data_NUT
#
_chem_comp.id NUT
_chem_comp.name "4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C30 H30 Cl2 N4 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "Nutlin 3a"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2012-10-12
_chem_comp.pdbx_modified_date 2021-03-01
_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 581.490
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code NUT
_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 4HG7
_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
NUT O3 O3 O 0 1 N N N -23.667 5.839 -16.568 2.397 -0.980 -0.849 O3 NUT 1
NUT C25 C25 C 0 1 N N N -23.015 6.538 -15.757 1.311 -1.194 -0.347 C25 NUT 2
NUT N2 N2 N 0 1 N N N -21.695 6.402 -15.710 0.673 -2.356 -0.591 N2 NUT 3
NUT C29 C29 C 0 1 N N N -21.006 5.564 -16.697 -0.534 -2.739 0.158 C29 NUT 4
NUT C28 C28 C 0 1 N N N -19.624 6.037 -17.066 -0.440 -4.196 0.520 C28 NUT 5
NUT O2 O2 O 0 1 N N N -19.027 5.438 -17.957 -1.221 -4.641 1.334 O2 NUT 6
NUT N3 N3 N 0 1 N N N -19.096 7.088 -16.423 0.461 -5.021 -0.014 N3 NUT 7
NUT C27 C27 C 0 1 N N N -19.765 7.777 -15.316 1.515 -4.612 -0.933 C27 NUT 8
NUT C26 C26 C 0 1 N N N -20.851 6.955 -14.647 1.151 -3.291 -1.624 C26 NUT 9
NUT N1 N1 N 0 1 N N N -23.728 7.387 -14.970 0.748 -0.273 0.460 N1 NUT 10
NUT C10 C10 C 0 1 N N N -25.032 7.173 -14.710 1.231 0.995 0.697 C10 NUT 11
NUT C9 C9 C 0 1 Y N N -25.716 5.849 -14.559 2.465 1.515 0.075 C9 NUT 12
NUT C3 C3 C 0 1 Y N N -27.003 5.643 -15.033 2.420 2.663 -0.719 C3 NUT 13
NUT C2 C2 C 0 1 Y N N -27.636 4.390 -14.872 3.572 3.145 -1.298 C2 NUT 14
NUT C5 C5 C 0 1 Y N N -25.021 4.742 -13.878 3.687 0.861 0.282 C5 NUT 15
NUT O1 O1 O 0 1 N N N -23.751 4.950 -13.415 3.740 -0.253 1.056 O1 NUT 16
NUT C6 C6 C 0 1 N N N -23.077 3.927 -12.640 4.992 -0.939 1.122 C6 NUT 17
NUT C8 C8 C 0 1 N N N -22.445 2.900 -13.586 5.780 -0.445 2.336 C8 NUT 18
NUT C7 C7 C 0 1 N N N -22.063 4.596 -11.718 4.743 -2.443 1.252 C7 NUT 19
NUT C4 C4 C 0 1 Y N N -25.678 3.512 -13.732 4.840 1.354 -0.304 C4 NUT 20
NUT C1 C1 C 0 1 Y N N -26.973 3.348 -14.207 4.784 2.492 -1.095 C1 NUT 21
NUT O O O 0 1 N N N -27.557 2.127 -14.022 5.916 2.973 -1.669 O NUT 22
NUT C C C 0 1 N N N -28.863 1.822 -14.540 5.788 4.152 -2.466 C NUT 23
NUT C18 C18 C 0 1 N N R -23.330 8.774 -14.740 -0.493 -0.446 1.234 C18 NUT 24
NUT C19 C19 C 0 1 Y N N -22.897 9.233 -13.374 -1.661 -0.697 0.316 C19 NUT 25
NUT C24 C24 C 0 1 Y N N -22.198 10.451 -13.326 -2.639 -1.606 0.675 C24 NUT 26
NUT C23 C23 C 0 1 Y N N -21.867 10.994 -12.087 -3.711 -1.837 -0.166 C23 NUT 27
NUT C22 C22 C 0 1 Y N N -22.260 10.321 -10.942 -3.805 -1.159 -1.368 C22 NUT 28
NUT CL1 CL1 CL 0 0 N N N -21.928 11.079 -9.376 -5.151 -1.448 -2.426 CL1 NUT 29
NUT C21 C21 C 0 1 Y N N -22.988 9.123 -10.942 -2.825 -0.250 -1.728 C21 NUT 30
NUT C20 C20 C 0 1 Y N N -23.300 8.579 -12.190 -1.757 -0.016 -0.883 C20 NUT 31
NUT C11 C11 C 0 1 N N S -24.792 9.367 -15.038 -0.651 0.905 1.958 C11 NUT 32
NUT N N N 0 1 N N N -25.707 8.251 -14.709 0.508 1.691 1.512 N NUT 33
NUT C12 C12 C 0 1 Y N N -25.194 10.617 -14.301 -1.933 1.580 1.540 C12 NUT 34
