data_GMD # _chem_comp.id GMD _chem_comp.name "(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-hydroxybutyl)sulfanyl]methyl}pyrrolidin-3-ol" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H25 N5 O2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms hydroxybutylthio-DADMe-Immucillin-A _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-05-29 _chem_comp.pdbx_modified_date 2020-06-17 _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 351.467 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GMD _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 4WKO _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 GMD C C1 C 0 1 N N N -39.766 -43.633 17.433 -8.665 1.400 0.111 C GMD 1 GMD OXT O1 O 0 1 N N N -39.967 -42.230 17.275 -9.909 1.053 0.723 OXT GMD 2 GMD CA C2 C 0 1 N N N -38.579 -44.043 16.582 -7.619 0.333 0.443 CA GMD 3 GMD CB C3 C 0 1 N N N -38.841 -43.930 15.077 -6.287 0.704 -0.211 CB GMD 4 GMD CG C4 C 0 1 N N N -37.719 -44.675 14.360 -5.241 -0.363 0.121 CG GMD 5 GMD "S5'" S1 S 0 1 N N N -37.944 -44.853 12.616 -3.662 0.077 -0.655 "S5'" GMD 6 GMD "C5'" C5 C 0 1 N N N -36.625 -45.932 12.177 -2.569 -1.283 -0.155 "C5'" GMD 7 GMD "C4'" C6 C 0 1 N N S -35.270 -45.219 12.126 -1.174 -1.057 -0.740 "C4'" GMD 8 GMD "C1'" C7 C 0 1 N N N -34.162 -46.256 12.098 -0.508 0.169 -0.079 "C1'" GMD 9 GMD "C3'" C8 C 0 1 N N R -35.077 -44.436 10.845 -0.252 -2.247 -0.402 "C3'" GMD 10 GMD "O3'" O2 O 0 1 N N N -34.040 -43.456 10.955 0.264 -2.830 -1.600 "O3'" GMD 11 GMD "C2'" C9 C 0 1 N N N -34.600 -45.491 9.871 0.894 -1.641 0.437 "C2'" GMD 12 GMD "N1'" N1 N 0 1 N N N -33.615 -46.205 10.718 0.924 -0.205 0.047 "N1'" GMD 13 GMD C10 C10 C 0 1 N N N -33.243 -47.505 10.152 1.593 0.605 1.074 C10 GMD 14 GMD C9 C11 C 0 1 Y N N -34.188 -48.671 10.295 3.066 0.290 1.082 C9 GMD 15 GMD C8 C12 C 0 1 Y N N -34.058 -49.745 11.186 3.706 -0.524 1.942 C8 GMD 16 GMD N7 N2 N 0 1 Y N N -35.072 -50.646 11.007 5.036 -0.565 1.641 N7 GMD 17 GMD C5 C13 C 0 1 Y N N -35.896 -50.244 10.025 5.292 0.239 0.554 C5 GMD 18 GMD C4 C14 C 0 1 Y N N -35.392 -48.983 9.507 4.069 0.805 0.155 C4 GMD 19 GMD N3 N3 N 0 1 Y N N -36.013 -48.316 8.504 4.047 1.634 -0.892 N3 GMD 20 GMD C2 C15 C 0 1 Y N N -37.139 -48.845 7.966 5.155 1.918 -1.540 C2 GMD 21 GMD N1 N4 N 0 1 Y N N -37.693 -50.016 8.394 6.325 1.408 -1.198 N1 GMD 22 GMD C6 C16 C 0 1 Y N N -37.131 -50.750 9.391 6.441 0.571 -0.172 C6 GMD 23 GMD N6 N5 N 0 1 N N N -37.680 -51.924 9.813 7.674 0.044 0.176 N6 GMD 24 GMD H1 H1 H 0 1 N N N -40.664 -44.177 17.105 -8.794 1.457 -0.969 H1 GMD 25 GMD H2 H2 H 0 1 N N N -39.563 -43.863 18.489 -8.331 2.366 0.490 H2 GMD 26 GMD H3 H3 H 0 1 N N N -40.708 -41.954 17.802 -10.620 1.687 0.554 H3 GMD 27 GMD H4 H4 H 0 1 N N N -38.328 -45.088 16.815 -7.490 0.275 1.524 H4 GMD 28 GMD H5 H5 H 0 1 N N N -37.727 -43.396 16.837 -7.953 -0.633 0.065 H5 GMD 29 GMD H6 H6 H 0 1 N N N -38.843 -42.872 14.774 -6.416 0.762 -1.292 H6 GMD 30 GMD H7 H7 H 0 1 N N N -39.812 -44.384 14.829 -5.953 1.670 0.167 H7 GMD 31 GMD H8 H8 H 0 1 N N N -37.640 -45.680 14.799 -5.112 -0.421 1.202 H8 GMD 32 GMD H9 H9 H 0 1 N N N -36.781 -44.126 14.530 -5.575 -1.329 -0.257 H9 GMD 33 GMD H10 H10 H 0 1 N N N -36.835 -46.360 11.186 -2.507 -1.318 0.932 H10 GMD 34 GMD H11 H11 H 0 1 N N N -36.569 -46.741 12.921 -2.970 -2.226 -0.527 H11 GMD 35 GMD H12 H12 H 0 1 N N N -35.155 -44.560 12.999 -1.234 -0.919 -1.819 H12 GMD 36 GMD H13 H13 H 0 1 N N N -34.564 -47.256 12.317 -0.617 1.049 -0.714 H13 GMD 37 GMD H14 H14 H 0 1 N N N -33.381 -46.006 12.832 -0.942 0.354 0.904 H14 GMD 38 GMD