data_PVX # _chem_comp.id PVX _chem_comp.name "N-(2-amino-5-{formyl[(6aS,8R,9R,9aR)-9-hydroxy-4-methoxy-1,11-dioxo-1,6a,8,9,9a,11-hexahydrocyclopenta[c]furo[3',2':4,5]furo[2,3-h]chromen-8-yl]amino}-6-oxo-1,6-dihydropyrimidin-4-yl)-2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosylamine" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C27 H26 N5 O15 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2011-01-18 _chem_comp.pdbx_modified_date 2011-08-05 _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 691.494 _chem_comp.one_letter_code ? _chem_comp.three_letter_code PVX _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 3PVX _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 PVX O O O 0 1 N N N 124.937 87.725 38.838 -4.766 0.171 -2.917 O PVX 1 PVX P P P 0 1 N N N 130.603 90.865 45.326 5.678 -3.791 -0.798 P PVX 2 PVX C1 C1 C 0 1 N N N 125.234 83.920 35.346 -7.718 -1.977 0.361 C1 PVX 3 PVX N1 N1 N 0 1 N N N 126.035 85.176 42.856 2.093 2.767 -1.579 N1 PVX 4 PVX O1 O1 O 0 1 N N N 125.269 83.025 34.500 -8.470 -2.501 1.157 O1 PVX 5 PVX C2 C2 C 0 1 N N N 125.277 84.773 41.823 1.164 3.166 -2.420 C2 PVX 6 PVX N2 N2 N 0 1 N N N 123.925 85.264 41.742 1.500 3.397 -3.729 N2 PVX 7 PVX C3 C3 C 0 1 N N N 124.349 85.781 36.668 -6.966 -0.976 -1.561 C3 PVX 8 PVX N3 N3 N 0 1 N N N 125.815 83.851 40.802 -0.123 3.355 -2.020 N3 PVX 9 PVX C4 C4 C 0 1 N N N 127.100 83.399 40.898 -0.474 3.132 -0.736 C4 PVX 10 PVX O4 O4 O 0 1 N N N 127.493 82.641 40.023 -1.627 3.299 -0.369 O4 PVX 11 PVX C5 C5 C 0 1 N N N 127.943 83.825 42.008 0.509 2.707 0.169 C5 PVX 12 PVX C6 C6 C 0 1 N N N 127.336 84.708 42.933 1.809 2.530 -0.293 C6 PVX 13 PVX N6 N6 N 0 1 N N N 128.127 85.167 44.053 2.803 2.110 0.573 N6 PVX 14 PVX N7 N7 N 0 1 N N N 129.376 83.341 42.124 0.186 2.463 1.519 N7 PVX 15 PVX O7 O7 O 0 1 N N N 130.617 85.420 41.759 1.012 0.273 1.155 O7 PVX 16 PVX C8 C8 C 0 1 N N N 129.568 82.268 42.914 -0.212 3.479 2.310 C8 PVX 17 PVX O8 O8 O 0 1 N N N 130.674 81.759 43.105 -0.403 3.288 3.493 O8 PVX 18 PVX C9 C9 C 0 1 N N R 130.323 83.970 39.889 -1.124 0.510 2.227 C9 PVX 19 PVX O9 O9 O 0 1 N N N 131.387 83.311 39.252 -1.342 0.120 3.585 O9 PVX 20 PVX CM CM C 0 1 N N N 124.637 88.822 39.747 -4.174 0.804 -4.053 CM PVX 21 PVX O10 O10 O 0 1 N N N 128.448 84.291 37.363 -4.100 -1.535 1.518 O10 PVX 22 PVX C11 C11 C 0 1 N N N 127.540 83.743 36.377 -5.390 -1.906 1.619 C11 PVX 23 PVX O11 O11 O 0 1 N N N 127.988 82.809 35.712 -5.786 -2.435 2.643 O11 PVX 24 PVX C1D C1D C 0 1 N N