data_VPD # _chem_comp.id VPD _chem_comp.name "6-chloro-N-cyclopentyl-1-{5-O-[(2R)-1-hydroxy-3-methoxy-2-phosphonopropan-2-yl]-beta-D-ribofuranosyl}-1H-pyrazolo[3,4-d]pyrimidin-4-amine" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H29 Cl N5 O9 P" _chem_comp.mon_nstd_parent_comp_id ADN _chem_comp.pdbx_synonyms OP-0105244 _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-08-31 _chem_comp.pdbx_modified_date 2021-03-01 _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 537.888 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VPD _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 7JV8 _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 VPD C5 C1 C 0 1 N N R 45.920 -28.638 -38.980 -5.083 -0.539 0.735 C5 VPD 1 VPD C6 C2 C 0 1 N N N 46.729 -27.365 -38.690 -5.486 -1.106 2.098 C6 VPD 2 VPD C8 C3 C 0 1 N N N 46.856 -29.764 -39.446 -6.196 0.373 0.213 C8 VPD 3 VPD O9 O1 O 0 1 N N N 47.884 -30.029 -38.500 -7.430 -0.349 0.189 O9 VPD 4 VPD C12 C4 C 0 1 N N N 44.691 -30.277 -37.598 -3.395 0.765 -0.357 C12 VPD 5 VPD C16 C5 C 0 1 N N R 41.741 -30.274 -35.485 0.128 1.450 -0.128 C16 VPD 6 VPD C21 C6 C 0 1 Y N N 38.265 -30.828 -36.274 3.220 -0.486 -0.026 C21 VPD 7 VPD C24 C7 C 0 1 N N N 35.775 -31.932 -37.694 6.774 -1.669 0.361 C24 VPD 8 VPD C27 C8 C 0 1 N N N 34.193 -30.453 -38.708 8.829 -2.129 -0.870 C27 VPD 9 VPD C30 C9 C 0 1 Y N N 37.799 -30.353 -33.621 4.493 1.733 0.790 C30 VPD 10 VPD C33 C10 C 0 1 Y N N 39.306 -30.520 -35.363 2.525 0.726 0.150 C33 VPD 11 VPD C34 C11 C 0 1 N N R 42.343 -31.659 -35.148 -0.261 1.889 -1.563 C34 VPD 12 VPD C37 C12 C 0 1 N N S 43.375 -31.814 -36.252 -1.728 2.348 -1.374 C37 VPD 13 VPD O1 O2 O 0 1 N N N 45.544 -27.794 -41.457 -3.567 -2.618 -0.094 O1 VPD 14 VPD P2 P1 P 0 1 N N N 44.734 -28.305 -40.323 -4.818 -1.908 -0.439 P2 VPD 15 VPD O3 O3 O 0 1 N N N 43.977 -29.640 -40.764 -6.057 -2.933 -0.356 O3 VPD 16 VPD O4 O4 O 0 1 N N N 43.626 -27.250 -39.864 -4.707 -1.319 -1.933 O4 VPD 17 VPD O7 O5 O 0 1 N N N 45.872 -26.261 -38.400 -5.806 -0.032 2.985 O7 VPD 18 VPD C10 C13 C 0 1 N N N 48.783 -31.057 -38.933 -8.540 0.416 -0.286 C10 VPD 19 VPD O11 O6 O 0 1 N N N 45.181 -28.948 -37.798 -3.876 0.214 0.870 O11 VPD 20 VPD C13 C14 C 0 1 N N R 43.849 -30.366 -36.349 -2.178 1.650 -0.077 C13 VPD 21 VPD O15 O7 O 0 1 N N N 42.616 -29.625 -36.426 -1.080 0.841 0.377 O15 VPD 22 VPD N18 N1 N 0 1 Y N N 40.449 -30.512 -36.077 1.222 0.476 -0.166 N18 VPD 23 VPD N19 N2 N 0 1 Y N N 40.178 -30.812 -37.404 1.110 -0.871 -0.533 N19 VPD 24 VPD C20 C15 C 0 1 Y N N 38.900 -30.993 -37.532 2.276 -1.447 -0.449 C20 VPD 25 VPD C22 C16 C 0 1 Y N N 36.938 -30.882 -35.729 4.603 -0.507 0.238 C22 VPD 26 VPD N23 N3 N 0 1 N N N 35.784 -31.191 -36.424 5.335 -1.667 0.082 N23 VPD 27 VPD C25 C17 C 0 1 N N N 34.517 -32.776 -37.956 7.241 -3.092 0.712 C25 VPD 28 VPD C26 C18 C 0 1 N N N 33.435 -31.775 -38.450 8.292 -3.484 -0.347 C26 VPD 29 VPD C28 C19 C 0 1 N N N 35.662 -30.907 -38.799 7.557 -1.244 -0.899 C28 VPD 30 VPD N29 N4 N 0 1 Y