data_XL6
#
_chem_comp.id XL6
_chem_comp.name "N-[2-({5-[(2,6-dichloro-3,5-dimethoxyphenyl)methoxy]pyrimidin-2-yl}amino)-3-methylphenyl]propanamide"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C23 H24 Cl2 N4 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-10-28
_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 491.367
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code XL6
_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 6BFR
_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
XL6 C1 C1 C 0 1 Y N N N N N 2.717 -21.383 8.415 -5.909 -0.729 -0.101 C1 XL6 1
XL6 C2 C2 C 0 1 Y N N N N N 3.402 -20.166 8.404 -4.546 -0.976 -0.007 C2 XL6 2
XL6 C3 C3 C 0 1 Y N N N N N 4.551 -19.983 7.633 -3.676 0.052 0.306 C3 XL6 3
XL6 C4 C4 C 0 1 Y N N N N N 4.988 -21.049 6.864 -4.161 1.328 0.525 C4 XL6 4
XL6 C5 C5 C 0 1 Y N N N N N 4.323 -22.273 6.855 -5.523 1.579 0.431 C5 XL6 5
XL6 C6 C6 C 0 1 Y N N N N N 3.180 -22.429 7.625 -6.396 0.551 0.113 C6 XL6 6
XL6 O1 O1 O 0 1 N N N N N N 1.606 -21.462 9.209 -6.764 -1.740 -0.408 O1 XL6 7
XL6 O2 O2 O 0 1 N N N N N N 4.832 -23.257 6.060 -6.000 2.834 0.647 O2 XL6 8
XL6 C7 C7 C 0 1 N N N N N N 0.861 -22.679 9.260 -8.153 -1.413 -0.488 C7 XL6 9
XL6 C8 C8 C 0 1 N N N N N N 4.777 -24.610 6.519 -7.412 3.020 0.534 C8 XL6 10
XL6 CL1 CL1 CL 0 0 N N N N N N 2.842 -18.867 9.407 -3.934 -2.577 -0.281 CL1 XL6 11
XL6 CL2 CL2 CL 0 0 N N N N N N 6.404 -20.850 5.895 -3.066 2.617 0.919 CL2 XL6 12
XL6 C9 C9 C 0 1 N N N N N N 5.306 -18.682 7.628 -2.197 -0.219 0.409 C9 XL6 13
XL6 O3 O3 O 0 1 N N N N N N 6.428 -18.799 8.513 -1.587 -0.026 -0.869 O3 XL6 14
XL6 C10 C10 C 0 1 Y N N N N N 7.545 -18.033 8.276 -0.245 -0.231 -0.950 C10 XL6 15
XL6 C11 C11 C 0 1 Y N N N N N 8.781 -18.557 8.595 0.428 -0.065 -2.155 C11 XL6 16
XL6 N1 N1 N 0 1 Y N N N N N 9.908 -17.864 8.401 1.734 -0.273 -2.197 N1 XL6 17
XL6 C12 C12 C 0 1 Y N N N N N 9.770 -16.624 7.882 2.398 -0.635 -1.110 C12 XL6 18
XL6 N2 N2 N 0 1 Y N N N N N 8.599 -16.044 7.543 1.789 -0.802 0.054 N2 XL6 19
XL6 C13 C13 C 0 1 Y N N N N N 7.489 -16.752 7.750 0.486 -0.606 0.171 C13 XL6 20
XL6 N3 N3 N 0 1 N N N N N N 10.899 -15.902 7.651 3.767 -0.844 -1.193 N3 XL6 21
XL6 C14 C14 C 0 1 Y N N N N N 11.035 -14.554 7.236 4.505 -1.114 -0.035 C14 XL6 22
XL6 C15 C15 C 0 1 Y N N N N N 11.461 -13.583 8.167 5.521 -0.246 0.365 C15 XL6 23
XL6 C16 C16 C 0 1 Y N N N N N 11.597 -12.239 7.715 6.248 -0.518 1.514 C16 XL6 24
XL6 C17 C17 C 0 1 Y N N N N N 11.292 -11.907 6.417 5.966 -1.648 2.259 C17 XL6 25
XL6 C18 C18 C 0 1 Y N N N N N 10.864 -12.877 5.528 4.959 -2.509 1.863 C18 XL6 26
XL6 C19 C19 C 0 1 Y N N N N N 10.727 -14.206 5.913 4.225 -2.242 0.722 C19 XL6 27
XL6 C20 C20 C 0 1 N N N N N N 10.265 -15.228 4.908 3.128 -3.183 0.295 C20 XL6 28
