data_V0V # _chem_comp.id V0V _chem_comp.name "(3S,5R,9R,19E)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9,19-tetrahydroxy-8,8,20-trimethyl-10,14-dioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphahenicos-19-en-21-oic acid 3,5-dioxide (non-preferred name)" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C25 H40 N7 O19 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-06-11 _chem_comp.pdbx_modified_date 2020-07-03 _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 867.607 _chem_comp.one_letter_code ? _chem_comp.three_letter_code V0V _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 6WFH _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 V0V C8 C1 C 0 1 Y N N 13.228 0.568 2.983 -2.915 -3.805 -0.173 C8 V0V 1 V0V N9 N1 N 0 1 Y N N 12.491 1.172 3.937 -4.034 -3.670 -0.939 N9 V0V 2 V0V C4 C2 C 0 1 Y N N 12.578 2.476 3.812 -4.084 -4.747 -1.787 C4 V0V 3 V0V C5 C3 C 0 1 Y N N 13.508 2.654 2.668 -2.952 -5.525 -1.493 C5 V0V 4 V0V N7 N2 N 0 1 Y N N 13.889 1.426 2.195 -2.279 -4.891 -0.502 N7 V0V 5 V0V N3 N3 N 0 1 Y N N 12.100 3.533 4.465 -4.918 -5.154 -2.739 N3 V0V 6 V0V C2 C4 C 0 1 Y N N 12.462 4.719 4.025 -4.688 -6.270 -3.399 C2 V0V 7 V0V N1 N4 N 0 1 Y N N 13.304 4.997 2.987 -3.639 -7.034 -3.157 N1 V0V 8 V0V C6 C5 C 0 1 Y N N 13.838 4.007 2.262 -2.750 -6.707 -2.224 C6 V0V 9 V0V N6 N5 N 0 1 N N N 14.635 4.184 1.195 -1.653 -7.513 -1.979 N6 V0V 10 V0V "C1'" C6 C 0 1 N N R 11.643 0.473 4.952 -5.006 -2.575 -0.870 "C1'" V0V 11 V0V "C2'" C7 C 0 1 N N R 10.684 -0.523 4.305 -6.150 -2.932 0.105 "C2'" V0V 12 V0V "O2'" O1 O 0 1 N N N 9.491 0.193 4.036 -7.287 -3.414 -0.613 "O2'" V0V 13 V0V "C3'" C8 C 0 1 N N S 10.504 -1.526 5.413 -6.478 -1.594 0.804 "C3'" V0V 14 V0V "O3'" O2 O 0 1 N N N 9.609 -0.886 6.295 -7.828 -1.208 0.540 "O3'" V0V 15 V0V "C4'" C9 C 0 1 N N R 11.801 -1.540 6.175 -5.493 -0.587 0.169 "C4'" V0V 16 V0V "O4'" O3 O 0 1 N N N 12.441 -0.307 5.813 -4.394 -1.395 -0.306 "O4'" V0V 17 V0V "C5'" C10 C 0 1 N N N 12.693 -2.643 5.744 -5.006 0.415 1.218 "C5'" V0V 18 V0V "O5'" O4 O 0 1 N N N 12.567 -2.589 4.332 -4.190 1.405 0.588 "O5'" V0V 19 V0V P1 P1 P 0 1 N N N 13.280 -3.743 3.508 -3.507 2.620 1.393 P1 V0V 20 V0V O11 O5 O 0 1 N N N 12.149 -4.578 3.070 -2.695 2.079 2.507 O11 V0V 21 V0V O12 O6 O 0 1 N N N 14.474 -4.280 4.349 -4.652 3.585 1.983 O12 V0V 22 V0V O6 O7 O 0 1 N N N 13.912 -3.410 2.114 -2.559 3.458 0.397 O6 V0V 23 V0V P2 P2 P 0 1 N N N 15.524 -3.628 2.031 -1.332 4.477 0.614 P2 V0V 24 V0V O21 O8 O 0 1 N N N 15.862 -5.105 2.061 -1.896 5.896 1.126 O21 V0V 25 V0V O22 O9 O 0 1 N N N 16.010 -2.881 0.763 -0.403 3.923 1.624 O22 V0V 26 V0V O7 O10 O 0 1 N N N 16.242 -3.115 3.393 -0.551 4.681 -0.779 O7 V0V 27 V0V CPB C11 C 0 1 N N N 16.121 -1.748 3.785 0.650 5.447 -0.893 CPB V0V 28 V0V CPA C12 C 0 1 N N N 17.383 -0.952 3.670 1.126 5.436 -2.347 CPA V0V 29 V0V CP7 C13 C 0 1 N N R 18.304 -1.216 2.519 2.411 6.257 -2.469 CP7 V0V 30 V0V CP9 C14 C 0 1 N N N 17.534 0.243 4.533 1.397 3.995 -2.784 CP9 V0V 31 V0V CP8 C15 C 0 1 N N N 18.126 -1.881 4.686 0.045 6.046 -3.242 CP8 V0V 32 V0V OP3 O11 O 0 1 N N N 17.545 -0.657 1.461 2.128 7.630 -2.197 OP3 V0V 33 V0V CP6 C16 C 0 1 N N N 19.659 -0.635 2.482 3.428 5.748 -1.480 CP6 V0V 34 V0V OP2 O12 O 0 1 N N N 20.616 -1.281 2.915 3.739 6.429 -0.526 OP2 V0V 35 V0V NP2 N6 N 0 1 N N N 19.842 0.574 1.975 3.991 4.536 -1.655 NP2 V0V 36 V0V CP5 C17 C 0 1 N N N 21.166 1.155 1.934 4.905 4.000 -0.643 CP5 V0V 37 V0V CP4 C18 C 0 1 N N N 21.856 1.004 0.589 5.399 2.620 -1.083 CP4 V0V 38 V0V CP3 C19 C 0 1 N N N 21.156 1.844 -0.475 6.340 2.069 -0.042 CP3 V0V 39 V0V OP1 O13 O 0 1 N N N 20.041 2.300 -0.321 6.590 2.716 0.953 OP1 V0V 40 V0V NP1 N7 N 0 1 N N N 21.797 1.978 -1.621 6.903 0.857 -0.217 NP1 V0V 41 V0V CP2 C20 C 0 1 N N N 21.215 2.651 -2.784 7.817 0.321 0.794 CP2 V0V 42 V0V CP1 C21 C 0 1 N N N 21.780 4.046 -2.913 8.311 -1.059 0.355 CP1 V0V 43 V0V P3 P3 P 0 1 N N N 8.301 -1.670 6.932 -8.914 -0.966 1.703 P3 V0V 44 V0V O31 O14 O 0 1 N N N 8.742 -2.528 8.083 -9.200 -2.354 2.468 O31 V0V 45 V0V O32 O15 O 0 1 N N N 7.797 -2.546 5.816 -8.393 0.030 2.666 O32 V0V 46 V0V O33 O16 O 0 1 N N N 7.351 -0.575 7.462 -10.283 -0.419 1.054 O33 V0V 47 V0V S S1 S 0 1 N N N 23.494 4.122 -3.571 9.441 -1.721 1.605 S V0V 48 V0V CS1 C22 C 0 1 N N N 24.021 5.746 -3.273 9.844 -3.268 0.864 CS1 V0V 49 V0V OS1 O17 O 0 1 N N N 23.323 6.508 -2.650 9.304 -3.608 -0.326 OS1 V0V 50 V0V CS2 C23 C 0 1 N N N 25.239 6.140 -3.649 10.701 -4.124 1.494 CS2 V0V 51 V0V CS3 C24 C 0 1 N N N 26.141 5.128 -4.348 11.204 -3.803 2.877 CS3 V0V 52 V0V CS4 C25 C 0 1 N N N 25.911 7.372 -3.261 11.113 -5.300 0.853 CS4 V0V 53 V0V OS4 O18 O 0 1 N N N 27.178 7.314 -3.338 10.627 -6.370 1.174 OS4 V0V 54 V0V OS5 O19 O 0 1 N N N 