R 127.562 86.182 44.919 4.143 1.816 0.061 C1D PVX 25 PVX O1P O1P O 0 1 N N N 129.256 90.856 45.970 4.469 -4.408 0.067 O1P PVX 26 PVX C2A C2A C 0 1 N N N 123.993 84.790 35.531 -8.063 -1.493 -1.003 C2A PVX 27 PVX C2D C2D C 0 1 N N N 128.140 85.994 46.313 5.203 2.223 1.103 C2D PVX 28 PVX O3P O3P O 0 1 N N N 131.750 91.510 46.003 6.970 -4.242 -0.233 O3P PVX 29 PVX "C3'" "C3'" C 0 1 N N S 128.275 87.438 46.759 5.972 0.912 1.394 "C3'" PVX 30 PVX "O3'" "O3'" O 0 1 N N N 126.961 87.954 47.195 7.376 1.157 1.502 "O3'" PVX 31 PVX C3A C3A C 0 1 N N N 125.794 85.385 37.042 -5.829 -1.078 -0.623 C3A PVX 32 PVX O2P O2P O 0 1 N Y N 130.434 91.565 43.891 5.556 -4.291 -2.324 O2P PVX 33 PVX C4A C4A C 0 1 Y N N 126.648 85.971 38.042 -4.474 -0.697 -0.699 C4A PVX 34 PVX C4B C4B C 0 1 Y N N 126.258 87.094 38.927 -3.957 -0.074 -1.857 C4B PVX 35 PVX C4D C4D C 0 1 N N R 128.791 88.143 45.508 5.654 0.063 0.137 C4D PVX 36 PVX O4D O4D O 0 1 N N N 127.991 87.510 44.485 4.283 0.403 -0.161 O4D PVX 37 PVX C5B C5B C 0 1 Y N N 127.242 87.563 39.909 -2.629 0.285 -1.906 C5B PVX 38 PVX C5D C5D C 0 1 N N N 130.270 87.863 45.231 5.788 -1.429 0.447 C5D PVX 39 PVX O5D O5D O 0 1 N N N 131.032 89.168 44.979 5.604 -2.183 -0.753 O5D PVX 40 PVX C5M C5M C 0 1 Y N N 128.512 86.933 39.993 -1.782 0.035 -0.819 C5M PVX 41 PVX C6A C6A C 0 1 N N S 130.575 86.290 40.663 0.087 -0.495 0.377 C6A PVX 42 PVX O6A O6A O 0 1 N N N 129.557 87.262 40.885 -0.460 0.316 -0.674 O6A PVX 43 PVX C8A C8A C 0 1 N N R 130.510 84.021 41.397 0.284 1.106 2.062 C8A PVX 44 PVX C9A C9A C 0 1 N N R 130.255 85.415 39.429 -1.143 -0.725 1.303 C9A PVX 45 PVX C9B C9B C 0 1 Y N N 128.848 85.905 39.155 -2.291 -0.581 0.321 C9B PVX 46 PVX CA1 CA1 C 0 1 Y N N 127.957 85.395 38.178 -3.619 -0.945 0.402 CA1 PVX 47 PVX CB1 CB1 C 0 1 N N N 126.231 84.335 36.252 -6.284 -1.691 0.558 CB1 PVX 48 PVX HN2 HN2 H 0 1 N N N 123.576 85.886 42.443 2.414 3.266 -4.026 HN2 PVX 49 PVX HN2A HN2A H 0 0 N N N 123.335 84.982 40.985 0.823 3.692 -4.359 HN2A PVX 50 PVX H3 H3 H 0 1 N N N 123.735 86.560 37.095 -6.917 -0.547 -2.552 H3 PVX 51 PVX HN3 HN3 H 0 1 N N N 125.238 83.558 40.040 -0.790 3.650 -2.660 HN3 PVX 52 PVX H8 H8 H 0 1 N N N 128.710 81.832 43.405 -0.361 4.463 1.891 H8 PVX 53 PVX H9 H9 H 0 1 N N N 129.413 83.408 39.633 -1.880 1.230 1.914 H9 PVX 54 PVX HO9 HO9 H 0 1 N N N 131.236 83.298 38.314 -1.295 0.851 4.216 HO9 PVX 55 PVX HM HM H 0 1 N N N 123.616 89.187 39.558 -3.368 0.180 -4.438 HM PVX 56 PVX HMA HMA H 0 1 N N N 124.714 88.469 40.786 -4.929 