data_2DY
#
_chem_comp.id 2DY
_chem_comp.name "(3S,10aS)-2-[(2S)-2-cyclohexyl-2-{[(2S)-2-(methylamino)butanoyl]amino}acetyl]-N-[(4R)-3,4-dihydro-2H-chromen-4-yl]-1,2,3,4,10,10a-hexahydropyrazino[1,2-a]indole-3-carboxamide"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C34 H45 N5 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2013-09-25
_chem_comp.pdbx_modified_date 2013-12-06
_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 587.752
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 2DY
_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 4MU7
_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
2DY C1 C1 C 0 1 N N N 21.170 -7.446 -11.646 -5.940 -1.510 3.283 C1 2DY 1
2DY C2 C2 C 0 1 N N N 22.254 -6.459 -11.212 -4.522 -1.894 2.858 C2 2DY 2
2DY C3 C3 C 0 1 N N S 23.626 -7.133 -11.304 -4.507 -2.219 1.363 C3 2DY 3
2DY N5 N5 N 0 1 N N N 24.625 -6.198 -10.745 -5.325 -3.414 1.114 N5 2DY 4
2DY C6 C6 C 0 1 N N N 25.980 -6.792 -10.584 -5.615 -3.564 -0.319 C6 2DY 5
2DY C7 C7 C 0 1 N N N 23.929 -7.461 -12.730 -3.091 -2.478 0.919 C7 2DY 6
2DY O8 O8 O 0 1 N N N 24.373 -6.599 -13.450 -2.631 -3.599 0.981 O8 2DY 7
2DY N9 N9 N 0 1 N N N 23.696 -8.699 -13.172 -2.334 -1.464 0.453 N9 2DY 8
2DY C10 C10 C 0 1 N N S 23.974 -9.184 -14.515 -0.957 -1.716 0.022 C10 2DY 9
2DY C12 C12 C 0 1 N N N 25.165 -10.081 -14.093 -0.957 -2.191 -1.433 C12 2DY 10
2DY C13 C13 C 0 1 N N N 25.072 -11.554 -14.505 -1.781 -3.475 -1.551 C13 2DY 11
2DY C14 C14 C 0 1 N N N 26.229 -12.383 -13.906 -1.781 -3.949 -3.005 C14 2DY 12
2DY C15 C15 C 0 1 N N N 27.338 -11.519 -13.269 -2.395 -2.866 -3.895 C15 2DY 13
2DY C16 C16 C 0 1 N N N 27.701 -10.325 -14.168 -1.572 -1.582 -3.777 C16 2DY 14
2DY C17 C17 C 0 1 N N N 26.495 -9.420 -14.474 -1.571 -1.108 -2.323 C17 2DY 15
2DY C18 C18 C 0 1 N N N 22.794 -9.923 -15.100 -0.155 -0.446 0.135 C18 2DY 16
2DY O19 O19 O 0 1 N N N 21.983 -10.394 -14.319 -0.656 0.617 -0.163 O19 2DY 17
2DY N20 N20 N 0 1 N N N 22.629 -10.093 -16.448 1.120 -0.491 0.570 N20 2DY 18
2DY C21 C21 C 0 1 N N N 23.628 -9.544 -17.415 1.699 -1.768 1.033 C21 2DY 19
2DY C22 C22 C 0 1 N N S 23.588 -10.410 -18.676 3.029 -1.935 0.301 C22 2DY 20
2DY C24 C24 C 0 1 N N N 24.522 -9.873 -19.791 3.896 -3.072 0.878 C24 2DY 21
