data_2VL
#

_chem_comp.id                                   2VL
_chem_comp.name                                 
;N-{3-[6-({4-[(2R)-1,4-dimethyl-3-oxopiperazin-2-yl]phenyl}amino)-4-methyl-5-oxo-4,5-dihydropyrazin-2-yl]-2-methylphenyl
}-4,5,6,7-tetrahydro-1-benzothiophene-2-carboxamide
;

_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C33 H36 N6 O3 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        GDC0834
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2014-02-25
_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                       596.742
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    2VL
_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       4OTF
_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
2VL  C1   C1   C  0  1  N  N  N  -38.071  27.649   -6.950   0.145   2.243   0.999  C1   2VL   1  
2VL  C2   C2   C  0  1  Y  N  N  -39.047  27.739   -8.115   0.076   2.660  -0.448  C2   2VL   2  
2VL  C3   C3   C  0  1  Y  N  N  -38.593  27.992   -9.433   1.229   3.068  -1.113  C3   2VL   3  
2VL  C4   C4   C  0  1  Y  N  N  -39.531  28.075  -10.467   1.159   3.447  -2.453  C4   2VL   4  
2VL  C5   C5   C  0  1  Y  N  N  -40.889  27.893  -10.209  -0.050   3.417  -3.117  C5   2VL   5  
2VL  C6   C6   C  0  1  Y  N  N  -41.333  27.638   -8.920  -1.196   3.012  -2.457  C6   2VL   6  
2VL  C7   C7   C  0  1  Y  N  N  -40.418  27.575   -7.870  -1.136   2.633  -1.122  C7   2VL   7  
2VL  N8   N8   N  0  1  N  N  N  -40.793  27.279   -6.547  -2.296   2.218  -0.460  N8   2VL   8  
2VL  C9   C9   C  0  1  N  N  N  -40.936  28.200   -5.572  -3.244   1.532  -1.128  C9   2VL   9  
2VL  O10  O10  O  0  1  N  N  N  -40.769  29.379   -5.802  -3.126   1.337  -2.324  O10  2VL  10  
2VL  C11  C11  C  0  1  Y  N  N  -41.209  27.813   -4.191  -4.418   1.020  -0.415  C11  2VL  11  
2VL  C12  C12  C  0  1  Y  N  N  -41.033  26.594   -3.587  -5.438   0.315  -0.977  C12  2VL  12  
2VL  C13  C13  C  0  1  Y  N  N  -41.330  26.607   -2.215  -6.428  -0.054  -0.085  C13  2VL  13  
2VL  C14  C14  C  0  1  Y  N  N  -41.717  27.817   -1.739  -6.201   0.353   1.185  C14  2VL  14  
2VL  S15  S15  S  0  1  Y  N  N  -41.690  28.981   -2.985  -4.729   1.209   1.303  S15  2VL  15  
2VL  C16  C16  C  0  1  N  N  N  -42.095  28.125   -0.288  -7.132   0.077   2.351  C16  2VL  16  
2VL  C17  C17  C  0  1  N  N  N  -42.283  26.822    0.498  -8.499  -0.337   1.801  C17  2VL  17  
2VL  C18  C18  C  0  1  N  N  N  -41.132  25.855    0.160  -8.304  -1.443   0.760  C18  2VL  18  
2VL  C19  C19  C  0  1  N  N  N  -41.262  25.386   -1.297  -7.663  -0.846  -0.494  C19  2VL  19  