0.941 -4.827 HMA PVX 57 PVX HMB HMB H 0 1 N N N 125.354 89.640 39.584 -3.774 1.775 -3.760 HMB PVX 58 PVX H1D H1D H 0 1 N N N 126.466 86.095 44.896 4.312 2.358 -0.870 H1D PVX 59 PVX HO1P HO1P H 0 0 N N N 129.302 91.303 46.807 3.590 -4.154 -0.247 HO1P PVX 60 PVX H2A H2A H 0 1 N N N 123.063 84.728 34.985 -9.038 -1.552 -1.464 H2A PVX 61 PVX H2D H2D H 0 1 N N N 127.477 85.411 46.969 5.875 2.976 0.690 H2D PVX 62 PVX H2DA H2DA H 0 0 N N N 129.104 85.465 46.301 4.724 2.594 2.009 H2DA PVX 63 PVX "H3'" "H3'" H 0 1 N N N 128.946 87.585 47.618 5.593 0.430 2.296 "H3'" PVX 64 PVX "HO3'" "HO3'" H 0 0 N Y N 127.052 88.858 47.473 7.616 1.758 2.221 "HO3'" PVX 65 PVX H4D H4D H 0 1 N N N 128.716 89.238 45.578 6.307 0.342 -0.690 H4D PVX 66 PVX H5B H5B H 0 1 N N N 127.001 88.385 40.566 -2.236 0.763 -2.791 H5B PVX 67 PVX H5D H5D H 0 1 N N N 130.708 87.354 46.102 6.780 -1.629 0.853 H5D PVX 68 PVX H5DA H5DA H 0 0 N N N 130.353 87.221 44.341 5.031 -1.718 1.177 H5DA PVX 69 PVX H6A H6A H 0 1 N N N 131.523 86.827 40.513 0.525 -1.421 0.005 H6A PVX 70 PVX H8A H8A H 0 1 N N N 131.418 83.475 41.692 0.789 1.131 3.027 H8A PVX 71 PVX H9A H9A H 0 1 N N N 130.906 85.475 38.544 -1.123 -1.674 1.839 H9A PVX 72 PVX H25 H25 H 0 1 N N N 128.304 84.367 44.626 2.612 2.010 1.518 H25 PVX 73 PVX HO2P HO2P H 0 0 N Y N 131.099 92.235 43.785 5.593 -5.252 -2.427 HO2P PVX 74 # 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 PVX O C4B SING N N 1 PVX O CM SING N N 2 PVX P O1P SING N N 3 PVX P O3P DOUB N N 4 PVX C1 C2A SING N N 5 PVX C1 CB1 SING N N 6 PVX N1 C6 SING N N 7 PVX O1 C1 DOUB N N 8 PVX C2 N1 DOUB N N 9 PVX N2 C2 SING N N 10 PVX N2 HN2 SING N N 11 PVX N2 HN2A SING N N 12 PVX C3 C3A SING N N 13 PVX C3 H3 SING N N 14 PVX N3 C2 SING N N 15 PVX N3 C4 SING N N 16 PVX N3 HN3 SING N N 17 PVX C4 C5 SING N N 18 PVX O4 C4 DOUB N N 19 PVX C5 N7 SING N N 20 PVX C5 C6 DOUB N N 21 PVX C6 N6 SING N N 22 PVX N6 C1D SING N N 23 PVX N7 C8 SING N N 24 PVX C8 O8 DOUB N N 25 PVX C8 H8 SING N N 26 PVX C9 C8A SING N N 27 PVX C9 H9 SING N N 28 PVX O9 C9 SING N N 29 PVX O9 HO9 SING N N 30 PVX CM HM SING N N 31 PVX CM HMA SING N N 32 PVX CM HMB SING N N 33 PVX O10 CA1 SING N N 34 PVX C11 O10 SING N N 35 PVX O11 C11 DOUB N N 36 PVX C1D C2D SING N N 37 PVX C1D H1D SING N N 38 PVX O1P HO1P SING N N 39 PVX C2A C3 DOUB N N 40 PVX C2A H2A SING N N 41 PVX C2D "C3'" SING N N 42 PVX C2D H2D SING N N 43 PVX C2D H2DA SING N N 44 PVX "C3'" "O3'" SING N N 45 PVX "C3'" "H3'" SING N N 46 PVX "O3'" "HO3'" SING N N 47 PVX