NUT C17 C17 C 0 1 Y N N -24.980 11.874 -14.865 -1.994 2.264 0.340 C17 NUT 35
NUT C16 C16 C 0 1 Y N N -25.355 13.035 -14.145 -3.169 2.883 -0.043 C16 NUT 36
NUT C15 C15 C 0 1 Y N N -25.935 12.921 -12.864 -4.283 2.818 0.774 C15 NUT 37
NUT CL CL CL 0 0 N N N -26.417 14.360 -11.915 -5.759 3.595 0.293 CL NUT 38
NUT C14 C14 C 0 1 Y N N -26.156 11.677 -12.254 -4.221 2.134 1.975 C14 NUT 39
NUT C13 C13 C 0 1 Y N N -25.791 10.528 -13.019 -3.047 1.511 2.355 C13 NUT 40
NUT H1 H1 H 0 1 N N N -21.616 5.540 -17.612 -0.604 -2.141 1.066 H1 NUT 41
NUT H2 H2 H 0 1 N N N -20.922 4.547 -16.285 -1.416 -2.569 -0.460 H2 NUT 42
NUT H3 H3 H 0 1 N N N -18.198 7.419 -16.714 0.411 -5.960 0.226 H3 NUT 43
NUT H4 H4 H 0 1 N N N -19.009 8.033 -14.559 2.445 -4.485 -0.379 H4 NUT 44
NUT H5 H5 H 0 1 N N N -20.220 8.699 -15.706 1.651 -5.385 -1.689 H5 NUT 45
NUT H6 H6 H 0 1 N N N -21.452 7.594 -13.983 0.364 -3.462 -2.358 H6 NUT 46
NUT H7 H7 H 0 1 N N N -20.400 6.140 -14.062 2.031 -2.876 -2.116 H7 NUT 47
NUT H9 H9 H 0 1 N N N -27.526 6.447 -15.529 1.481 3.173 -0.879 H9 NUT 48
NUT H10 H10 H 0 1 N N N -28.631 4.234 -15.261 3.536 4.033 -1.911 H10 NUT 49
NUT H11 H11 H 0 1 N N N -23.816 3.404 -12.014 5.562 -0.742 0.214 H11 NUT 50
NUT H12 H12 H 0 1 N N N -21.934 2.124 -12.997 5.210 -0.642 3.244 H12 NUT 51
NUT H13 H13 H 0 1 N N N -23.230 2.436 -14.201 6.736 -0.968 2.386 H13 NUT 52
NUT H14 H14 H 0 1 N N N -21.717 3.403 -14.240 5.957 0.627 2.243 H14 NUT 53
NUT H15 H15 H 0 1 N N N -22.578 5.318 -11.068 4.181 -2.795 0.387 H15 NUT 54
NUT H16 H16 H 0 1 N N N -21.571 3.832 -11.099 5.699 -2.966 1.302 H16 NUT 55
NUT H17 H17 H 0 1 N N N -21.308 5.120 -12.322 4.173 -2.640 2.160 H17 NUT 56
NUT H18 H18 H 0 1 N N N -25.175 2.688 -13.248 5.783 0.853 -0.146 H18 NUT 57
NUT H19 H19 H 0 1 N N N -29.132 0.789 -14.274 5.402 4.966 -1.853 H19 NUT 58
NUT H20 H20 H 0 1 N N N -29.600 2.515 -14.108 6.765 4.429 -2.864 H20 NUT 59
NUT H21 H21 H 0 1 N N N -28.857 1.929 -15.635 5.101 3.961 -3.290 H21 NUT 60
NUT H22 H22 H 0 1 N N N -22.628 9.125 -15.511 -0.387 -1.259 1.952 H22 NUT 61
NUT H23 H23 H 0 1 N N N -21.921 10.959 -14.238 -2.566 -2.135 1.614 H23 NUT 62
NUT H24 H24 H 0 1 N N N -21.316 11.920 -12.020 -4.475 -2.547 0.115 H24 NUT 63
NUT H25 H25 H 0 1 N N N -23.292 8.645 -10.023 -2.898 0.279 -2.666 H25 NUT 64
NUT H26 H26 H 0 1 N N N -23.853 7.653 -12.249 -0.995 0.697 -1.161 H26 NUT 65
NUT H27 H27 H 0 1 N N N -24.850 9.566 -16.118 -0.628 0.765 3.038 H27 NUT 66
NUT H30 H30 H 0 1 N N N -24.532 11.962 -15.844 -1.124 2.314 -0.298 H30 NUT 67
NUT H31 H31 H 0 1 N N N -25.196 14.011 -14.579 -3.217 3.417 -0.981 H31 NUT 68
NUT H32 H32 H 0 1 N N N -26.578 11.593 -11.263 -5.090 2.084 2.614 H32 NUT 69
NUT H33 H33 H 0 1 N N N -25.978 9.549 -12.603 -3.000 0.973 3.290 H33 NUT 70
# #
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
NUT O2 C28 DOUB N N 1
NUT C28 C29 SING N N 2
NUT C28 N3 SING N N 3
NUT C29 N2 SING N N 4
NUT O3 C25 DOUB N N 5
NUT N3 C27 SING N N 6
NUT C25 N2 SING N N 7
NUT C25 N1 SING N N 8
NUT N2 C26 SING N N 9
NUT C27 C26 SING N N 10
