data_39B # _chem_comp.id 39B _chem_comp.name "(S)-2,4-DIAMINO-5-((7,8-DICARBAUNDECABORAN-7-YL)METHYL)-6-METHYLPYRIMIDINE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C8 H9 B9 N4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2005-09-30 _chem_comp.pdbx_modified_date 2023-09-25 _chem_comp.pdbx_ambiguous_flag Y _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 258.483 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 39B _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 2C2T _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 39B N1 N1 N 0 1 Y N N 2.434 28.987 -6.208 2.434 28.987 -6.208 N1 39B 1 39B C2 C2 C 0 1 Y N N 2.052 27.688 -6.097 2.052 27.688 -6.097 C2 39B 2 39B N3 N3 N 0 1 Y N N 1.995 27.041 -4.939 1.995 27.041 -4.939 N3 39B 3 39B C4 C4 C 0 1 Y N N 2.296 27.696 -3.817 2.296 27.696 -3.817 C4 39B 4 39B C5 C5 C 0 1 Y N N 2.717 29.075 -3.808 2.717 29.075 -3.808 C5 39B 5 39B C6 C6 C 0 1 Y N N 2.780 29.691 -5.035 2.780 29.691 -5.035 C6 39B 6 39B "N2'" "N2'" N 0 1 N N N 1.827 26.999 -7.230 1.827 26.999 -7.230 "N2'" 39B 7 39B "N4'" "N4'" N 0 1 N N N 2.191 26.976 -2.651 2.191 26.976 -2.651 "N4'" 39B 8 39B "C6'" "C6'" C 0 1 N N N 3.227 31.132 -5.261 3.227 31.132 -5.261 "C6'" 39B 9 39B "C5'" "C5'" C 0 1 N N N 3.148 29.793 -2.543 3.148 29.793 -2.543 "C5'" 39B 10 39B C1C C1C C 1 1 N N N 2.144 30.691 -1.827 2.144 30.691 -1.827 C1C 39B 11 39B C2C C2C C 0 1 N N S 2.456 32.205 -1.675 2.456 32.205 -1.675 C2C 39B 12 39B B4 B4 B 0 1 N N N 0.591 30.385 -1.985 0.591 30.385 -1.985 B4 39B 13 39B B5 B5 B 0 1 N N N 1.344 30.061 -0.438 1.344 30.061 -0.438 B5 39B 14 39B B6 B6 B 0 1 N N N 2.617 31.247 -0.251 2.617 31.247 -0.251 B6 39B 15 39B B7 B7 B 0 1 N N N 1.891 32.834 -0.180 1.891 32.834 -0.180 B7 39B 16 39B B8 B8 B 0 1 N N N 1.122 33.134 -1.741 1.122 33.134 -1.741 B8 39B 17 39B B9 B9 B 0 1 N N N -0.255 31.967 -1.911 -0.255 31.967 -1.911 B9 39B 18 39B B10 B10 B 0 1 N N N -0.183 30.890 -0.501 -0.183 30.890 -0.501 B10 39B 19 39B B11 B11 B 0 1 N N N 1.083 31.455 0.583 1.083 31.455 0.583 B11 39B 20 39B B12 B12 B 0 1 N N N 0.137 32.644 -0.350 0.137 32.644 -0.350 B12 39B 21 39B "H2'1" "H2'1" H 0 0 N N N 1.988 27.592 -8.019 1.988 27.592 -8.019 "H2'1" 39B 22 39B "H2'2" "H2'2" H 0 0 N N N 2.446 26.215 -7.271 2.446 26.215 -7.272 "H2'2" 39B 23 39B "H4'1" "H4'1" H 0 0 N N N 1.893 26.044 -2.860 1.893 26.044 -2.860 "H4'1" 39B 24 39B "H4'2" "H4'2" H 0 0 N N N 3.081 26.948 -2.196 3.081 26.948 -2.196 "H4'2" 39B 25 39B "H5'1" "H5'1" H 0 0 N N N 3.461 29.021 -1.824 3.461 29.021 -1.824 "H5'1" 39B 26 39B "H5'2" "H5'2" H 0 