C3A C4A SING N N 48 PVX O2P P SING N N 49 PVX C4A CA1 DOUB Y N 50 PVX C4A C4B SING Y N 51 PVX C4B C5B DOUB Y N 52 PVX C4D "C3'" SING N N 53 PVX C4D H4D SING N N 54 PVX O4D C1D SING N N 55 PVX O4D C4D SING N N 56 PVX C5B C5M SING Y N 57 PVX C5B H5B SING N N 58 PVX C5D C4D SING N N 59 PVX C5D H5D SING N N 60 PVX C5D H5DA SING N N 61 PVX O5D P SING N N 62 PVX O5D C5D SING N N 63 PVX C5M O6A SING N N 64 PVX C6A O7 SING N N 65 PVX C6A O6A SING N N 66 PVX C6A H6A SING N N 67 PVX C8A N7 SING N N 68 PVX C8A O7 SING N N 69 PVX C8A H8A SING N N 70 PVX C9A C9 SING N N 71 PVX C9A C6A SING N N 72 PVX C9A H9A SING N N 73 PVX C9B C5M DOUB Y N 74 PVX C9B C9A SING N N 75 PVX CA1 C9B SING Y N 76 PVX CB1 C11 SING N N 77 PVX CB1 C3A DOUB N N 78 PVX N6 H25 SING N N 79 PVX O2P HO2P SING N N 80 # 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 PVX SMILES ACDLabs 12.01 "O=P(O)(O)OCC7OC(NC=1N=C(N)NC(=O)C=1N(C=O)C5OC6Oc4cc(OC)c3c(OC(=O)C=2C(=O)C=CC=23)c4C6C5O)CC7O" PVX SMILES_CANONICAL CACTVS 3.370 "COc1cc2O[C@H]3O[C@H]([C@H](O)[C@H]3c2c4OC(=O)C5=C(C=CC5=O)c14)N(C=O)C6=C(N[C@H]7C[C@H](O)[C@@H](CO[P](O)(O)=O)O7)N=C(N)NC6=O" PVX SMILES CACTVS 3.370 "COc1cc2O[CH]3O[CH]([CH](O)[CH]3c2c4OC(=O)C5=C(C=CC5=O)c14)N(C=O)C6=C(N[CH]7C[CH](O)[CH](CO[P](O)(O)=O)O7)N=C(N)NC6=O" PVX SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "COc1cc2c(c3c1C4=C(C(=O)C=C4)C(=O)O3)[C@@H]5[C@H]([C@@H](O[C@@H]5O2)N(C=O)C6=C(N=C(NC6=O)N)N[C@H]7C[C@@H]([C@H](O7)COP(=O)(O)O)O)O" PVX SMILES "OpenEye OEToolkits" 1.7.0 "COc1cc2c(c3c1C4=C(C(=O)C=C4)C(=O)O3)C5C(C(OC5O2)N(C=O)C6=C(N=C(NC6=O)N)NC7CC(C(O7)COP(=O)(O)O)O)O" PVX InChI InChI 1.03 ;InChI=1S/C27H26N5O15P/c1-42-11-5-12-17(21-16(11)8-2-3-9(34)15(8)25(38)46-21)18-20(36)24(47-26(18)45-12)32(7-33)19-22(30-27(28)31-23(19)37)29-14-4-10(35)13(44-14)6-43-48(39,40)41/h2-3,5,7,10,13-14,18,20,24,26,35-36H,4,6H2,1H3,(H2,39,40,41)(H4,28,29,30,31,37)/t10-,13+,14+,18+,20+,24+,26-/m0/s1 ; PVX InChIKey InChI 1.03 OKIQEPDWYKTICF-MHRKVAGWSA-N # 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 PVX "SYSTEMATIC NAME" ACDLabs 12.01 "N-(2-amino-5-{formyl[(6aS,8R,9R,9aR)-9-hydroxy-4-methoxy-1,11-dioxo-1,6a,8,9,9a,11-hexahydrocyclopenta[c]furo[3',2':4,5]furo[2,3-h]chromen-8-yl]amino}-6-oxo-1,6-dihydropyrimidin-4-yl)-2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosylamine" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site PVX "Create component" 2011-01-18 RCSB PVX "Modify aromatic_flag" 2011-06-04 RCSB PVX "Modify descriptor" 2011-06-04 RCSB #