data_XL8
#
_chem_comp.id XL8
_chem_comp.name "N-[3,5-dichloro-2-({5-[(2,6-dichloro-3,5-dimethoxyphenyl)methoxy]pyrimidin-2-yl}amino)phenyl]propanamide"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C22 H20 Cl4 N4 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-11-05
_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 546.231
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code XL8
_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 6BIS
_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
XL8 C1 C1 C 0 1 Y N N N N N 22.230 -3.741 -6.386 6.444 -0.777 0.236 C1 XL8 1
XL8 C2 C2 C 0 1 Y N N N N N 20.999 -4.394 -6.372 5.066 -0.947 0.249 C2 XL8 2
XL8 C3 C3 C 0 1 Y N N N N N 19.933 -3.977 -7.174 4.245 0.012 -0.316 C3 XL8 3
XL8 C4 C4 C 0 1 Y N N N N N 20.125 -2.848 -7.952 4.794 1.141 -0.894 C4 XL8 4
XL8 C5 C5 C 0 1 Y N N N N N 21.343 -2.161 -7.953 6.172 1.315 -0.909 C5 XL8 5
XL8 C6 C6 C 0 1 Y N N N N N 22.395 -2.620 -7.174 6.996 0.357 -0.338 C6 XL8 6
XL8 O1 O1 O 0 1 N N N N N N 23.223 -4.196 -5.569 7.251 -1.720 0.791 O1 XL8 7
XL8 O2 O2 O 0 1 N N N N N N 21.468 -1.066 -8.754 6.711 2.425 -1.477 O2 XL8 8
XL8 C7 C7 C 0 1 N N N N N N 24.548 -4.302 -6.082 8.659 -1.480 0.741 C7 XL8 9
XL8 C8 C8 C 0 1 N N N N N N 22.689 -0.333 -8.741 8.136 2.538 -1.456 C8 XL8 10
XL8 CL1 CL1 CL 0 0 N N N N N N 20.809 -5.809 -5.393 4.374 -2.364 0.974 CL1 XL8 11
XL8 CL2 CL2 CL 0 0 N N N N N N 18.852 -2.364 -9.027 3.761 2.343 -1.602 CL2 XL8 12
XL8 C9 C9 C 0 1 N N N N N N 18.631 -4.741 -7.214 2.750 -0.175 -0.301 C9 XL8 13
XL8 O3 O3 O 0 1 N N N N N N 18.811 -5.964 -7.955 2.209 0.405 0.887 O3 XL8 14
XL8 C10 C10 C 0 1 Y N N N N N 17.978 -7.033 -7.716 0.862 0.322 1.057 C10 XL8 15
XL8 C11 C11 C 0 1 Y N N N N N 16.701 -6.964 -7.175 0.253 0.860 2.185 C11 XL8 16
XL8 N1 N1 N 0 1 Y N N N N N 15.962 -8.065 -7.009 -1.060 0.762 2.317 N1 XL8 17
XL8 C12 C12 C 0 1 Y N N N N N 16.523 -9.241 -7.372 -1.791 0.161 1.391 C12 XL8 18
XL8 N2 N2 N 0 1 Y N N N N N 17.754 -9.380 -7.903 -1.245 -0.363 0.304 N2 XL8 19
XL8 C13 C13 C 0 1 Y N N N N N 18.463 -8.265 -8.085 0.061 -0.297 0.104 C13 XL8 20
XL8 N3 N3 N 0 1 N N N N N N 15.839 -10.399 -7.153 -3.165 0.077 1.563 N3 XL8 21
XL8 C14 C14 C 0 1 Y N N N N N 14.501 -10.536 -6.719 -3.969 -0.448 0.543 C14 XL8 22
XL8 C15 C15 C 0 1 Y N N N N N 13.519 -10.981 -7.619 -4.995 0.321 -0.005 C15 XL8 23
XL8 C16 C16 C 0 1 Y N N N N N 12.202 -11.072 -7.175 -5.787 -0.203 -1.015 C16 XL8 24
XL8 C17 C17 C 0 1 Y N N N N N 11.885 -10.680 -5.885 -5.558 -1.487 -1.477 C17 XL8 25
XL8 C18 C18 C 0 1 Y N N N N N 12.837 -10.190 -5.011 -4.540 -2.251 -0.934 C18 XL8 26