NUT C11 C18 SING N N 11
NUT C11 N SING N N 12
NUT C11 C12 SING N N 13
NUT C3 C2 DOUB Y N 14
NUT C3 C9 SING Y N 15
NUT N1 C18 SING N N 16
NUT N1 C10 SING N N 17
NUT C2 C1 SING Y N 18
NUT C17 C12 DOUB Y N 19
NUT C17 C16 SING Y N 20
NUT C18 C19 SING N N 21
NUT C10 N DOUB N N 22
NUT C10 C9 SING N N 23
NUT C9 C5 DOUB Y N 24
NUT C O SING N N 25
NUT C12 C13 SING Y N 26
NUT C1 O SING N N 27
NUT C1 C4 DOUB Y N 28
NUT C16 C15 DOUB Y N 29
NUT C5 C4 SING Y N 30
NUT C5 O1 SING N N 31
NUT C8 C6 SING N N 32
NUT O1 C6 SING N N 33
NUT C19 C24 DOUB Y N 34
NUT C19 C20 SING Y N 35
NUT C24 C23 SING Y N 36
NUT C13 C14 DOUB Y N 37
NUT C15 C14 SING Y N 38
NUT C15 CL SING N N 39
NUT C6 C7 SING N N 40
NUT C20 C21 DOUB Y N 41
NUT C23 C22 DOUB Y N 42
NUT C21 C22 SING Y N 43
NUT C22 CL1 SING N N 44
NUT C29 H1 SING N N 45
NUT C29 H2 SING N N 46
NUT N3 H3 SING N N 47
NUT C27 H4 SING N N 48
NUT C27 H5 SING N N 49
NUT C26 H6 SING N N 50
NUT C26 H7 SING N N 51
NUT C3 H9 SING N N 52
NUT C2 H10 SING N N 53
NUT C6 H11 SING N N 54
NUT C8 H12 SING N N 55
NUT C8 H13 SING N N 56
NUT C8 H14 SING N N 57
NUT C7 H15 SING N N 58
NUT C7 H16 SING N N 59
NUT C7 H17 SING N N 60
NUT C4 H18 SING N N 61
NUT C H19 SING N N 62
NUT C H20 SING N N 63
NUT C H21 SING N N 64
NUT C18 H22 SING N N 65
NUT C24 H23 SING N N 66
NUT C23 H24 SING N N 67
NUT C21 H25 SING N N 68
NUT C20 H26 SING N N 69
NUT C11 H27 SING N N 70
NUT C17 H30 SING N N 71
NUT C16 H31 SING N N 72
NUT C14 H32 SING N N 73
NUT C13 H33 SING N N 74
# #
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
NUT SMILES ACDLabs 12.01 "O=C5NCCN(C(=O)N3C(=NC(c1ccc(Cl)cc1)C3c2ccc(Cl)cc2)c4ccc(OC)cc4OC(C)C)C5"
NUT InChI InChI 1.03 "InChI=1S/C30H30Cl2N4O4/c1-18(2)40-25-16-23(39-3)12-13-24(25)29-34-27(19-4-8-21(31)9-5-19)28(20-6-10-22(32)11-7-20)36(29)30(38)35-15-14-33-26(37)17-35/h4-13,16,18,27-28H,14-15,17H2,1-3H3,(H,33,37)/t27-,28+/m0/s1"
NUT InChIKey InChI 1.03 BDUHCSBCVGXTJM-WUFINQPMSA-N
NUT SMILES_CANONICAL CACTVS 3.370 "COc1ccc(c(OC(C)C)c1)C2=N[C@H]([C@H](N2C(=O)N3CCNC(=O)C3)c4ccc(Cl)cc4)c5ccc(Cl)cc5"
NUT SMILES CACTVS 3.370 "COc1ccc(c(OC(C)C)c1)C2=N[CH]([CH](N2C(=O)N3CCNC(=O)C3)c4ccc(Cl)cc4)c5ccc(Cl)cc5"
NUT SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC(C)Oc1cc(ccc1C2=N[C@H]([C@H](N2C(=O)N3CCNC(=O)C3)c4ccc(cc4)Cl)c5ccc(cc5)Cl)OC"
NUT SMILES "OpenEye OEToolkits" 1.7.6 "CC(C)Oc1cc(ccc1C2=NC(C(N2C(=O)N3CCNC(=O)C3)c4ccc(cc4)Cl)c5ccc(cc5)Cl)OC"
# #
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
NUT "SYSTEMATIC NAME" ACDLabs 12.01 "4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one"
NUT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "4-[[(4S,5R)-4,5-bis(4-chlorophenyl)-2-(4-methoxy-2-propan-2-yloxy-phenyl)-4,5-dihydroimidazol-1-yl]carbonyl]piperazin-2-one"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
NUT "Create component" 2012-10-12 RCSB
NUT "Initial release" 2013-04-24 RCSB
NUT "Modify synonyms" 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id NUT
_pdbx_chem_comp_synonyms.name "Nutlin 3a"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##