data_B39
# 
_chem_comp.id                                    B39 
_chem_comp.name                                  "[(1S,2S,4R)-4-{4-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-2-hydroxycyclopentyl]methyl sulfamate" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H25 N5 O4 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2009-04-17 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        443.519 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     B39 
_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        3GZN 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              Y 
# 
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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
B39 C4   C4   C 0 1 N N R N N N 8.687  89.106 41.149 -1.628 0.227  -0.254 C4   B39 1  
B39 C5   C5   C 0 1 N N N N N N 10.203 89.450 41.232 -2.619 -0.934 -0.032 C5   B39 2  
B39 C6   C6   C 0 1 N N S N N N 10.284 90.933 41.640 -3.901 -0.571 -0.801 C6   B39 3  
B39 C8   C8   C 0 1 N N N N N N 11.463 91.620 40.938 -5.082 -0.474 0.166  C8   B39 4  
B39 C10  C10  C 0 1 Y N N N N N 8.033  87.114 44.063 1.459  -1.421 -1.217 C10  B39 5  
B39 C13  C13  C 0 1 Y N N N N N 7.429  87.092 41.970 0.785  0.040  0.420  C13  B39 6  
B39 C15  C15  C 0 1 Y N N N N N 5.996  85.529 40.996 2.091  0.942  2.086  C15  B39 7  
B39 C17  C17  C 0 1 Y N N N N N 6.466  85.304 43.259 3.134  -0.499 0.616  C17  B39 8  
B39 C20  C20  C 0 1 N N N N N N 5.757  85.937 46.442 6.450  -2.208 0.688  C20  B39 9  
B39 C21  C21  C 0 1 Y N N N N N 6.714  83.765 46.683 6.303  0.188  0.324  C21  B39 10 
B39 C22  C22  C 0 1 Y N N N N N 6.367  84.215 47.969 7.309  -0.275 -0.503 C22  B39 11 
B39 C24  C24  C 0 1 Y N N N N N 6.574  81.966 48.802 7.973  1.984  -0.959 C24  B39 12 
B39 C26  C26  C 0 1 Y N N N N N 6.992  82.416 46.463 6.133  1.550  0.508  C26  B39 13 
B39 C19  C19  C 0 1 N N N N N N 6.118  85.726 47.909 7.287  -1.788 -0.538 C19  B39 14 
B39 C23  C23  C 0 1 Y N N N N N 6.296  83.314 49.028 8.143  0.626  -1.144 C23  B39 15 
B39 C25  C25  C 0 1 Y N N N N N 6.920  81.517 47.525 6.965  2.447  -0.133 C25  B39 16 
B39 C1   C1   C 0 1 N N S N N N 6.720  84.976 45.742 5.536  -0.983 0.901  C1   B39 17 
B39 N18  N18  N 0 1 N N N N N N 6.255  84.597 44.386 4.269  -1.162 0.187  N18  B39 18 
B39 N16  N16  N 0 1 Y N N N N N 5.845  84.881 42.141 3.173  0.306  1.674  N16  B39 19 
B39 N14  N14  N 0 1 Y N N N N N 6.770  86.614 40.900 0.925  0.823  1.488  N14  B39 20 
B39 C12  C12  C 0 1 Y N N N N N 7.287  86.443 43.187 1.912  -0.658 -0.055 C12  B39 21 
B39 C11  C11  C 0 1 Y N N N N N 8.626  88.137 43.451 0.152  -1.156 -1.370 C11  B39 22 
B39 N7   N7   N 0 1 Y N N N N N 8.258  88.116 42.173 -0.263 -0.283 -0.397 N7   B39 23 
B39 C3   C3   C 0 1 N N N N N N 7.931  90.425 41.393 -2.103 0.885  -1.573 C3   B39 24 
B39 C2   C2   C 0 1 N N S N N N 8.957  91.534 41.172 -3.645 0.799  -1.462 C2   B39 25 
B39 O9   O9   O 0 1 N N N N N N 9.022  91.821 39.778 -4.148 1.853  -0.639 O9   B39 26 
B39 O27  O27  O 0 1 N N N N N N 12.329 92.252 41.872 -6.286 -0.251 -0.572 O27  B39 27 
B39 S28  S28  S 0 1 N N N N N N 12.832 93.578 41.718 -7.531 -0.137 0.295  S28  B39 28 
B39 O29  O29  O 0 1 N N N N N N 13.300 93.830 40.324 -8.639 -0.122 -0.594 O29  B39 29 
B39 O30  O30  O 0 1 N N N N N N 11.758 94.566 42.017 -7.384 -1.092 1.337  O30  B39 30 
B39 N31  N31  N 0 1 N N N N N N 14.062 93.804 42.767 -7.492 1.352  1.018  N31  B39 31 
