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 
# 