XL8 C19 C19 C 0 1 Y N N N N N 14.154 -10.135 -5.432 -3.742 -1.733 0.070 C19 XL8 27
XL8 N4 N4 N 0 1 N N N N N N 13.960 -11.433 -8.890 -5.225 1.621 0.465 N4 XL8 28
XL8 C20 C20 C 0 1 N N N N N N 13.295 -11.364 -10.065 -6.481 2.108 0.512 C20 XL8 29
XL8 C21 C21 C 0 1 N N N N N N 14.032 -11.945 -11.254 -6.742 3.463 1.118 C21 XL8 30
XL8 C22 C22 C 0 1 N N N N N N 15.464 -11.473 -11.402 -8.239 3.774 1.047 C22 XL8 31
XL8 O4 O4 O 0 1 N N N N N N 12.150 -10.955 -10.143 -7.402 1.455 0.067 O4 XL8 32
XL8 CL3 CL3 CL 0 0 N N N N N N 15.367 -9.589 -4.319 -2.461 -2.692 0.743 CL3 XL8 33
XL8 CL4 CL4 CL 0 0 N N N N N N 10.232 -10.746 -5.343 -6.551 -2.141 -2.742 CL4 XL8 34
XL8 H1 H1 H 0 1 N N N N N N 23.342 -2.101 -7.184 8.068 0.491 -0.349 H1 XL8 35
XL8 H2 H2 H 0 1 N N N N N N 25.217 -4.682 -5.296 8.977 -1.397 -0.298 H2 XL8 36
XL8 H3 H3 H 0 1 N N N N N N 24.556 -4.995 -6.937 8.888 -0.553 1.266 H3 XL8 37
XL8 H4 H4 H 0 1 N N N N N N 24.894 -3.311 -6.410 9.185 -2.307 1.217 H4 XL8 38
XL8 H5 H5 H 0 1 N N N N N N 22.617 0.513 -9.441 8.434 3.468 -1.941 H5 XL8 39
XL8 H6 H6 H 0 1 N N N N N N 22.878 0.046 -7.726 8.485 2.538 -0.424 H6 XL8 40
XL8 H7 H7 H 0 1 N N N N N N 23.515 -0.992 -9.046 8.575 1.694 -1.988 H7 XL8 41
XL8 H8 H8 H 0 1 N N N N N N 17.861 -4.127 -7.703 2.314 0.312 -1.174 H8 XL8 42
XL8 H9 H9 H 0 1 N N N N N N 18.314 -4.978 -6.188 2.516 -1.239 -0.325 H9 XL8 43
XL8 H10 H10 H 0 1 N N N N N N 16.299 -6.005 -6.884 0.843 1.352 2.944 H10 XL8 44
XL8 H11 H11 H 0 1 N N N N N N 19.443 -8.332 -8.534 0.501 -0.725 -0.785 H11 XL8 45
XL8 H12 H12 H 0 1 N N N N N N 16.341 -11.248 -7.318 -3.569 0.382 2.391 H12 XL8 46
XL8 H13 H13 H 0 1 N N N N N N 11.432 -11.446 -7.833 -6.582 0.390 -1.441 H13 XL8 47
XL8 H14 H14 H 0 1 N N N N N N 12.559 -9.858 -4.022 -4.366 -3.253 -1.298 H14 XL8 48
XL8 H15 H15 H 0 1 N N N N N N 14.868 -11.851 -8.920 -4.481 2.171 0.756 H15 XL8 49
XL8 H16 H16 H 0 1 N N N N N N 13.484 -11.668 -12.166 -6.420 3.463 2.160 H16 XL8 50
XL8 H17 H17 H 0 1 N N N N N N 14.041 -13.040 -11.150 -6.187 4.221 0.566 H17 XL8 51
XL8 H18 H18 H 0 1 N N N N N N 15.916 -11.944 -12.287 -8.794 3.015 1.599 H18 XL8 52
XL8 H19 H19 H 0 1 N N N N N N 15.479 -10.380 -11.521 -8.427 4.753 1.485 H19 XL8 53
XL8 H20 H20 H 0 1 N N N N N N 16.036 -11.752 -10.505 -8.561 3.773 0.005 H20 XL8 54
#
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
XL8 C22 C21 SING N N 1
XL8 C21 C20 SING N N 2
XL8 O4 C20 DOUB N N 3
XL8 C20 N4 SING N N 4
XL8 CL2 C4 SING N N 5
XL8 N4 C15 SING N N 6
XL8 O2 C8 SING N N 7
XL8 O2 C5 SING N N 8
XL8 C13 N2 DOUB Y N 9