2VL  C20  C20  C  0  1  N  N  N  -37.159  28.199   -9.795   2.528   3.100  -0.397  C20  2VL  20  
2VL  C21  C21  C  0  1  N  N  N  -36.294  28.877   -8.975   3.215   4.272  -0.317  C21  2VL  21  
2VL  N22  N22  N  0  1  N  N  N  -34.986  29.066   -9.324   4.410   4.336   0.332  N22  2VL  22  
2VL  C23  C23  C  0  1  N  N  N  -34.528  28.608  -10.512   4.912   3.219   0.901  C23  2VL  23  
2VL  O24  O24  O  0  1  N  N  N  -33.363  28.755  -10.895   5.980   3.247   1.489  O24  2VL  24  
2VL  C25  C25  C  0  1  N  N  N  -35.466  27.885  -11.363   4.147   1.971   0.797  C25  2VL  25  
2VL  N26  N26  N  0  1  N  N  N  -36.714  27.706  -10.972   2.996   1.975   0.161  N26  2VL  26  
2VL  N27  N27  N  0  1  N  N  N  -34.955  27.412  -12.551   4.628   0.802   1.372  N27  2VL  27  
2VL  C28  C28  C  0  1  Y  N  N  -35.663  26.953  -13.668   3.950  -0.404   1.174  C28  2VL  28  
2VL  C29  C29  C  0  1  Y  N  N  -37.042  26.770  -13.701   3.310  -0.653  -0.033  C29  2VL  29  
2VL  C30  C30  C  0  1  Y  N  N  -37.640  26.297  -14.873   2.642  -1.846  -0.226  C30  2VL  30  
2VL  C31  C31  C  0  1  Y  N  N  -36.863  26.013  -15.991   2.609  -2.792   0.782  C31  2VL  31  
2VL  C32  C32  C  0  1  Y  N  N  -35.493  26.190  -15.959   3.245  -2.548   1.985  C32  2VL  32  
2VL  C33  C33  C  0  1  Y  N  N  -34.896  26.665  -14.799   3.920  -1.359   2.183  C33  2VL  33  
2VL  C34  C34  C  0  1  N  N  R  -37.478  25.503  -17.273   1.874  -4.090   0.570  C34  2VL  34  
2VL  C36  C36  C  0  1  N  N  N  -38.542  26.478  -17.700   2.741  -5.033  -0.215  C36  2VL  35  
2VL  O37  O37  O  0  1  N  N  N  -38.180  27.595  -18.016   3.918  -5.113   0.068  O37  2VL  36  
2VL  N38  N38  N  0  1  N  N  N  -39.849  26.152  -17.711   2.270  -5.788  -1.213  N38  2VL  37  
2VL  C39  C39  C  0  1  N  N  N  -40.304  24.812  -17.335   0.879  -5.741  -1.656  C39  2VL  38  
2VL  C40  C40  C  0  1  N  N  N  -39.226  23.792  -17.719   0.007  -5.100  -0.575  C40  2VL  39  
2VL  N41  N41  N  0  1  N  N  N  -37.981  24.143  -17.002   0.626  -3.830  -0.160  N41  2VL  40  
2VL  C42  C42  C  0  1  N  N  N  -36.914  23.141  -17.152  -0.303  -3.033   0.652  C42  2VL  41  
2VL  C43  C43  C  0  1  N  N  N  -40.861  27.138  -18.126   3.190  -6.703  -1.893  C43  2VL  42  
2VL  C44  C44  C  0  1  N  N  N  -34.087  29.785   -8.406   5.142   5.602   0.412  C44  2VL  43  
2VL  H1   H1   H  0  1  N  N  N  -37.932  28.647   -6.510   0.255   1.161   1.060  H1   2VL  44  
2VL  H2   H2   H  0  1  N  N  N  -38.472  26.965   -6.188   1.000   2.723   1.475  H2   2VL  45  
2VL  H3   H3   H  0  1  N  N  N  -37.104  27.270   -7.311  -0.771   2.544   1.508  H3   2VL  46  
2VL  H4   H4   H  0  1  N  N  N  -39.201  28.282  -11.474   2.052   3.764  -2.971  H4   2VL  47  