H15 H15 H 0 1 N N N -36.028 -43.996 10.509 -0.795 -2.993 0.179 H15 GMD 39 GMD H16 H16 H 0 1 N N N -34.309 -42.776 11.562 0.851 -3.584 -1.449 H16 GMD 40 GMD H17 H17 H 0 1 N N N -34.126 -45.043 8.985 0.680 -1.742 1.501 H17 GMD 41 GMD H18 H18 H 0 1 N N N -35.420 -46.153 9.554 1.841 -2.122 0.191 H18 GMD 42 GMD H20 H20 H 0 1 N N N -32.295 -47.801 10.625 1.449 1.663 0.853 H20 GMD 43 GMD H21 H21 H 0 1 N N N -33.084 -47.352 9.074 1.167 0.377 2.051 H21 GMD 44 GMD H22 H22 H 0 1 N N N -33.266 -49.847 11.914 3.236 -1.064 2.751 H22 GMD 45 GMD H23 H23 H 0 1 N N N -35.184 -51.488 11.535 5.701 -1.084 2.120 H23 GMD 46 GMD H24 H24 H 0 1 N N N -37.621 -48.313 7.159 5.108 2.594 -2.381 H24 GMD 47 GMD H25 H25 H 0 1 N N N -38.507 -52.115 9.284 8.465 0.285 -0.332 H25 GMD 48 GMD H26 H26 H 0 1 N N N -37.022 -52.666 9.682 7.747 -0.566 0.926 H26 GMD 49 # # 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 GMD C2 N1 DOUB Y N 1 GMD C2 N3 SING Y N 2 GMD N1 C6 SING Y N 3 GMD N3 C4 DOUB Y N 4 GMD C6 N6 SING N N 5 GMD C6 C5 DOUB Y N 6 GMD C4 C5 SING Y N 7 GMD C4 C9 SING Y N 8 GMD "C2'" "N1'" SING N N 9 GMD "C2'" "C3'" SING N N 10 GMD C5 N7 SING Y N 11 GMD C10 C9 SING N N 12 GMD C10 "N1'" SING N N 13 GMD C9 C8 DOUB Y N 14 GMD "N1'" "C1'" SING N N 15 GMD "C3'" "O3'" SING N N 16 GMD "C3'" "C4'" SING N N 17 GMD N7 C8 SING Y N 18 GMD "C1'" "C4'" SING N N 19 GMD "C4'" "C5'" SING N N 20 GMD "C5'" "S5'" SING N N 21 GMD "S5'" CG SING N N 22 GMD CG CB SING N N 23 GMD CB CA SING N N 24 GMD CA C SING N N 25 GMD OXT C SING N N 26 GMD C H1 SING N N 27 GMD C H2 SING N N 28 GMD OXT H3 SING N N 29 GMD CA H4 SING N N 30 GMD CA H5 SING N N 31 GMD CB H6 SING N N 32 GMD CB H7 SING N N 33 GMD CG H8 SING N N 34 GMD CG H9 SING N N 35 GMD "C5'" H10 SING N N 36 GMD "C5'" H11 SING N N 37 GMD "C4'" H12 SING N N 38 GMD "C1'" H13 SING N N 39 GMD "C1'" H14 SING N N 40 GMD "C3'" H15 SING N N 41 GMD "O3'" H16 SING N N 42 GMD "C2'" H17 SING N N 43 GMD "C2'" H18 SING N N 44 GMD C10 H20 SING N N 45 GMD C10 H21 SING N N 46 GMD C8 H22 SING N N 47 GMD N7 H23 SING N N 48 GMD C2 H24 SING N N 49 GMD N6 H25 SING N N 50 GMD N6 H26 SING N N 51 # # 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 GMD SMILES ACDLabs 12.01 "C(O)CCCSCC1CN(CC1O)Cc2cnc3c2ncnc3N" GMD InChI InChI 1.03 "InChI=1S/C16H25N5O2S/c17-16-15-14(19-10-20-16)11(5-18-15)6-21-7-12(13(23)8-21)9-24-4-2-1-3-22/h5,10,12-13,18,22-23H,1-4,6-9H2,(H2,17,19,20)/t12-,13+/m1/s1" GMD InChIKey InChI 1.03 LDGNPMXZDVLXIT-OLZOCXBDSA-N GMD SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2c(CN3C[C@H](O)[C@@H](CSCCCCO)C3)c[nH]c12" GMD SMILES CACTVS 3.385 "Nc1ncnc2c(CN3C[CH](O)[CH](CSCCCCO)C3)c[nH]c12" GMD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1c(c2c([nH]1)c(ncn2)N)CN3C[C@@H]([C@H](C3)O)CSCCCCO" GMD SMILES "OpenEye OEToolkits" 2.0.6 "c1c(c2c([nH]1)c(ncn2)N)CN3CC(C(C3)O)CSCCCCO" # # 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 GMD "SYSTEMATIC NAME" ACDLabs 12.01 "(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-hydroxybutyl)sulfanyl]methyl}pyrrolidin-3-ol" GMD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(3~{R},4~{S})-1-[(4-azanyl-5~{H}-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-(4-oxidanylbutylsulfanylmethyl)pyrrolidin-3-ol" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site GMD "Create component" 2018-05-29 RCSB GMD "Initial release" 2018-06-06 RCSB GMD "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id GMD _pdbx_chem_comp_synonyms.name hydroxybutylthio-DADMe-Immucillin-A _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##