B39 H4   H4   H 0 1 N N N N N N 8.475  88.657 40.168 -1.684 0.938  0.571  H4   B39 32 
B39 H5   H5   H 0 1 N N N N N N 10.703 88.815 41.978 -2.200 -1.862 -0.423 H5   B39 33 
B39 H5A  H5A  H 0 1 N N N N N N 10.707 89.272 40.271 -2.838 -1.041 1.030  H5A  B39 34 
B39 H6   H6   H 0 1 N N N N N N 10.443 91.062 42.721 -4.105 -1.322 -1.564 H6   B39 35 
B39 H8   H8   H 0 1 N N N N N N 12.034 90.863 40.381 -5.168 -1.403 0.730  H8   B39 36 
B39 H8A  H8A  H 0 1 N N N N N N 11.063 92.389 40.262 -4.920 0.355  0.855  H8A  B39 37 
B39 H10  H10  H 0 1 N N N N N N 8.140  86.866 45.109 2.062  -2.070 -1.835 H10  B39 38 
B39 H15  H15  H 0 1 N N N N N N 5.480  85.171 40.117 2.167  1.586  2.949  H15  B39 39 
B39 H20  H20  H 0 1 N N N N N N 4.705  85.693 46.235 5.859  -3.098 0.467  H20  B39 40 
B39 H20A H20A H 0 0 N N N N N N 5.853  86.981 46.108 7.088  -2.372 1.556  H20A B39 41 
B39 H24  H24  H 0 1 N N N N N N 6.521  81.264 49.621 8.625  2.684  -1.460 H24  B39 42 
B39 H26  H26  H 0 1 N N N N N N 7.261  82.071 45.476 5.347  1.912  1.154  H26  B39 43 
B39 H19  H19  H 0 1 N N N N N N 7.009  86.301 48.200 8.300  -2.182 -0.458 H19  B39 44 
B39 H19A H19A H 0 0 N N N N N N 5.339  86.069 48.606 6.816  -2.138 -1.457 H19A B39 45 
B39 H23  H23  H 0 1 N N N N N N 6.028  83.656 50.017 8.929  0.266  -1.790 H23  B39 46 
B39 H25  H25  H 0 1 N N N N N N 7.132  80.471 47.361 6.831  3.509  0.013  H25  B39 47 
B39 H1   H1   H 0 1 N N N N N N 7.715  85.414 45.577 5.353  -0.828 1.964  H1   B39 48 
B39 HN18 HN18 H 0 0 N N N N N N 5.259  84.551 44.468 4.227  -1.747 -0.586 HN18 B39 49 
B39 H11  H11  H 0 1 N N N N N N 9.288  88.856 43.911 -0.479 -1.568 -2.144 H11  B39 50 
B39 H3   H3   H 0 1 N N N N N N 7.089  90.527 40.693 -1.777 1.924  -1.626 H3   B39 51 
B39 H3A  H3A  H 0 1 N N N N N N 7.503  90.465 42.405 -1.745 0.323  -2.435 H3A  B39 52 
B39 H2   H2   H 0 1 N N N N N N 8.713  92.464 41.707 -4.101 0.836  -2.452 H2   B39 53 
B39 HO9  HO9  H 0 1 N N N N N N 9.036  92.762 39.648 -4.013 2.738  -1.007 HO9  B39 54 
B39 HN31 HN31 H 0 0 N N N N N N 14.925 93.850 42.264 -6.754 1.957  0.842  HN31 B39 55 
B39 HN3A HN3A H 0 0 N N N N N N 13.921 94.659 43.266 -8.206 1.620  1.617  HN3A B39 56 
# 
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 
B39 C4  C5   SING N N 1  
B39 C4  N7   SING N N 2  
B39 C4  C3   SING N N 3  
B39 C5  C6   SING N N 4  
B39 C6  C8   SING N N 5  
B39 C6  C2   SING N N 6  
B39 C8  O27  SING N N 7  
B39 C10 C12  SING Y N 8  
B39 C10 C11  DOUB Y N 9  
B39 C13 N14  DOUB Y N 10 
B39 C13 C12  SING Y N 11 
B39 C13 N7   SING Y N 12 
B39 C15 N16  DOUB Y N 13 
B39 C15 N14  SING Y N 14 
B39 C17 N18  SING N N 15 
B39 C17 N16  SING Y N 16 
B39 C17 C12  DOUB Y N 17 
B39 C20 C19  SING N N 18 
B39 C20 C1   SING N N 19 
B39 C21 C22  DOUB Y N 20 
B39 C21 C26  SING Y N 21 
B39 C21 C1   SING N N 22 
B39 C22 C19  SING N N 23 
B39 C22 C23  SING Y N 24 
B39 C24 C23  DOUB Y N 25 
B39 C24 C25  SING Y N 26 
B39 C26 C25  DOUB Y N 27 
B39 C1  N18  SING N N 28 
B39 C11 N7   SING Y N 29 
B39 C3  C2   SING N N 30 
B39 C2  O9   SING N N 31 
B39 O27 S28  SING N N 32 
B39 S28 O29  DOUB N N 33 
B39 S28 O30  DOUB N N 34 
B39 S28 N31  SING N N 35 
B39 C4  H4   SING N N 36 
B39 C5  H5   SING N N 37 
B39 C5  H5A  SING N N 38 
B39 C6  H6   SING N N 39 
B39 C8  H8   SING N N 40 
B39 C8  H8A  SING N N 41 
B39 C10 H10  SING N N 42 
B39 C15 H15  SING N N 43 