XL8 C13 C10 SING Y N 10
XL8 O3 C10 SING N N 11
XL8 O3 C9 SING N N 12
XL8 C5 C4 DOUB Y N 13
XL8 C5 C6 SING Y N 14
XL8 C4 C3 SING Y N 15
XL8 N2 C12 SING Y N 16
XL8 C10 C11 DOUB Y N 17
XL8 C15 C16 DOUB Y N 18
XL8 C15 C14 SING Y N 19
XL8 C12 N3 SING N N 20
XL8 C12 N1 DOUB Y N 21
XL8 C9 C3 SING N N 22
XL8 C11 N1 SING Y N 23
XL8 C16 C17 SING Y N 24
XL8 C6 C1 DOUB Y N 25
XL8 C3 C2 DOUB Y N 26
XL8 N3 C14 SING N N 27
XL8 C14 C19 DOUB Y N 28
XL8 C1 C2 SING Y N 29
XL8 C1 O1 SING N N 30
XL8 C2 CL1 SING N N 31
XL8 C7 O1 SING N N 32
XL8 C17 CL4 SING N N 33
XL8 C17 C18 DOUB Y N 34
XL8 C19 C18 SING Y N 35
XL8 C19 CL3 SING N N 36
XL8 C6 H1 SING N N 37
XL8 C7 H2 SING N N 38
XL8 C7 H3 SING N N 39
XL8 C7 H4 SING N N 40
XL8 C8 H5 SING N N 41
XL8 C8 H6 SING N N 42
XL8 C8 H7 SING N N 43
XL8 C9 H8 SING N N 44
XL8 C9 H9 SING N N 45
XL8 C11 H10 SING N N 46
XL8 C13 H11 SING N N 47
XL8 N3 H12 SING N N 48
XL8 C16 H13 SING N N 49
XL8 C18 H14 SING N N 50
XL8 N4 H15 SING N N 51
XL8 C21 H16 SING N N 52
XL8 C21 H17 SING N N 53
XL8 C22 H18 SING N N 54
XL8 C22 H19 SING N N 55
XL8 C22 H20 SING N N 56
#
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
XL8 SMILES ACDLabs 12.01 "c1(c(Cl)c(c(c(c1)OC)Cl)COc3cnc(Nc2c(cc(cc2NC(CC)=O)Cl)Cl)nc3)OC"
XL8 InChI InChI 1.03 "InChI=1S/C22H20Cl4N4O4/c1-4-18(31)29-15-6-11(23)5-14(24)21(15)30-22-27-8-12(9-28-22)34-10-13-19(25)16(32-2)7-17(33-3)20(13)26/h5-9H,4,10H2,1-3H3,(H,29,31)(H,27,28,30)"
XL8 InChIKey InChI 1.03 PKLZCNWCSPPNIU-UHFFFAOYSA-N
XL8 SMILES_CANONICAL CACTVS 3.385 "CCC(=O)Nc1cc(Cl)cc(Cl)c1Nc2ncc(OCc3c(Cl)c(OC)cc(OC)c3Cl)cn2"
XL8 SMILES CACTVS 3.385 "CCC(=O)Nc1cc(Cl)cc(Cl)c1Nc2ncc(OCc3c(Cl)c(OC)cc(OC)c3Cl)cn2"
XL8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CCC(=O)Nc1cc(cc(c1Nc2ncc(cn2)OCc3c(c(cc(c3Cl)OC)OC)Cl)Cl)Cl"
XL8 SMILES "OpenEye OEToolkits" 2.0.6 "CCC(=O)Nc1cc(cc(c1Nc2ncc(cn2)OCc3c(c(cc(c3Cl)OC)OC)Cl)Cl)Cl"
#
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
XL8 "SYSTEMATIC NAME" ACDLabs 12.01 "N-[3,5-dichloro-2-({5-[(2,6-dichloro-3,5-dimethoxyphenyl)methoxy]pyrimidin-2-yl}amino)phenyl]propanamide"
XL8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "~{N}-[2-[[5-[[2,6-bis(chloranyl)-3,5-dimethoxy-phenyl]methoxy]pyrimidin-2-yl]amino]-3,5-bis(chloranyl)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
XL8 "Create component" 2017-11-05 RCSB
XL8 "Initial release" 2019-07-10 RCSB
XL8 "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id XL8
_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 C22
_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 ?
#