N N 36.780 -30.646 -34.421 5.187 0.617 0.639 N29 VPD 31 VPD CL31 CL1 CL 0 0 N N N 37.500 -30.073 -31.938 5.321 3.164 1.318 CL31 VPD 32 VPD N32 N5 N 0 1 Y N N 39.040 -30.298 -34.065 3.199 1.801 0.555 N32 VPD 33 VPD O36 O8 O 0 1 N N N 42.968 -31.635 -33.865 0.559 2.973 -2.004 O36 VPD 34 VPD O39 O9 O 0 1 N N N 44.457 -32.657 -35.874 -1.792 3.768 -1.227 O39 VPD 35 VPD H1 H1 H 0 1 N N N 47.385 -27.546 -37.826 -6.356 -1.752 1.980 H1 VPD 36 VPD H2 H2 H 0 1 N N N 47.342 -27.121 -39.570 -4.658 -1.683 2.510 H2 VPD 37 VPD H3 H3 H 0 1 N N N 46.264 -30.680 -39.593 -6.295 1.238 0.868 H3 VPD 38 VPD H4 H4 H 0 1 N N N 47.318 -29.469 -40.400 -5.950 0.706 -0.795 H4 VPD 39 VPD H5 H5 H 0 1 N N N 44.079 -30.568 -38.465 -3.108 -0.043 -1.031 H5 VPD 40 VPD H6 H6 H 0 1 N N N 45.545 -30.964 -37.505 -4.180 1.363 -0.820 H6 VPD 41 VPD H7 H7 H 0 1 N N N 41.647 -29.682 -34.563 0.405 2.313 0.476 H7 VPD 42 VPD H8 H8 H 0 1 N N N 36.683 -32.542 -37.814 6.995 -0.990 1.185 H8 VPD 43 VPD H9 H9 H 0 1 N N N 34.049 -29.746 -37.878 9.570 -1.717 -0.185 H9 VPD 44 VPD H10 H10 H 0 1 N N N 33.865 -29.986 -39.648 9.249 -2.239 -1.870 H10 VPD 45 VPD H11 H11 H 0 1 N N N 41.572 -32.440 -35.221 -0.202 1.051 -2.256 H11 VPD 46 VPD H12 H12 H 0 1 N N N 42.901 -32.135 -37.191 -2.340 2.025 -2.216 H12 VPD 47 VPD H13 H13 H 0 1 N N N 44.194 -29.845 -41.666 -6.912 -2.535 -0.571 H13 VPD 48 VPD H14 H14 H 0 1 N N N 43.684 -26.473 -40.407 -4.566 -1.993 -2.612 H14 VPD 49 VPD H15 H15 H 0 1 N N N 46.397 -25.489 -38.225 -6.071 -0.319 3.870 H15 VPD 50 VPD H16 H16 H 0 1 N N N 49.554 -31.218 -38.165 -8.687 1.282 0.359 H16 VPD 51 VPD H17 H17 H 0 1 N N N 48.223 -31.990 -39.092 -8.343 0.750 -1.304 H17 VPD 52 VPD H18 H18 H 0 1 N N N 49.262 -30.752 -39.875 -9.438 -0.202 -0.274 H18 VPD 53 VPD H19 H19 H 0 1 N N N 44.437 -30.092 -35.461 -2.429 2.396 0.678 H19 VPD 54 VPD H20 H20 H 0 1 N N N 38.396 -31.233 -38.456 2.486 -2.482 -0.673 H20 VPD 55 VPD H21 H21 H 0 1 N N N 35.337 -30.317 -36.615 4.898 -2.481 -0.212 H21 VPD 56 VPD H22 H22 H 0 1 N N N 34.188 -33.271 -37.031 7.690 -3.104 1.705 H22 VPD 57 VPD H23 H23 H 0 1 N N N 34.718 -33.535 -38.726 6.398 -3.782 0.675 H23 VPD 58 VPD H24 H24 H 0 1 N N N 32.662 -31.632 -37.681 7.826 -4.048 -1.156 H24 VPD 59 VPD H25 H25 H 0 1 N N N 32.968 -32.139 -39.377 9.096 -4.063 0.108 H25 VPD 60 VPD H26 H26 H 0 1 N N N 35.876 -31.358 -39.779 6.972 -1.446 -1.796 H26 VPD 61 VPD H27 H27 H 0 1 N N N 36.347 -30.064 -38.627 7.825 -0.189 -0.845 H27 VPD 62 VPD H28 H28 H 0 1 N N N 42.305 -31.538 -33.191 0.354 3.283 -2.897 H28 VPD 63 VPD H29 H29 H 0 1 N N N 44.154 -33.555 -35.816 -1.465 4.259 -1.993 H29 VPD 64 # # 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 VPD O1 P2 DOUB N N 1 VPD O3 P2 SING N N 2 VPD P2 O4 SING N N 3 VPD P2 C5 SING N N 4 VPD C8 C5 SING N N 5 VPD C8 O9 SING N N 6 VPD C5 C6 SING N N 7 VPD C5 O11 SING N N 8 VPD C10 O9 SING N N 9 VPD C28 C27 SING N N 10 VPD C28 C24 SING N N 11 VPD C27 C26 SING N N 12 VPD C6 O7 SING N N 13 VPD C26 C25 SING N N 14 VPD C25 C24 