25.453 8.332 -2.636 12.048 -5.247 -0.119 OS5 V0V 55 V0V H1 H1 H 0 1 N N N 13.280 -0.504 2.866 -2.601 -3.110 0.592 H1 V0V 56 V0V H2 H2 H 0 1 N N N 12.046 5.570 4.544 -5.385 -6.573 -4.167 H2 V0V 57 V0V H3 H3 H 0 1 N N N 14.763 5.162 1.032 -1.011 -7.265 -1.295 H3 V0V 58 V0V H4 H4 H 0 1 N N N 15.522 3.756 1.367 -1.524 -8.327 -2.491 H4 V0V 59 V0V H5 H5 H 0 1 N N N 11.063 1.215 5.521 -5.404 -2.359 -1.862 H5 V0V 60 V0V H6 H6 H 0 1 N N N 11.126 -0.981 3.408 -5.815 -3.671 0.832 H6 V0V 61 V0V H7 H7 H 0 1 N N N 8.858 -0.387 3.630 -7.120 -4.220 -1.120 H7 V0V 62 V0V H8 H8 H 0 1 N N N 10.188 -2.519 5.061 -6.305 -1.672 1.878 H8 V0V 63 V0V H9 H9 H 0 1 N N N 11.611 -1.593 7.257 -5.967 -0.065 -0.662 H9 V0V 64 V0V H10 H10 H 0 1 N N N 12.351 -3.611 6.139 -5.865 0.897 1.686 H10 V0V 65 V0V H11 H11 H 0 1 N N N 13.731 -2.464 6.060 -4.423 -0.107 1.976 H11 V0V 66 V0V H12 H12 H 0 1 N N N 14.349 -5.206 4.523 -5.223 3.976 1.308 H12 V0V 67 V0V H13 H13 H 0 1 N N N 16.333 -5.339 1.270 -2.513 6.318 0.512 H13 V0V 68 V0V H14 H14 H 0 1 N N N 15.358 -1.275 3.149 0.457 6.474 -0.582 H14 V0V 69 V0V H15 H15 H 0 1 N N N 15.792 -1.720 4.834 1.420 5.013 -0.255 H15 V0V 70 V0V H16 H16 H 0 1 N N N 18.383 -2.304 2.379 2.809 6.161 -3.480 H16 V0V 71 V0V H17 H17 H 0 1 N N N 16.755 0.236 5.310 0.467 3.427 -2.759 H17 V0V 72 V0V H18 H18 H 0 1 N N N 18.526 0.229 5.008 1.797 3.992 -3.798 H18 V0V 73 V0V H19 H19 H 0 1 N N N 17.433 1.152 3.922 2.120 3.540 -2.107 H19 V0V 74 V0V H20 H20 H 0 1 N N N 17.609 -1.852 5.656 -0.095 7.095 -2.980 H20 V0V 75 V0V H21 H21 H 0 1 N N N 18.131 -2.912 4.304 0.351 5.969 -4.285 H21 V0V 76 V0V H22 H22 H 0 1 N N N 19.162 -1.532 4.812 -0.892 5.508 -3.098 H22 V0V 77 V0V H23 H23 H 0 1 N N N 16.957 -1.315 1.110 1.770 7.790 -1.313 H23 V0V 78 V0V H24 H24 H 0 1 N N N 19.062 1.088 1.619 3.791 4.019 -2.451 H24 V0V 79 V0V H25 H25 H 0 1 N N N 21.785 0.664 2.699 5.756 4.672 -0.530 H25 V0V 80 V0V H26 H26 H 0 1 N N N 21.082 2.228 2.163 4.382 3.912 0.309 H26 V0V 81 V0V H27 H27 H 0 1 N N N 21.831 -0.054 0.288 4.549 1.949 -1.196 H27 V0V 82 V0V H28 H28 H 0 1 N N N 22.901 1.335 0.680 5.923 2.708 -2.035 H28 V0V 83 V0V H29 H29 H 0 1 N N N 22.721 1.603 -1.698 6.703 0.340 -1.013 H29 V0V 84 V0V H30 H30 H 0 1 N N N 20.123 2.710 -2.661 8.668 0.993 0.908 H30 V0V 85 V0V H31 H31 H 0 1 N N N 21.451 2.077 -3.692 7.294 0.233 1.747 H31 V0V 86 V0V H32 H32 H 0 1 N