2DY C25 C25 C 0 1 Y N N 23.592 -9.601 -20.962 5.287 -2.506 0.709 C25 2DY 22
2DY C26 C26 C 0 1 Y N N 23.891 -9.238 -22.266 6.510 -3.139 0.720 C26 2DY 23
2DY C27 C27 C 0 1 Y N N 22.815 -9.041 -23.140 7.638 -2.349 0.530 C27 2DY 24
2DY C28 C28 C 0 1 Y N N 21.497 -9.190 -22.732 7.536 -0.987 0.338 C28 2DY 25
2DY C29 C29 C 0 1 Y N N 21.181 -9.552 -21.426 6.313 -0.336 0.333 C29 2DY 26
2DY C30 C30 C 0 1 Y N N 22.250 -9.781 -20.540 5.171 -1.112 0.531 C30 2DY 27
2DY N31 N31 N 0 1 N N N 22.239 -10.085 -19.193 3.848 -0.737 0.630 N31 2DY 28
2DY C32 C32 C 0 1 N N N 21.086 -10.549 -18.445 3.352 0.459 -0.023 C32 2DY 29
2DY C33 C33 C 0 1 N N S 21.465 -10.831 -16.952 1.938 0.729 0.577 C33 2DY 30
2DY C35 C35 C 0 1 N N N 21.721 -12.310 -16.763 1.262 1.825 -0.206 C35 2DY 31
2DY O36 O36 O 0 1 N N N 22.869 -12.735 -16.649 0.668 1.561 -1.230 O36 2DY 32
2DY N37 N37 N 0 1 N N N 20.651 -13.130 -16.731 1.317 3.098 0.232 N37 2DY 33
2DY C38 C38 C 0 1 N N R 20.762 -14.583 -16.528 0.659 4.163 -0.530 C38 2DY 34
2DY C40 C40 C 0 1 N N N 20.976 -15.283 -17.879 1.347 5.499 -0.235 C40 2DY 35
2DY C41 C41 C 0 1 N N N 19.638 -15.654 -18.525 0.472 6.626 -0.798 C41 2DY 36
2DY O42 O42 O 0 1 N N N 18.968 -16.533 -17.622 -0.764 6.637 -0.082 O42 2DY 37
2DY C43 C43 C 0 1 Y N N 18.702 -16.051 -16.376 -1.422 5.458 0.066 C43 2DY 38
2DY C44 C44 C 0 1 Y N N 17.576 -16.522 -15.694 -2.766 5.489 0.426 C44 2DY 39
2DY C45 C45 C 0 1 Y N N 17.294 -16.027 -14.425 -3.467 4.312 0.591 C45 2DY 40
2DY C46 C46 C 0 1 Y N N 18.118 -15.070 -13.852 -2.835 3.098 0.397 C46 2DY 41
2DY C47 C47 C 0 1 Y N N 19.241 -14.610 -14.533 -1.502 3.064 0.036 C47 2DY 42
2DY C48 C48 C 0 1 Y N N 19.533 -15.093 -15.802 -0.793 4.241 -0.132 C48 2DY 43
2DY H1 H1 H 0 1 N N N 20.185 -6.962 -11.580 -6.264 -0.636 2.718 H1 2DY 44
2DY H2 H2 H 0 1 N N N 21.355 -7.761 -12.684 -6.617 -2.342 3.085 H2 2DY 45
2DY H3 H3 H 0 1 N N N 21.191 -8.326 -10.987 -5.951 -1.278 4.348 H3 2DY 46
2DY H4 H4 H 0 1 N N N 22.233 -5.579 -11.871 -3.845 -1.063 3.056 H4 2DY 47
2DY H5 H5 H 0 1 N N N 22.069 -6.144 -10.174 -4.198 -2.768 3.423 H5 2DY 48
2DY H6 H6 H 0 1 N N N 23.611 -8.059 -10.710 -4.915 -1.377 0.804 H6 2DY 49
2DY H7 H7 H 0 1 N N N 24.697 -5.410 -11.357 -4.878 -4.241 1.480 H7 2DY 50
2DY H9 H9 H 0 1 N N N 26.664 -6.039 -10.165 -6.088 -2.655 -0.690 H9 2DY 51