SING N N 15 VPD O11 C12 SING N N 16 VPD C24 N23 SING N N 17 VPD C12 C13 SING N N 18 VPD C20 N19 DOUB Y N 19 VPD C20 C21 SING Y N 20 VPD N19 N18 SING Y N 21 VPD O15 C13 SING N N 22 VPD O15 C16 SING N N 23 VPD N23 C22 SING N N 24 VPD C13 C37 SING N N 25 VPD C21 C22 DOUB Y N 26 VPD C21 C33 SING Y N 27 VPD C37 O39 SING N N 28 VPD C37 C34 SING N N 29 VPD N18 C16 SING N N 30 VPD N18 C33 SING Y N 31 VPD C22 N29 SING Y N 32 VPD C16 C34 SING N N 33 VPD C33 N32 DOUB Y N 34 VPD C34 O36 SING N N 35 VPD N29 C30 DOUB Y N 36 VPD N32 C30 SING Y N 37 VPD C30 CL31 SING N N 38 VPD C6 H1 SING N N 39 VPD C6 H2 SING N N 40 VPD C8 H3 SING N N 41 VPD C8 H4 SING N N 42 VPD C12 H5 SING N N 43 VPD C12 H6 SING N N 44 VPD C16 H7 SING N N 45 VPD C24 H8 SING N N 46 VPD C27 H9 SING N N 47 VPD C27 H10 SING N N 48 VPD C34 H11 SING N N 49 VPD C37 H12 SING N N 50 VPD O3 H13 SING N N 51 VPD O4 H14 SING N N 52 VPD O7 H15 SING N N 53 VPD C10 H16 SING N N 54 VPD C10 H17 SING N N 55 VPD C10 H18 SING N N 56 VPD C13 H19 SING N N 57 VPD C20 H20 SING N N 58 VPD N23 H21 SING N N 59 VPD C25 H22 SING N N 60 VPD C25 H23 SING N N 61 VPD C26 H24 SING N N 62 VPD C26 H25 SING N N 63 VPD C28 H26 SING N N 64 VPD C28 H27 SING N N 65 VPD O36 H28 SING N N 66 VPD O39 H29 SING N N 67 # # 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 VPD SMILES ACDLabs 12.01 "C(CO)(OCC1C(C(C(O1)n4c2c(c(nc(Cl)n2)NC3CCCC3)cn4)O)O)(COC)P(=O)(O)O" VPD InChI InChI 1.03 "InChI=1S/C19H29ClN5O9P/c1-32-9-19(8-26,35(29,30)31)33-7-12-13(27)14(28)17(34-12)25-16-11(6-21-25)15(23-18(20)24-16)22-10-4-2-3-5-10/h6,10,12-14,17,26-28H,2-5,7-9H2,1H3,(H,22,23,24)(H2,29,30,31)/t12-,13-,14-,17-,19-/m1/s1" VPD InChIKey InChI 1.03 BQCRMLSBGAKPFW-RTPDKIPNSA-N VPD SMILES_CANONICAL CACTVS 3.385 "COC[C@](CO)(OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2ncc3c(NC4CCCC4)nc(Cl)nc23)[P](O)(O)=O" VPD SMILES CACTVS 3.385 "COC[C](CO)(OC[CH]1O[CH]([CH](O)[CH]1O)n2ncc3c(NC4CCCC4)nc(Cl)nc23)[P](O)(O)=O" VPD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COC[C@](CO)(OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2c3c(cn2)c(nc(n3)Cl)NC4CCCC4)O)O)P(=O)(O)O" VPD SMILES "OpenEye OEToolkits" 2.0.7 "COCC(CO)(OCC1C(C(C(O1)n2c3c(cn2)c(nc(n3)Cl)NC4CCCC4)O)O)P(=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 VPD "SYSTEMATIC NAME" ACDLabs 12.01 "6-chloro-N-cyclopentyl-1-{5-O-[(2R)-1-hydroxy-3-methoxy-2-phosphonopropan-2-yl]-beta-D-ribofuranosyl}-1H-pyrazolo[3,4-d]pyrimidin-4-amine" VPD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R})-2-[[(2~{R},3~{S},4~{R},5~{R})-5-[6-chloranyl-4-(cyclopentylamino)pyrazolo[3,4-d]pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy]-1-methoxy-3-oxidanyl-propan-2-yl]phosphonic 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 VPD "Create component" 2020-08-31 RCSB VPD "Initial release" 2020-09-23 RCSB VPD "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id VPD _pdbx_chem_comp_synonyms.name OP-0105244 _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##