2VL  H5   H5   H  0  1  N  N  N  -41.601  27.951  -11.019  -0.102   3.711  -4.155  H5   2VL  48  
2VL  H6   H6   H  0  1  N  N  N  -42.386  27.489   -8.730  -2.140   2.991  -2.982  H6   2VL  49  
2VL  H7   H7   H  0  1  N  N  N  -40.965  26.322   -6.314  -2.418   2.424   0.480  H7   2VL  50  
2VL  H8   H8   H  0  1  N  N  N  -40.699  25.712   -4.114  -5.472   0.067  -2.028  H8   2VL  51  
2VL  H9   H9   H  0  1  N  N  N  -41.294  28.718    0.178  -6.724  -0.728   2.961  H9   2VL  52  
2VL  H10  H10  H  0  1  N  N  N  -43.034  28.698   -0.271  -7.238   0.979   2.954  H10  2VL  53  
2VL  H11  H11  H  0  1  N  N  N  -42.277  27.039    1.576  -9.122  -0.709   2.615  H11  2VL  54  
2VL  H12  H12  H  0  1  N  N  N  -43.243  26.361    0.222  -8.981   0.523   1.336  H12  2VL  55  
2VL  H13  H13  H  0  1  N  N  N  -41.177  24.984    0.830  -7.654  -2.217   1.168  H13  2VL  56  
2VL  H14  H14  H  0  1  N  N  N  -40.170  26.371    0.294  -9.270  -1.877   0.504  H14  2VL  57  
2VL  H15  H15  H  0  1  N  N  N  -42.179  24.789   -1.411  -8.374  -0.185  -0.988  H15  2VL  58  
2VL  H16  H16  H  0  1  N  N  N  -40.389  24.772   -1.565  -7.373  -1.648  -1.173  H16  2VL  59  
2VL  H17  H17  H  0  1  N  N  N  -36.653  29.269   -8.035   2.808   5.162  -0.775  H17  2VL  60  
2VL  H18  H18  H  0  1  N  N  N  -33.958  27.394  -12.625   5.433   0.822   1.912  H18  2VL  61  
2VL  H19  H19  H  0  1  N  N  N  -37.643  26.991  -12.831   3.335   0.086  -0.821  H19  2VL  62  
2VL  H20  H20  H  0  1  N  N  N  -38.710  26.152  -14.910   2.145  -2.040  -1.165  H20  2VL  63  
2VL  H21  H21  H  0  1  N  N  N  -34.893  25.961  -16.827   3.217  -3.289   2.770  H21  2VL  64  
2VL  H22  H22  H  0  1  N  N  N  -33.827  26.813  -14.771   4.417  -1.169   3.123  H22  2VL  65  
2VL  H23  H23  H  0  1  N  N  N  -36.700  25.458  -18.049   1.641  -4.536   1.537  H23  2VL  66  
2VL  H24  H24  H  0  1  N  N  N  -41.239  24.578  -17.865   0.811  -5.154  -2.572  H24  2VL  67  
2VL  H25  H25  H  0  1  N  N  N  -40.479  24.773  -16.250   0.527  -6.754  -1.848  H25  2VL  68  
2VL  H26  H26  H  0  1  N  N  N  -39.550  22.781  -17.430  -0.988  -4.907  -0.976  H26  2VL  69  
2VL  H27  H27  H  0  1  N  N  N  -39.052  23.825  -18.805  -0.065  -5.769   0.282  H27  2VL  70  
2VL  H29  H29  H  0  1  N  N  N  -36.023  23.467  -16.595   0.161  -2.079   0.902  H29  2VL  71  
2VL  H30  H30  H  0  1  N  N  N  -37.260  22.175  -16.756  -1.218  -2.855   0.088  H30  2VL  72  
2VL  H31  H31  H  0  1  N  N  N  -36.661  23.032  -18.217  -0.540  -3.573   1.569  H31  2VL  73  
2VL  H32  H32  H  0  1  N  N  N  -41.861  26.684  -18.067   4.182  -6.619  -1.448  H32  2VL  74  