2DY H10 H10 H 0 1 N N N 25.924 -7.655 -9.904 -4.686 -3.738 -0.861 H10 2DY 52
2DY H11 H11 H 0 1 N N N 26.354 -7.122 -11.564 -6.286 -4.410 -0.467 H11 2DY 53
2DY H12 H12 H 0 1 N N N 23.296 -9.348 -12.525 -2.702 -0.568 0.404 H12 2DY 54
2DY H13 H13 H 0 1 N N N 24.312 -8.379 -15.184 -0.513 -2.485 0.654 H13 2DY 55
2DY H14 H14 H 0 1 N N N 25.147 -10.085 -12.993 0.067 -2.385 -1.752 H14 2DY 56
2DY H15 H15 H 0 1 N N N 24.116 -11.965 -14.149 -1.343 -4.246 -0.917 H15 2DY 57
2DY H16 H16 H 0 1 N N N 25.114 -11.622 -15.602 -2.805 -3.280 -1.232 H16 2DY 58
2DY H17 H17 H 0 1 N N N 25.817 -13.048 -13.132 -0.757 -4.143 -3.324 H17 2DY 59
2DY H18 H18 H 0 1 N N N 26.676 -12.988 -14.709 -2.367 -4.864 -3.089 H18 2DY 60
2DY H19 H19 H 0 1 N N N 28.234 -12.140 -13.118 -2.395 -3.204 -4.931 H19 2DY 61
2DY H20 H20 H 0 1 N N N 26.985 -11.142 -12.298 -3.419 -2.672 -3.576 H20 2DY 62
2DY H21 H21 H 0 1 N N N 28.102 -10.709 -15.118 -0.548 -1.776 -4.096 H21 2DY 63
2DY H22 H22 H 0 1 N N N 28.471 -9.725 -13.661 -2.009 -0.811 -4.411 H22 2DY 64
2DY H23 H23 H 0 1 N N N 26.601 -8.484 -13.906 -2.595 -0.913 -2.004 H23 2DY 65
2DY H24 H24 H 0 1 N N N 26.484 -9.196 -15.551 -0.985 -0.193 -2.239 H24 2DY 66
2DY H25 H25 H 0 1 N N N 24.634 -9.576 -16.971 1.867 -1.733 2.109 H25 2DY 67
2DY H26 H26 H 0 1 N N N 23.372 -8.504 -17.667 1.030 -2.592 0.786 H26 2DY 68
2DY H27 H27 H 0 1 N N N 23.741 -11.480 -18.470 2.884 -2.044 -0.774 H27 2DY 69
2DY H28 H28 H 0 1 N N N 25.279 -10.624 -20.061 3.668 -3.243 1.930 H28 2DY 70
2DY H29 H29 H 0 1 N N N 25.023 -8.948 -19.468 3.774 -3.989 0.300 H29 2DY 71
2DY H30 H30 H 0 1 N N N 24.912 -9.112 -22.594 6.589 -4.206 0.871 H30 2DY 72
2DY H31 H31 H 0 1 N N N 23.017 -8.764 -24.164 8.614 -2.811 0.533 H31 2DY 73
2DY H32 H32 H 0 1 N N N 20.701 -9.022 -23.442 8.437 -0.410 0.187 H32 2DY 74
2DY H33 H33 H 0 1 N N N 20.155 -9.653 -21.105 6.246 0.731 0.183 H33 2DY 75
2DY H34 H34 H 0 1 N N N 20.301 -9.779 -18.478 4.028 1.292 0.166 H34 2DY 76
2DY H35 H35 H 0 1 N N N 20.709 -11.476 -18.902 3.266 0.286 -1.096 H35 2DY 77
2DY H36 H36 H 0 1 N N N 20.592 -10.561 -16.339 2.039 1.036 1.618 H36 2DY 78
2DY H37 H37 H 0 1 N N N 19.741 -12.733 -16.851 1.792 3.310 1.051 H37 2DY 79
2DY H38 H38 H 0 1 N N N 21.641 -14.786 -15.899 0.732 3.946 -1.595 H38 2DY 80
