data_39E
# 
_chem_comp.id                                    39E 
_chem_comp.name                                  "(R)-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 H20 B9 N4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_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                   OBS 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        269.570 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     39E 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_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 
39E N1     N1     N 0 1 Y N N 2.434  28.987 -6.208 2.434  28.987 -6.208 N1     39E 1  
39E C2     C2     C 0 1 Y N N 2.052  27.688 -6.097 2.052  27.688 -6.097 C2     39E 2  
39E N3     N3     N 0 1 Y N N 1.995  27.041 -4.939 1.995  27.041 -4.939 N3     39E 3  
39E C4     C4     C 0 1 Y N N 2.296  27.696 -3.817 2.296  27.696 -3.817 C4     39E 4  
39E C5     C5     C 0 1 Y N N 2.717  29.075 -3.808 2.717  29.075 -3.808 C5     39E 5  
39E C6     C6     C 0 1 Y N N 2.780  29.691 -5.035 2.780  29.691 -5.035 C6     39E 6  
39E "N2'"  "N2'"  N 0 1 N N N 1.827  26.999 -7.230 1.827  26.999 -7.230 "N2'"  39E 7  
39E "N4'"  "N4'"  N 0 1 N N N 2.191  26.976 -2.651 2.191  26.976 -2.651 "N4'"  39E 8  
39E "C6'"  "C6'"  C 0 1 N N N 3.227  31.132 -5.261 3.227  31.132 -5.261 "C6'"  39E 9  
39E "C5'"  "C5'"  C 0 1 N N N 3.131  29.740 -2.519 3.131  29.740 -2.519 "C5'"  39E 10 
39E C1C    C1C    C 0 1 N N N 2.200  30.727 -1.820 2.200  30.727 -1.820 C1C    39E 11 
39E C2C    C2C    C 0 1 N N N 0.662  30.518 -1.839 0.662  30.518 -1.839 C2C    39E 12 
39E B4     B4     B 0 1 N N N 2.622  32.266 -1.795 2.622  32.266 -1.795 B4     39E 13 
39E B5     B5     B 0 1 N N N 2.734  31.348 -0.308 2.734  31.348 -0.308 B5     39E 14 
39E B6     B6     B 0 1 N N N 1.459  30.150 -0.357 1.459  30.150 -0.357 B6     39E 15 
39E B7     B7     B 0 1 N N N -0.076 30.985 -0.363 -0.076 30.985 -0.363 B7     39E 16 
39E B8     B8     B 0 1 N N N -0.161 31.925 -1.860 -0.161 31.925 -1.860 B8     39E 17 
39E B9     B9     B 0 1 N N N 1.103  33.221 -1.779 1.103  33.221 -1.779 B9     39E 18 
39E B10    B10    B 0 1 N N N 2.019  32.931 -0.292 2.019  32.931 -0.292 B10    39E 19 
39E B11    B11    B 0 1 N N N 1.267  31.612 0.602  1.267  31.612 0.602  B11    39E 20 
39E B12    B12    B 0 1 N N N 0.243  32.728 -0.337 0.243  32.728 -0.337 B12    39E 21 
39E "H2'1" "H2'1" H 0 0 N N N 1.988  27.592 -8.019 1.771  27.633 -8.001 "H2'1" 39E 22 
39E HA2    HA2    H 0 1 N N N 2.446  26.215 -7.271 2.576  26.355 -7.382 HA2    39E 23 
39E HA1    HA1    H 0 1 N N N 1.893  26.044 -2.860 2.165  25.999 -2.863 HA1    39E 24 
39E HB2    HB2    H 0 1 N N N 3.081  26.948 -2.196 2.980  27.170 -2.068 HB2    39E 25 
39E HB1    HB1    H 0 1 N N N 3.332  28.933 -1.799 3.301  28.925 -1.800 HB1    39E 26 
39E HC2    HC2    H 0 1 N N N 4.064  30.283 -2.731 3.984  30.366 -2.819 HC2    39E 27 
39E HC1    HC1    H 0 1 N N N 3.195  31.362 -6.336 3.335  31.639 -4.291 HC1    39E 28 
39E HD2    HD2    H 0 1 N N N 2.554  31.814 -4.720 4.193  31.138 -5.787 HD2    39E 29 
39E HE3    HE3    H 0 1 N N N 4.254  31.260 -4.889 2.475  31.658 -5.868 HE3    39E 30 
39E HB4    HB4    H 0 1 N N N 3.601  32.714 -2.325 2.934  32.901 -2.764 HB4    39E 31 
39E HB5    HB5    H 0 1 N N N ?      ?      ?      0.000  0.000  0.000  HB5    39E 32 
39E HB6    HB6    H 0 1 N N N ?      ?      ?      0.000  0.000  0.000  HB6    39E 33 
39E HB7    HB7    H 0 1 N N N ?      ?      ?      0.000  0.000  0.000  HB7    39E 34 
39E HB9    HB9    H 0 1 N N N ?      ?      ?      0.000  0.000  0.000  HB9    39E 35 
39E HB10   HB10   H 0 0 N N N ?      ?      ?      0.000  0.000  0.000  HB10   39E 36 