2VL  H33  H33  H  0  1  N  N  N  -40.816  28.012  -17.460   2.830  -7.726  -1.786  H33  2VL  75  
2VL  H34  H34  H  0  1  N  N  N  -40.662  27.454  -19.161   3.244  -6.445  -2.951  H34  2VL  76  
2VL  H35  H35  H  0  1  N  N  N  -34.641  30.074   -7.501   4.836   6.143   1.308  H35  2VL  77  
2VL  H36  H36  H  0  1  N  N  N  -33.247  29.131   -8.128   6.212   5.401   0.458  H36  2VL  78  
2VL  H37  H37  H  0  1  N  N  N  -33.701  30.687   -8.903   4.923   6.205  -0.469  H37  2VL  79  
#   #
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
2VL  C43  N38  SING  N  N   1  
2VL  O37  C36  DOUB  N  N   2  
2VL  C40  C39  SING  N  N   3  
2VL  C40  N41  SING  N  N   4  
2VL  N38  C36  SING  N  N   5  
2VL  N38  C39  SING  N  N   6  
2VL  C36  C34  SING  N  N   7  
2VL  C34  N41  SING  N  N   8  
2VL  C34  C31  SING  N  N   9  
2VL  C42  N41  SING  N  N  10  
2VL  C31  C32  DOUB  Y  N  11  
2VL  C31  C30  SING  Y  N  12  
2VL  C32  C33  SING  Y  N  13  
2VL  C30  C29  DOUB  Y  N  14  
2VL  C33  C28  DOUB  Y  N  15  
2VL  C29  C28  SING  Y  N  16  
2VL  C28  N27  SING  N  N  17  
2VL  N27  C25  SING  N  N  18  
2VL  C25  N26  DOUB  N  N  19  
2VL  C25  C23  SING  N  N  20  
2VL  N26  C20  SING  N  N  21  
2VL  O24  C23  DOUB  N  N  22  
2VL  C23  N22  SING  N  N  23  
2VL  C4   C5   DOUB  Y  N  24  
2VL  C4   C3   SING  Y  N  25  
2VL  C5   C6   SING  Y  N  26  
2VL  C20  C3   SING  N  N  27  
2VL  C20  C21  DOUB  N  N  28  
2VL  C3   C2   DOUB  Y  N  29  
2VL  N22  C21  SING  N  N  30  
2VL  N22  C44  SING  N  N  31  
2VL  C6   C7   DOUB  Y  N  32  
2VL  C2   C7   SING  Y  N  33  
2VL  C2   C1   SING  N  N  34  
2VL  C7   N8   SING  N  N  35  
2VL  N8   C9   SING  N  N  36  
2VL  O10  C9   DOUB  N  N  37  
2VL  C9   C11  SING  N  N  38  
2VL  C11  C12  DOUB  Y  N  39  
2VL  C11  S15  SING  Y  N  40  
2VL  C12  C13  SING  Y  N  41  
2VL  S15  C14  SING  Y  N  42  
2VL  C13  C14  DOUB  Y  N  43  
2VL  C13  C19  SING  N  N  44  
2VL  C14  C16  SING  N  N  45  
2VL  C19  C18  SING  N  N  46  
2VL  C16  C17  SING  N  N  47  
2VL  C18  C17  SING  N  N  48  
2VL  C1   H1   SING  N  N  49  
2VL  C1   H2   SING  N  N  50  
2VL  C1   H3   SING  N  N  51  
2VL  C4   H4   SING  N  N  52  
2VL  C5   H5   SING  N  N  53  
2VL  C6   H6   SING  N  N  54  
2VL  N8   H7   SING  N  N  55  
2VL  C12  H8   SING  N  N  56  
2VL  C16  H9   SING  N  N  57  
2VL  C16  H10  SING  N  N  58  
2VL  C17  H11  SING  N  N  59  
2VL  C17  H12  SING  N  N  60  
2VL  C18  H13  SING  N  N  61  
2VL  C18  H14  SING  N  N  62  
2VL  C19  H15  SING  N  N  63  
2VL  C19  H16  SING  N  N  64  
2VL  C21  H17  SING  N  N  65  