N N 21.775 4.511 -1.916 7.460 -1.731 0.242 H32 V0V 87 V0V H33 H33 H 0 1 N N N 21.128 4.619 -3.589 8.834 -0.971 -0.597 H33 V0V 88 V0V H34 H34 H 0 1 N N N 8.610 -3.443 7.865 -9.545 -3.054 1.897 H34 V0V 89 V0V H35 H35 H 0 1 N N N 6.531 -0.607 6.983 -10.984 -0.251 1.699 H35 V0V 90 V0V H37 H37 H 0 1 N N N 27.103 5.601 -4.593 10.526 -4.227 3.618 H37 V0V 91 V0V H38 H38 H 0 1 N N N 26.314 4.270 -3.682 12.199 -4.228 3.010 H38 V0V 92 V0V H39 H39 H 0 1 N N N 25.656 4.783 -5.273 11.252 -2.721 3.005 H39 V0V 93 V0V H40 H40 H 0 1 N N N 26.166 8.871 -2.316 12.267 -6.108 -0.502 H40 V0V 94 V0V H36 H36 H 0 1 N N N 22.492 6.090 -2.455 9.521 -4.505 -0.615 H36 V0V 95 # # 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 V0V CS3 CS2 SING N N 1 V0V CS2 CS1 DOUB N E 2 V0V CS2 CS4 SING N N 3 V0V S CS1 SING N N 4 V0V S CP1 SING N N 5 V0V OS4 CS4 DOUB N N 6 V0V CS1 OS1 SING N N 7 V0V CS4 OS5 SING N N 8 V0V CP1 CP2 SING N N 9 V0V CP2 NP1 SING N N 10 V0V NP1 CP3 SING N N 11 V0V CP3 OP1 DOUB N N 12 V0V CP3 CP4 SING N N 13 V0V CP4 CP5 SING N N 14 V0V O22 P2 DOUB N N 15 V0V N6 C6 SING N N 16 V0V OP3 CP7 SING N N 17 V0V CP5 NP2 SING N N 18 V0V NP2 CP6 SING N N 19 V0V P2 O21 SING N N 20 V0V P2 O6 SING N N 21 V0V P2 O7 SING N N 22 V0V O6 P1 SING N N 23 V0V N7 C5 SING Y N 24 V0V N7 C8 DOUB Y N 25 V0V C6 C5 DOUB Y N 26 V0V C6 N1 SING Y N 27 V0V CP6 CP7 SING N N 28 V0V CP6 OP2 DOUB N N 29 V0V CP7 CPA SING N N 30 V0V C5 C4 SING Y N 31 V0V C8 N9 SING Y N 32 V0V N1 C2 DOUB Y N 33 V0V O11 P1 DOUB N N 34 V0V O7 CPB SING N N 35 V0V P1 "O5'" SING N N 36 V0V P1 O12 SING N N 37 V0V CPA CPB SING N N 38 V0V CPA CP9 SING N N 39 V0V CPA CP8 SING N N 40 V0V C4 N9 SING Y N 41 V0V C4 N3 DOUB Y N 42 V0V N9 "C1'" SING N N 43 V0V C2 N3 SING Y N 44 V0V "O2'" "C2'" SING N N 45 V0V "C2'" "C1'" SING N N 46 V0V "C2'" "C3'" SING N N 47 V0V "O5'" "C5'" SING N N 48 V0V "C1'" "O4'" SING N N 49 V0V "C3'" "C4'" SING N N 50 V0V "C3'" "O3'" SING N N 51 V0V "C5'" "C4'" SING N N 52 V0V "O4'" "C4'" SING N N 53 V0V O32 P3 DOUB N N 54 V0V "O3'" P3 SING N N 55 V0V P3 O33 SING N N 56 V0V P3 O31 SING N N 57 V0V C8 H1 SING N N 58 V0V C2 H2 SING N N 59 V0V N6 H3 SING N N 60 V0V N6 H4 SING N N 61 V0V "C1'" H5 SING N N 62 V0V "C2'" H6 SING N N 63 V0V "O2'" H7 SING N N 64 V0V "C3'" H8 SING N N 65 V0V "C4'" H9 SING N N 66 V0V "C5'" H10 SING N N 67 V0V "C5'" H11 SING N N 68 V0V