39E H2C    H2C    H 0 1 N N N ?      ?      ?      0.000  0.000  0.000  H2C    39E 37 
39E HB8    HB8    H 0 1 N N N ?      ?      ?      0.000  0.000  0.000  HB8    39E 38 
39E HB9A   HB9A   H 0 0 N N N 1.135  33.208 -2.979 1.107  33.993 -2.698 HB9A   39E 39 
39E HB11   HB11   H 0 0 N N N ?      ?      ?      0.000  0.000  0.000  HB11   39E 40 
39E HB12   HB12   H 0 0 N N N ?      ?      ?      0.000  0.000  0.000  HB12   39E 41 
# 
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 
39E N1    C2     SING Y N 1  
39E C2    N3     DOUB Y N 2  
39E N3    C4     SING Y N 3  
39E C4    C5     DOUB Y N 4  
39E N1    C6     DOUB Y N 5  
39E C5    C6     SING Y N 6  
39E C2    "N2'"  SING N N 7  
39E C4    "N4'"  SING N N 8  
39E C6    "C6'"  SING N N 9  
39E C5    "C5'"  SING N N 10 
39E "C5'" C1C    SING N N 11 
39E C1C   C2C    SING N N 12 
39E C1C   B4     SING N N 13 
39E C1C   B5     SING N N 14 
39E B4    B5     SING N N 15 
39E B5    B6     SING N N 16 
39E C1C   B6     SING N N 17 
39E C2C   B6     SING N N 18 
39E B6    B7     SING N N 19 
39E C2C   B7     SING N N 20 
39E B7    B8     SING N N 21 
39E C2C   B8     SING N N 22 
39E B4    B10    SING N N 23 
39E B5    B10    SING N N 24 
39E B9    B10    SING N N 25 
39E B5    B11    SING N N 26 
39E B6    B11    SING N N 27 
39E B7    B11    SING N N 28 
39E B10   B11    SING N N 29 
39E B7    B12    SING N N 30 
39E B8    B12    SING N N 31 
39E B9    B12    SING N N 32 
39E B10   B12    SING N N 33 
39E B11   B12    SING N N 34 
39E "N2'" "H2'1" SING N N 35 
39E "N2'" HA2    SING N N 36 
39E "N4'" HA1    SING N N 37 
39E "N4'" HB2    SING N N 38 
39E "C5'" HB1    SING N N 39 
39E "C5'" HC2    SING N N 40 
39E "C6'" HC1    SING N N 41 
39E "C6'" HD2    SING N N 42 
39E "C6'" HE3    SING N N 43 
39E B4    HB4    SING N N 44 
39E B5    HB5    SING N N 45 
39E B6    HB6    SING N N 46 
39E B7    HB7    SING N N 47 
39E B8    HB9    SING N N 48 
39E B9    HB9    SING N N 49 
39E B10   HB10   SING N N 50 
39E C2C   H2C    SING N N 51 
39E B8    HB8    SING N N 52 
39E B9    HB9A   SING N N 53 
39E B11   HB11   SING N N 54 
39E B12   HB12   SING N N 55 
# 
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 
39E 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"                                                                  
39E InChI            InChI                1.06  "InChI=1S/C8H20B9N4/c1-3-4(5(18)21-6(19)20-3)2-8-7-11-13(7)12(7,8)14(8)9(8)15(14)10(22-11)16(11,13,15)17(12,13,14)15/h7,9-17H,2H2,1H3,(H4,18,19,20,21)" 
39E InChIKey         InChI                1.06  ITWYLEOPKOXNTM-UHFFFAOYSA-N                                                                                                                             
39E SMILES_CANONICAL CACTVS               3.385 "Cc1nc(N)nc(N)c1C[C+]234[BH-]5[BH]267[BH]389[CH]4%10[BH2]%11[BH]%12%13%14[BH2-][BH+]56%12[BH]78%13[BH]9%10%11%14"                                       
39E SMILES           CACTVS               3.385 "Cc1nc(N)nc(N)c1C[C+]234[BH-]5[BH]267[BH]389[CH]4%10[BH2]%11[BH]%12%13%14[BH2-][BH+]56%12[BH]78%13[BH]9%10%11%14"                                       
39E SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]1[BH]2[BH]345[BH]267[BH]18[BH]691[BH]732[BH]434[BH]292[CH]18C23([BH]54)Cc1c(nc(nc1N)N)C"                                                            
39E SMILES           "OpenEye OEToolkits" 2.0.7 "[H]1[BH]2[BH]345[BH]267[BH]18[BH]691[BH]732[BH]434[BH]292[CH]18C23([BH]54)Cc1c(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 
39E "Create component"   2005-09-30 EBI  
39E "Other modification" 2015-02-12 EBI  
39E "Modify descriptor"  2023-09-23 RCSB 
39E "Obsolete component" 2023-09-25 PDBE 
# 