2VL  N27  H18  SING  N  N  66  
2VL  C29  H19  SING  N  N  67  
2VL  C30  H20  SING  N  N  68  
2VL  C32  H21  SING  N  N  69  
2VL  C33  H22  SING  N  N  70  
2VL  C34  H23  SING  N  N  71  
2VL  C39  H24  SING  N  N  72  
2VL  C39  H25  SING  N  N  73  
2VL  C40  H26  SING  N  N  74  
2VL  C40  H27  SING  N  N  75  
2VL  C42  H29  SING  N  N  76  
2VL  C42  H30  SING  N  N  77  
2VL  C42  H31  SING  N  N  78  
2VL  C43  H32  SING  N  N  79  
2VL  C43  H33  SING  N  N  80  
2VL  C43  H34  SING  N  N  81  
2VL  C44  H35  SING  N  N  82  
2VL  C44  H36  SING  N  N  83  
2VL  C44  H37  SING  N  N  84  
#   #
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
2VL  SMILES            ACDLabs               12.01  "O=C1N(C)CCN(C)C1c2ccc(cc2)NC3=NC(=CN(C3=O)C)c4cccc(c4C)NC(=O)c5sc6c(c5)CCCC6"  
2VL  InChI             InChI                 1.03   "InChI=1S/C33H36N6O3S/c1-20-24(9-7-10-25(20)36-31(40)28-18-22-8-5-6-11-27(22)43-28)26-19-39(4)33(42)30(35-26)34-23-14-12-21(13-15-23)29-32(41)38(3)17-16-37(29)2/h7,9-10,12-15,18-19,29H,5-6,8,11,16-17H2,1-4H3,(H,34,35)(H,36,40)/t29-/m1/s1"  
2VL  InChIKey          InChI                 1.03   CDOOFZZILLRUQH-GDLZYMKVSA-N  
2VL  SMILES_CANONICAL  CACTVS                3.385  "CN1CCN(C)C(=O)[C@H]1c2ccc(NC3=NC(=CN(C)C3=O)c4cccc(NC(=O)c5sc6CCCCc6c5)c4C)cc2"  
2VL  SMILES            CACTVS                3.385  "CN1CCN(C)C(=O)[CH]1c2ccc(NC3=NC(=CN(C)C3=O)c4cccc(NC(=O)c5sc6CCCCc6c5)c4C)cc2"  
2VL  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "Cc1c(cccc1NC(=O)c2cc3c(s2)CCCC3)C4=CN(C(=O)C(=N4)Nc5ccc(cc5)[C@@H]6C(=O)N(CCN6C)C)C"  
2VL  SMILES            "OpenEye OEToolkits"  1.7.6  "Cc1c(cccc1NC(=O)c2cc3c(s2)CCCC3)C4=CN(C(=O)C(=N4)Nc5ccc(cc5)C6C(=O)N(CCN6C)C)C"  
#   #
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
2VL  "SYSTEMATIC NAME"  ACDLabs               12.01  "N-{3-[6-({4-[(2R)-1,4-dimethyl-3-oxopiperazin-2-yl]phenyl}amino)-4-methyl-5-oxo-4,5-dihydropyrazin-2-yl]-2-methylphenyl}-4,5,6,7-tetrahydro-1-benzothiophene-2-carboxamide"  
2VL  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "N-[3-[6-[[4-[(2R)-1,4-dimethyl-3-oxidanylidene-piperazin-2-yl]phenyl]amino]-4-methyl-5-oxidanylidene-pyrazin-2-yl]-2-methyl-phenyl]-4,5,6,7-tetrahydro-1-benzothiophene-2-carboxamide"  
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loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
2VL  "Create component"  2014-02-25  RCSB  
2VL  "Modify synonyms"   2015-01-22  RCSB  
2VL  "Initial release"   2015-01-28  RCSB  
2VL  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     2VL
_pdbx_chem_comp_synonyms.name        GDC0834
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