O12 H12 SING N N 69 V0V O21 H13 SING N N 70 V0V CPB H14 SING N N 71 V0V CPB H15 SING N N 72 V0V CP7 H16 SING N N 73 V0V CP9 H17 SING N N 74 V0V CP9 H18 SING N N 75 V0V CP9 H19 SING N N 76 V0V CP8 H20 SING N N 77 V0V CP8 H21 SING N N 78 V0V CP8 H22 SING N N 79 V0V OP3 H23 SING N N 80 V0V NP2 H24 SING N N 81 V0V CP5 H25 SING N N 82 V0V CP5 H26 SING N N 83 V0V CP4 H27 SING N N 84 V0V CP4 H28 SING N N 85 V0V NP1 H29 SING N N 86 V0V CP2 H30 SING N N 87 V0V CP2 H31 SING N N 88 V0V CP1 H32 SING N N 89 V0V CP1 H33 SING N N 90 V0V O31 H34 SING N N 91 V0V O33 H35 SING N N 92 V0V CS3 H37 SING N N 93 V0V CS3 H38 SING N N 94 V0V CS3 H39 SING N N 95 V0V OS5 H40 SING N N 96 V0V OS1 H36 SING N N 97 # # 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 V0V SMILES ACDLabs 12.01 "c3n(C1OC(C(C1O)OP(O)(O)=O)COP(O)(=O)OP(O)(OCC(C)(C)C(O)C(=O)NCCC(=O)NCCS/C(O)=C(/C(O)=O)C)=O)c2ncnc(c2n3)N" V0V InChI InChI 1.03 "InChI=1S/C25H40N7O19P3S/c1-12(23(37)38)24(39)55-7-6-27-14(33)4-5-28-21(36)18(35)25(2,3)9-48-54(45,46)51-53(43,44)47-8-13-17(50-52(40,41)42)16(34)22(49-13)32-11-31-15-19(26)29-10-30-20(15)32/h10-11,13,16-18,22,34-35,39H,4-9H2,1-3H3,(H,27,33)(H,28,36)(H,37,38)(H,43,44)(H,45,46)(H2,26,29,30)(H2,40,41,42)/b24-12+/t13-,16-,17-,18+,22-/m1/s1" V0V InChIKey InChI 1.03 RERUYCLVCZLHGP-JXZMNPEQSA-N V0V SMILES_CANONICAL CACTVS 3.385 "C\C(C(O)=O)=C(O)/SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23" V0V SMILES CACTVS 3.385 "CC(C(O)=O)=C(O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23" V0V SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C/C(=C(/O)\SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O)/C(=O)O" V0V SMILES "OpenEye OEToolkits" 2.0.7 "CC(=C(O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)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 V0V "SYSTEMATIC NAME" ACDLabs 12.01 "(3S,5R,9R,19E)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9,19-tetrahydroxy-8,8,20-trimethyl-10,14-dioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphahenicos-19-en-21-oic acid 3,5-dioxide (non-preferred name)" V0V "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(~{E})-3-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-2-methyl-3-oxidanyl-prop-2-enoic 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 V0V "Create component" 2020-06-11 RCSB V0V "Initial release" 2020-07-08 RCSB ##