XL6 N4 N4 N 0 1 N N N N N N 11.765 -14.007 9.482 5.806 0.898 -0.392 N4 XL6 29
XL6 C21 C21 C 0 1 N N N N N N 12.185 -13.320 10.566 7.002 1.508 -0.268 C21 XL6 30
XL6 C22 C22 C 0 1 N N N N N N 12.493 -14.132 11.771 7.271 2.795 -1.004 C22 XL6 31
XL6 C23 C23 C 0 1 N N N N N N 12.036 -15.532 11.966 8.691 3.273 -0.692 C23 XL6 32
XL6 O4 O4 O 0 1 N N N N N N 12.379 -12.101 10.551 7.861 1.021 0.437 O4 XL6 33
XL6 H1 H1 H 0 1 N N N N N N 2.647 -23.368 7.611 -7.456 0.745 0.039 H1 XL6 34
XL6 H2 H2 H 0 1 N N N N N N 0.008 -22.559 9.944 -8.304 -0.657 -1.259 H2 XL6 35
XL6 H3 H3 H 0 1 N N N N N N 0.492 -22.925 8.254 -8.722 -2.308 -0.740 H3 XL6 36
XL6 H4 H4 H 0 1 N N N N N N 1.509 -23.491 9.621 -8.491 -1.025 0.473 H4 XL6 37
XL6 H5 H5 H 0 1 N N N N N N 5.226 -25.272 5.764 -7.921 2.385 1.258 H5 XL6 38
XL6 H6 H6 H 0 1 N N N N N N 5.334 -24.700 7.463 -7.658 4.064 0.729 H6 XL6 39
XL6 H7 H7 H 0 1 N N N N N N 3.728 -24.899 6.683 -7.734 2.753 -0.473 H7 XL6 40
XL6 H8 H8 H 0 1 N N N N N N 5.659 -18.463 6.610 -1.752 0.466 1.131 H8 XL6 41
XL6 H9 H9 H 0 1 N N N N N N 4.647 -17.870 7.970 -2.037 -1.246 0.736 H9 XL6 42
XL6 H10 H10 H 0 1 N N N N N N 8.840 -19.552 9.012 -0.108 0.229 -3.045 H10 XL6 43
XL6 H11 H11 H 0 1 N N N N N N 6.530 -16.320 7.504 -0.004 -0.744 1.123 H11 XL6 44
XL6 H12 H12 H 0 1 N N N N N N 11.758 -16.394 7.795 4.213 -0.804 -2.054 H12 XL6 45
XL6 H13 H13 H 0 1 N N N N N N 11.942 -11.476 8.397 7.036 0.152 1.826 H13 XL6 46
XL6 H14 H14 H 0 1 N N N N N N 11.387 -10.883 6.089 6.534 -1.859 3.153 H14 XL6 47
XL6 H15 H15 H 0 1 N N N N N N 10.631 -12.595 4.512 4.740 -3.388 2.451 H15 XL6 48
XL6 H16 H16 H 0 1 N N N N N N 11.137 -15.654 4.391 2.215 -2.948 0.841 H16 XL6 49
XL6 H17 H17 H 0 1 N N N N N N 9.718 -16.030 5.426 2.951 -3.072 -0.775 H17 XL6 50
XL6 H18 H18 H 0 1 N N N N N N 9.602 -14.747 4.174 3.426 -4.209 0.509 H18 XL6 51
XL6 H19 H19 H 0 1 N N N N N N 11.648 -14.988 9.636 5.144 1.251 -1.006 H19 XL6 52
XL6 H20 H20 H 0 1 N N N N N N 13.591 -14.164 11.837 7.172 2.628 -2.076 H20 XL6 53
XL6 H21 H21 H 0 1 N N N N N N 12.091 -13.565 12.624 6.555 3.553 -0.686 H21 XL6 54
XL6 H22 H22 H 0 1 N N N N N N 12.397 -15.904 12.936 8.791 3.440 0.381 H22 XL6 55
XL6 H23 H23 H 0 1 N N N N N N 10.937 -15.565 11.946 9.408 2.516 -1.010 H23 XL6 56
XL6 H24 H24 H 0 1 N Y N N N N 12.436 -16.164 11.159 8.886 4.204 -1.224 H24 XL6 57
#
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
XL6 C20 C19 SING N N 1
XL6 C18 C19 DOUB Y N 2
XL6 C18 C17 SING Y N 3
XL6 CL2 C4 SING N N 4
XL6 C19 C14 SING Y N 5
XL6 O2 C8 SING N N 6
XL6 O2 C5 SING N N 7
XL6 C17 C16 DOUB Y N 8
XL6 C5 C4 DOUB Y N 9
XL6 C5 C6 SING Y N 10
XL6 C4 C3 SING Y N 11
XL6 C14 N3 SING N N 12
XL6 C14 C15 DOUB Y N 13
XL6 N2 C13 DOUB Y N 14