0 N N N 4.012 30.421 -2.806 4.012 30.421 -2.806 "H5'2" 39B 27 39B "H6'1" "H6'1" H 0 0 N N N 3.195 31.362 -6.336 3.195 31.362 -6.336 "H6'1" 39B 28 39B "H6'2" "H6'2" H 0 0 N N N 2.554 31.814 -4.720 2.554 31.814 -4.720 "H6'2" 39B 29 39B "H6'3" "H6'3" H 0 0 N N N 4.254 31.260 -4.889 4.254 31.260 -4.889 "H6'3" 39B 30 # 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 39B N1 C2 SING Y N 1 39B C2 N3 DOUB Y N 2 39B N3 C4 SING Y N 3 39B C4 C5 DOUB Y N 4 39B N1 C6 DOUB Y N 5 39B C5 C6 SING Y N 6 39B C2 "N2'" SING N N 7 39B C4 "N4'" SING N N 8 39B C6 "C6'" SING N N 9 39B C5 "C5'" SING N N 10 39B "C5'" C1C SING N N 11 39B C1C C2C SING N N 12 39B C1C B4 SING N N 13 39B C1C B5 SING N N 14 39B B4 B5 SING N N 15 39B C1C B6 SING N N 16 39B C2C B6 SING N N 17 39B B5 B6 SING N N 18 39B C2C B7 SING N N 19 39B B6 B7 SING N N 20 39B C2C B8 SING N N 21 39B B7 B8 SING N N 22 39B B9 B10 SING N N 23 39B B4 B10 SING N N 24 39B B5 B10 SING N N 25 39B B10 B11 SING N N 26 39B B5 B11 SING N N 27 39B B6 B11 SING N N 28 39B B7 B11 SING N N 29 39B B8 B12 SING N N 30 39B B9 B12 SING N N 31 39B B10 B12 SING N N 32 39B B11 B12 SING N N 33 39B B7 B12 SING N N 34 39B "N2'" "H2'1" SING N N 35 39B "N2'" "H2'2" SING N N 36 39B "N4'" "H4'1" SING N N 37 39B "N4'" "H4'2" SING N N 38 39B "C5'" "H5'1" SING N N 39 39B "C5'" "H5'2" SING N N 40 39B "C6'" "H6'1" SING N N 41 39B "C6'" "H6'2" SING N N 42 39B "C6'" "H6'3" SING N N 43 39B B8 B9 SING N N 44 39B B4 B9 SING N N 45 # 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 39B SMILES ACDLabs 10.04 "n1c(c(c(nc1N)N)CC29%12B8B%157%10B4[H]B53C2%11B36%13B45%15B67%14B89%10B%11%12%13%14)C" 39B InChI InChI 1.06 "InChI=1S/C8H9B9N4/c1-3-4(5(18)21-6(19)20-3)2-8-7-9-11-10(8)14(8)12(7,8)13(7,9)15(9,11)16(10,11,14)17(12,13,14)15/h2H2,1H3,(H4,18,19,20,21)/q+1" 39B InChIKey InChI 1.06 LMKIHIJGTSLZFQ-UHFFFAOYSA-N 39B SMILES_CANONICAL CACTVS 3.385 "Cc1nc(N)nc(N)c1C[C+]234[B-]56[B]78[B+]9%10[C@@]2%11[B]9%12%13[B]7%10%14[B]58%15[B]36%16[B]4%11%12[B]%13%14%15%16" 39B SMILES CACTVS 3.385 "Cc1nc(N)nc(N)c1C[C+]234[B-]56[B]78[B+]9%10[C]2%11[B]9%12%13[B]7%10%14[B]58%15[B]36%16[B]4%11%12[B]%13%14%15%16" 39B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "B123B45B167B289B31B823B966B744B622[C@@]45[C+]321Cc1c(nc(nc1N)N)C" 39B SMILES "OpenEye OEToolkits" 2.0.7 "B123B45B167B289B31B823B966B744B622C45[C+]321Cc1c(nc(nc1N)N)C" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 39B "Create component" 2005-09-30 EBI 39B "Other modification" 2015-02-12 EBI 39B "Modify descriptor" 2023-09-23 RCSB 39B "Modify charge" 2023-09-25 PDBE #