2DY H39 H39 H 0 1 N N N 21.564 -16.199 -17.720 1.460 5.625 0.842 H39 2DY 81
2DY H40 H40 H 0 1 N N N 21.524 -14.607 -18.551 2.327 5.521 -0.712 H40 2DY 82
2DY H41 H41 H 0 1 N N N 19.034 -14.749 -18.689 0.978 7.583 -0.671 H41 2DY 83
2DY H42 H42 H 0 1 N N N 19.810 -16.160 -19.487 0.281 6.449 -1.857 H42 2DY 84
2DY H43 H43 H 0 1 N N N 16.933 -17.262 -16.147 -3.261 6.436 0.578 H43 2DY 85
2DY H44 H44 H 0 1 N N N 16.432 -16.389 -13.885 -4.510 4.339 0.872 H44 2DY 86
2DY H45 H45 H 0 1 N N N 17.887 -14.680 -12.872 -3.383 2.176 0.528 H45 2DY 87
2DY H46 H46 H 0 1 N N N 19.887 -13.876 -14.074 -1.010 2.114 -0.115 H46 2DY 88
#
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
2DY C27 C28 DOUB Y N 1
2DY C27 C26 SING Y N 2
2DY C28 C29 SING Y N 3
2DY C26 C25 DOUB Y N 4
2DY C29 C30 DOUB Y N 5
2DY C25 C30 SING Y N 6
2DY C25 C24 SING N N 7
2DY C30 N31 SING N N 8
2DY C24 C22 SING N N 9
2DY N31 C22 SING N N 10
2DY N31 C32 SING N N 11
2DY C22 C21 SING N N 12
2DY C41 C40 SING N N 13
2DY C41 O42 SING N N 14
2DY C32 C33 SING N N 15
2DY C40 C38 SING N N 16
2DY O42 C43 SING N N 17
2DY C21 N20 SING N N 18
2DY C33 C35 SING N N 19
2DY C33 N20 SING N N 20
2DY C35 N37 SING N N 21
2DY C35 O36 DOUB N N 22
2DY N37 C38 SING N N 23
2DY C38 C48 SING N N 24
2DY N20 C18 SING N N 25
2DY C43 C48 DOUB Y N 26
2DY C43 C44 SING Y N 27
2DY C48 C47 SING Y N 28
2DY C44 C45 DOUB Y N 29
2DY C18 C10 SING N N 30
2DY C18 O19 DOUB N N 31
2DY C47 C46 DOUB Y N 32
2DY C10 C12 SING N N 33
2DY C10 N9 SING N N 34
2DY C13 C12 SING N N 35
2DY C13 C14 SING N N 36
2DY C17 C16 SING N N 37
2DY C17 C12 SING N N 38
2DY C45 C46 SING Y N 39
2DY C16 C15 SING N N 40
2DY C14 C15 SING N N 41
2DY O8 C7 DOUB N N 42
2DY N9 C7 SING N N 43
2DY C7 C3 SING N N 44
2DY C1 C2 SING N N 45
2DY C3 C2 SING N N 46
2DY C3 N5 SING N N 47
2DY N5 C6 SING N N 48
2DY C1 H1 SING N N 49
2DY C1 H2 SING N N 50
2DY C1 H3 SING N N 51
2DY C2 H4 SING N N 52
2DY C2 H5 SING N N 53
2DY C3 H6 SING N N 54
2DY N5 H7 SING N N 55
2DY C6 H9 SING N N 56
2DY C6 H10 SING N N 57
2DY C6 H11 SING N N 58
2DY N9 H12 SING N N 59
2DY C10 H13 SING N N 60
2DY C12 H14 SING N N 61
2DY C13 H15 SING N N 62
2DY C13 H16 SING N N 63
2DY C14 H17 SING N N 64
2DY C14 H18 SING N N 65
2DY C15 H19 SING N N 66
2DY C15 H20 SING N N 67