B39 C20 H20  SING N N 44 
B39 C20 H20A SING N N 45 
B39 C24 H24  SING N N 46 
B39 C26 H26  SING N N 47 
B39 C19 H19  SING N N 48 
B39 C19 H19A SING N N 49 
B39 C23 H23  SING N N 50 
B39 C25 H25  SING N N 51 
B39 C1  H1   SING N N 52 
B39 N18 HN18 SING N N 53 
B39 C11 H11  SING N N 54 
B39 C3  H3   SING N N 55 
B39 C3  H3A  SING N N 56 
B39 C2  H2   SING N N 57 
B39 O9  HO9  SING N N 58 
B39 N31 HN31 SING N N 59 
B39 N31 HN3A SING N N 60 
# 
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 
B39 SMILES           ACDLabs              10.04 "O=S(=O)(OCC5CC(n2c1ncnc(c1cc2)NC4c3ccccc3CC4)CC5O)N"                                                                                                                                                              
B39 SMILES_CANONICAL CACTVS               3.341 "N[S](=O)(=O)OC[C@@H]1C[C@H](C[C@@H]1O)n2ccc3c(N[C@H]4CCc5ccccc45)ncnc23"                                                                                                                                          
B39 SMILES           CACTVS               3.341 "N[S](=O)(=O)OC[CH]1C[CH](C[CH]1O)n2ccc3c(N[CH]4CCc5ccccc45)ncnc23"                                                                                                                                                
B39 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1ccc2c(c1)CC[C@@H]2Nc3c4ccn(c4ncn3)[C@@H]5C[C@H]([C@H](C5)O)COS(=O)(=O)N"                                                                                                                                        
B39 SMILES           "OpenEye OEToolkits" 1.5.0 "c1ccc2c(c1)CCC2Nc3c4ccn(c4ncn3)C5CC(C(C5)O)COS(=O)(=O)N"                                                                                                                                                          
B39 InChI            InChI                1.03  "InChI=1S/C21H25N5O4S/c22-31(28,29)30-11-14-9-15(10-19(14)27)26-8-7-17-20(23-12-24-21(17)26)25-18-6-5-13-3-1-2-4-16(13)18/h1-4,7-8,12,14-15,18-19,27H,5-6,9-11H2,(H2,22,28,29)(H,23,24,25)/t14-,15+,18-,19-/m0/s1" 
B39 InChIKey         InChI                1.03  MPUQHZXIXSTTDU-QXGSTGNESA-N                                                                                                                                                                                        
# 
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 
B39 "SYSTEMATIC NAME" ACDLabs              10.04 "[(1S,2S,4R)-4-{4-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-2-hydroxycyclopentyl]methyl sulfamate" 
B39 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(1S,2S,4R)-4-[4-[[(1S)-2,3-dihydro-1H-inden-1-yl]amino]pyrrolo[2,3-d]pyrimidin-7-yl]-2-hydroxy-cyclopentyl]methyl sulfamate"  
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
B39 "Create component"     2009-04-17 RCSB 
B39 "Modify aromatic_flag" 2011-06-04 RCSB 
B39 "Modify descriptor"    2011-06-04 RCSB 
B39 "Modify PCM"           2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            B39 
_pdbx_chem_comp_pcm.modified_residue_id                GLY 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid backbone" 
_pdbx_chem_comp_pcm.polypeptide_position               C-terminal 
_pdbx_chem_comp_pcm.comp_id_linking_atom               N31 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   C 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