XL6 N2 C12 SING Y N 15
XL6 C6 C1 DOUB Y N 16
XL6 C9 C3 SING N N 17
XL6 C9 O3 SING N N 18
XL6 C3 C2 DOUB Y N 19
XL6 N3 C12 SING N N 20
XL6 C16 C15 SING Y N 21
XL6 C13 C10 SING Y N 22
XL6 C12 N1 DOUB Y N 23
XL6 C15 N4 SING N N 24
XL6 C10 O3 SING N N 25
XL6 C10 C11 DOUB Y N 26
XL6 N1 C11 SING Y N 27
XL6 C2 C1 SING Y N 28
XL6 C2 CL1 SING N N 29
XL6 C1 O1 SING N N 30
XL6 O1 C7 SING N N 31
XL6 N4 C21 SING N N 32
XL6 O4 C21 DOUB N N 33
XL6 C21 C22 SING N N 34
XL6 C22 C23 SING N N 35
XL6 C6 H1 SING N N 36
XL6 C7 H2 SING N N 37
XL6 C7 H3 SING N N 38
XL6 C7 H4 SING N N 39
XL6 C8 H5 SING N N 40
XL6 C8 H6 SING N N 41
XL6 C8 H7 SING N N 42
XL6 C9 H8 SING N N 43
XL6 C9 H9 SING N N 44
XL6 C11 H10 SING N N 45
XL6 C13 H11 SING N N 46
XL6 N3 H12 SING N N 47
XL6 C16 H13 SING N N 48
XL6 C17 H14 SING N N 49
XL6 C18 H15 SING N N 50
XL6 C20 H16 SING N N 51
XL6 C20 H17 SING N N 52
XL6 C20 H18 SING N N 53
XL6 N4 H19 SING N N 54
XL6 C22 H20 SING N N 55
XL6 C22 H21 SING N N 56
XL6 C23 H22 SING N N 57
XL6 C23 H23 SING N N 58
XL6 C23 H24 SING N N 59
#
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
XL6 SMILES ACDLabs 12.01 "c1(OC)c(Cl)c(c(c(c1)OC)Cl)COc2cnc(nc2)Nc3c(NC(CC)=O)cccc3C"
XL6 InChI InChI 1.03 "InChI=1S/C23H24Cl2N4O4/c1-5-19(30)28-16-8-6-7-13(2)22(16)29-23-26-10-14(11-27-23)33-12-15-20(24)17(31-3)9-18(32-4)21(15)25/h6-11H,5,12H2,1-4H3,(H,28,30)(H,26,27,29)"
XL6 InChIKey InChI 1.03 HPDWTQKRQUCMTC-UHFFFAOYSA-N
XL6 SMILES_CANONICAL CACTVS 3.385 "CCC(=O)Nc1cccc(C)c1Nc2ncc(OCc3c(Cl)c(OC)cc(OC)c3Cl)cn2"
XL6 SMILES CACTVS 3.385 "CCC(=O)Nc1cccc(C)c1Nc2ncc(OCc3c(Cl)c(OC)cc(OC)c3Cl)cn2"
XL6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CCC(=O)Nc1cccc(c1Nc2ncc(cn2)OCc3c(c(cc(c3Cl)OC)OC)Cl)C"
XL6 SMILES "OpenEye OEToolkits" 2.0.6 "CCC(=O)Nc1cccc(c1Nc2ncc(cn2)OCc3c(c(cc(c3Cl)OC)OC)Cl)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
XL6 "SYSTEMATIC NAME" ACDLabs 12.01 "N-[2-({5-[(2,6-dichloro-3,5-dimethoxyphenyl)methoxy]pyrimidin-2-yl}amino)-3-methylphenyl]propanamide"
XL6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "~{N}-[2-[[5-[[2,6-bis(chloranyl)-3,5-dimethoxy-phenyl]methoxy]pyrimidin-2-yl]amino]-3-methyl-phenyl]propanamide"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
XL6 "Create component" 2017-10-28 RCSB
XL6 "Initial release" 2019-07-10 RCSB
XL6 "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id XL6
_pdbx_chem_comp_pcm.modified_residue_id CYS
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category "Covalent chemical modification"
_pdbx_chem_comp_pcm.position "Amino-acid side chain"
_pdbx_chem_comp_pcm.polypeptide_position "Any position"
_pdbx_chem_comp_pcm.comp_id_linking_atom C23
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#