2DY C16 H21 SING N N 68
2DY C16 H22 SING N N 69
2DY C17 H23 SING N N 70
2DY C17 H24 SING N N 71
2DY C21 H25 SING N N 72
2DY C21 H26 SING N N 73
2DY C22 H27 SING N N 74
2DY C24 H28 SING N N 75
2DY C24 H29 SING N N 76
2DY C26 H30 SING N N 77
2DY C27 H31 SING N N 78
2DY C28 H32 SING N N 79
2DY C29 H33 SING N N 80
2DY C32 H34 SING N N 81
2DY C32 H35 SING N N 82
2DY C33 H36 SING N N 83
2DY N37 H37 SING N N 84
2DY C38 H38 SING N N 85
2DY C40 H39 SING N N 86
2DY C40 H40 SING N N 87
2DY C41 H41 SING N N 88
2DY C41 H42 SING N N 89
2DY C44 H43 SING N N 90
2DY C45 H44 SING N N 91
2DY C46 H45 SING N N 92
2DY C47 H46 SING N N 93
#
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
2DY SMILES ACDLabs 12.01 "O=C(NC(C(=O)N3CC2N(c1ccccc1C2)CC3C(=O)NC4c5c(OCC4)cccc5)C6CCCCC6)C(NC)CC"
2DY InChI InChI 1.03
;InChI=1S/C34H45N5O4/c1-3-26(35-2)32(40)37-31(22-11-5-4-6-12-22)34(42)39-20-24-19-23-13-7-9-15-28(23)38(24)21-29(39)33(41)36-27-17-18-43-30-16-10-8-14-25(27)30/h7-10,13-16,22,24,26-27,29,31,35H,3-6,11-12,17-21H2,1-2H3,(H,36,41)(H,37,40)/t24-,26-,27+,29-,31-/m0/s1
;
2DY InChIKey InChI 1.03 TYXHMZBEDPKUQY-HDFVOGAFSA-N
2DY SMILES_CANONICAL CACTVS 3.385 "CC[C@H](NC)C(=O)N[C@@H](C1CCCCC1)C(=O)N2C[C@@H]3Cc4ccccc4N3C[C@H]2C(=O)N[C@@H]5CCOc6ccccc56"
2DY SMILES CACTVS 3.385 "CC[CH](NC)C(=O)N[CH](C1CCCCC1)C(=O)N2C[CH]3Cc4ccccc4N3C[CH]2C(=O)N[CH]5CCOc6ccccc56"
2DY SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC[C@@H](C(=O)N[C@@H](C1CCCCC1)C(=O)N2C[C@@H]3Cc4ccccc4N3C[C@H]2C(=O)N[C@@H]5CCOc6c5cccc6)NC"
2DY SMILES "OpenEye OEToolkits" 1.7.6 "CCC(C(=O)NC(C1CCCCC1)C(=O)N2CC3Cc4ccccc4N3CC2C(=O)NC5CCOc6c5cccc6)NC"
#
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
2DY "SYSTEMATIC NAME" ACDLabs 12.01 "(3S,10aS)-2-[(2S)-2-cyclohexyl-2-{[(2S)-2-(methylamino)butanoyl]amino}acetyl]-N-[(4R)-3,4-dihydro-2H-chromen-4-yl]-1,2,3,4,10,10a-hexahydropyrazino[1,2-a]indole-3-carboxamide"
2DY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(3S,10aS)-2-[(2S)-2-cyclohexyl-2-[[(2S)-2-(methylamino)butanoyl]amino]ethanoyl]-N-[(4R)-3,4-dihydro-2H-chromen-4-yl]-3,4,10,10a-tetrahydro-1H-pyrazino[1,2-a]indole-3-carboxamide"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
2DY "Create component" 2013-09-25 RCSB
2DY "Initial release" 2013-12-11 RCSB
#