000584905450
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
7SG O2P -9.555 -0.104 -3.489 ETKDGv3 1
7SG P -8.713 -0.243 -2.241 ETKDGv3 2
7SG O3P -7.196 0.454 -2.525 ETKDGv3 3
7SG O1P -8.535 -1.888 -1.879 ETKDGv3 4
7SG O4P -9.499 0.571 -0.962 ETKDGv3 5
7SG "C5'" -8.826 0.315 0.252 ETKDGv3 6
7SG C5P -7.686 1.293 0.459 ETKDGv3 7
7SG C4P -6.361 0.966 0.464 ETKDGv3 8
7SG "C4'" -5.894 -0.431 0.221 ETKDGv3 9
7SG C3P -5.355 2.059 0.698 ETKDGv3 10
7SG "O3'" -3.991 1.747 0.731 ETKDGv3 11
7SG C2P -5.779 3.331 0.875 ETKDGv3 12
7SG "C2'" -4.827 4.467 1.108 ETKDGv3 13
7SG N1P -7.181 3.625 0.844 ETKDGv3 14
7SG C6P -8.076 2.707 0.655 ETKDGv3 15
7SG O4 8.340 4.727 -0.349 ETKDGv3 16
7SG C4 8.196 3.510 -0.054 ETKDGv3 17
7SG N3 6.883 2.966 0.079 ETKDGv3 18
7SG C2 6.723 1.593 0.432 ETKDGv3 19
7SG O2 5.563 1.123 0.584 ETKDGv3 20
7SG C5 9.374 2.646 0.166 ETKDGv3 21
7SG C5M 10.760 3.227 0.090 ETKDGv3 22
7SG C6 9.201 1.358 0.509 ETKDGv3 23
7SG N1 7.890 0.765 0.619 ETKDGv3 24
7SG "C1'" 7.784 -0.648 1.018 ETKDGv3 25
7SG "O4'" 6.763 -1.296 0.296 ETKDGv3 26
7SG C2H 7.488 -0.777 2.501 ETKDGv3 27
7SG "C3'" 6.726 -2.075 2.577 ETKDGv3 28
7SG O3H 7.562 -3.140 2.962 ETKDGv3 29
7SG C4H 6.189 -2.268 1.147 ETKDGv3 30
7SG C5H 4.662 -2.144 1.097 ETKDGv3 31
7SG "O5'" 4.229 -2.297 -0.235 ETKDGv3 32
7SG PA 2.544 -2.040 -0.288 ETKDGv3 33
7SG O1A 2.033 -2.222 -1.892 ETKDGv3 34
7SG O2A 1.850 -3.075 0.572 ETKDGv3 35
7SG O3A 2.196 -0.472 0.283 ETKDGv3 36
7SG PB 0.568 -0.137 -0.077 ETKDGv3 37
7SG O1B 0.427 0.118 -1.563 ETKDGv3 38
7SG O2B 0.123 1.260 0.770 ETKDGv3 39
7SG O3B -0.430 -1.434 0.427 ETKDGv3 40
7SG O4Q -5.261 -2.138 -2.104 ETKDGv3 41
7SG C4Q -4.027 -2.393 -1.484 ETKDGv3 42
7SG C5Q -2.873 -1.635 -2.198 ETKDGv3 43
7SG O5Q -1.635 -1.767 -1.511 ETKDGv3 44
7SG C6Q -3.188 -0.172 -2.561 ETKDGv3 45
7SG C3Q -4.098 -2.076 0.027 ETKDGv3 46
7SG N3Q -4.635 -0.737 0.282 ETKDGv3 47
7SG C2Q -2.694 -2.179 0.641 ETKDGv3 48
7SG O2Q -2.282 -3.524 0.640 ETKDGv3 49
7SG C1Q -1.705 -1.316 -0.166 ETKDGv3 50
7SG H1 -6.816 -0.062 -3.281 ETKDGv3 51
7SG H2 -8.089 -2.276 -2.673 ETKDGv3 52
7SG H3 -8.580 -0.754 0.397 ETKDGv3 53
7SG H4 -9.557 0.500 1.068 ETKDGv3 54
7SG H5 -6.588 -1.213 -0.038 ETKDGv3 55
7SG H6 -3.257 2.429 0.880 ETKDGv3 56
7SG H7 -4.244 4.293 2.036 ETKDGv3 57
7SG H8 -4.140 4.572 0.242 ETKDGv3 58
7SG H9 -5.387 5.419 1.224 ETKDGv3 59
7SG H10 -9.122 2.988 0.642 ETKDGv3 60
7SG H11 6.045 3.572 -0.069 ETKDGv3 61
7SG H12 11.519 2.441 -0.110 ETKDGv3 62
7SG H13 10.821 3.971 -0.733 ETKDGv3 63
7SG H14 11.003 3.728 1.050 ETKDGv3 64
7SG H15 10.073 0.744 0.707 ETKDGv3 65
7SG H16 8.738 -1.177 0.795 ETKDGv3 66
7SG H17 6.838 0.057 2.848 ETKDGv3 67
7SG H18 8.421 -0.792 3.106 ETKDGv3 68
7SG H19 5.910 -1.988 3.328 ETKDGv3 69
7SG H20 8.309 -3.200 2.309 ETKDGv3 70
7SG H21 6.463 -3.278 0.766 ETKDGv3 71
7SG H22 4.223 -2.941 1.739 ETKDGv3 72
7SG H23 4.379 -1.145 1.499 ETKDGv3 73
7SG H24 2.603 -1.599 -2.409 ETKDGv3 74
7SG H25 -0.635 1.645 0.261 ETKDGv3 75
7SG H26 -5.240 -2.593 -2.986 ETKDGv3 76
7SG H27 -3.809 -3.484 -1.570 ETKDGv3 77
7SG H28 -2.734 -2.150 -3.174 ETKDGv3 78
7SG H29 -4.007 -0.134 -3.311 ETKDGv3 79
7SG H30 -2.289 0.302 -3.009 ETKDGv3 80
7SG H31 -3.500 0.426 -1.685 ETKDGv3 81
7SG H32 -4.752 -2.826 0.526 ETKDGv3 82
7SG H33 -2.741 -1.802 1.690 ETKDGv3 83
7SG H34 -1.580 -3.612 1.336 ETKDGv3 84
7SG H35 -2.056 -0.260 -0.108 ETKDGv3 85
#