data_XL5
#
_chem_comp.id XL5
_chem_comp.name "N-[2-({5-[(2,6-dichloro-3,5-dimethoxyphenyl)methoxy]pyrimidin-2-yl}amino)-3-fluorophenyl]propanamide"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C22 H21 Cl2 F 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 495.331
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code XL5
_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 6BIU
_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
XL5 C1 C1 C 0 1 Y N N N N N 20.913 -2.770 -8.630 5.954 -0.756 0.212 C1 XL5 1
XL5 C2 C2 C 0 1 Y N N N N N 19.715 -3.462 -8.615 4.589 -0.984 0.105 C2 XL5 2
XL5 C3 C3 C 0 1 Y N N N N N 19.519 -4.571 -7.782 3.745 0.037 -0.290 C3 XL5 3
XL5 C4 C4 C 0 1 Y N N N N N 20.567 -4.975 -6.968 4.258 1.288 -0.580 C4 XL5 4
XL5 C5 C5 C 0 1 Y N N N N N 21.777 -4.285 -6.980 5.623 1.520 -0.474 C5 XL5 5
XL5 C6 C6 C 0 1 Y N N N N N 21.947 -3.190 -7.810 6.471 0.498 -0.078 C6 XL5 6
XL5 O1 O1 O 0 1 N N N N N N 20.947 -1.703 -9.477 6.783 -1.759 0.605 O1 XL5 7
XL5 O2 O2 O 0 1 N N N N N N 22.788 -4.693 -6.172 6.127 2.750 -0.759 O2 XL5 8
XL5 C7 C7 C 0 1 N N N N N N 22.098 -0.869 -9.523 8.176 -1.452 0.693 C7 XL5 9
XL5 C8 C8 C 0 1 N N N N N N 24.063 -4.871 -6.769 7.540 2.918 -0.628 C8 XL5 10
XL5 CL1 CL1 CL 0 0 N N N N N N 18.452 -2.911 -9.671 3.941 -2.554 0.468 CL1 XL5 11
XL5 CL2 CL2 CL 0 0 N N N N N N 20.354 -6.350 -5.926 3.196 2.568 -1.076 CL2 XL5 12
XL5 C9 C9 C 0 1 N N N N N N 18.229 -5.336 -7.788 2.263 -0.214 -0.407 C9 XL5 13
XL5 O3 O3 O 0 1 N N N N N N 18.452 -6.532 -8.554 1.632 0.071 0.844 O3 XL5 14
XL5 C10 C10 C 0 1 Y N N N N N 17.621 -7.604 -8.353 0.285 -0.105 0.910 C10 XL5 15
XL5 C11 C11 C 0 1 Y N N N N N 16.325 -7.505 -7.865 -0.408 0.149 2.088 C11 XL5 16
XL5 N1 N1 N 0 1 Y N N N N N 15.559 -8.585 -7.725 -1.718 -0.033 2.116 N1 XL5 17
XL5 C12 C12 C 0 1 Y N N N N N 16.100 -9.766 -8.081 -2.368 -0.452 1.041 C12 XL5 18
XL5 N2 N2 N 0 1 Y N N N N N 17.347 -9.945 -8.556 -1.740 -0.703 -0.098 N2 XL5 19
XL5 C13 C13 C 0 1 Y N N N N N 18.103 -8.850 -8.688 -0.431 -0.537 -0.200 C13 XL5 20
XL5 N3 N3 N 0 1 N N N N N N 15.340 -10.878 -7.918 -3.741 -0.632 1.109 N3 XL5 21
XL5 C14 C14 C 0 1 Y N N N N N 14.025 -10.971 -7.427 -4.463 -0.958 -0.047 C14 XL5 22
XL5 C15 C15 C 0 1 Y N N N N N 13.037 -11.541 -8.236 -5.503 -0.135 -0.478 C15 XL5 23
XL5 C16 C16 C 0 1 Y N N N N N 11.717 -11.622 -7.715 -6.213 -0.463 -1.624 C16 XL5 24
XL5 C17 C17 C 0 1 Y N N N N N 11.430 -11.122 -6.454 -5.890 -1.603 -2.335 C17 XL5 25
XL5 C18 C18 C 0 1 Y N N N N N 12.416 -10.561 -5.669 -4.860 -2.421 -1.909 C18 XL5 26
XL5 C19 C19 C 0 1 Y N N N N N 13.696 -10.492 -6.167 -4.142 -2.099 -0.771 C19 XL5 27
XL5 N4 N4 N 0 1 N N N N N N 13.443 -12.070 -9.484 -5.829 1.021 0.244 N4 XL5 28
XL5 C20 C20 C 0 1 N N N N N N 12.796 -12.016 -10.660 -7.111 1.431 0.315 C20 XL5 29
XL5 C21 C21 C 0 1 N N N N N N 13.547 -12.665 -11.802 -7.478 2.609 1.180 C21 XL5 30
XL5 C22 C22 C 0 1 N N N N N N 14.870 -11.994 -12.108 -8.983 2.864 1.083 C22 XL5 31
XL5 O4 O4 O 0 1 N N N N N N 11.712 -11.491 -10.796 -7.969 0.852 -0.317 O4 XL5 32
XL5 F1 F1 F 0 1 N N N N N N 14.668 -9.937 -5.410 -3.132 -2.897 -0.360 F1 XL5 33
XL5 H1 H1 H 0 1 N N N N N N 22.889 -2.662 -7.818 7.532 0.677 0.004 H1 XL5 34
XL5 H2 H2 H 0 1 N N N N N N 21.941 -0.067 -10.259 8.723 -2.338 1.017 H2 XL5 35
XL5 H3 H3 H 0 1 N N N N N N 22.270 -0.427 -8.531 8.541 -1.137 -0.285 H3 XL5 36
XL5 H4 H4 H 0 1 N N N N N N 22.973 -1.468 -9.814 8.326 -0.648 1.413 H4 XL5 37
XL5 H5 H5 H 0 1 N N N N N N 24.783 -5.201 -6.006 7.810 3.942 -0.885 H5 XL5 38
XL5 H6 H6 H 0 1 N N N N N N 23.994 -5.632 -7.561 7.838 2.710 0.400 H6 XL5 39
XL5 H7 H7 H 0 1 N N N N N N 24.400 -3.919 -7.204 8.052 2.229 -1.301 H7 XL5 40
XL5 H8 H8 H 0 1 N N N N N N 17.435 -4.733 -8.252 1.845 0.431 -1.180 H8 XL5 41
XL5 H9 H9 H 0 1 N N N N N N 17.939 -5.595 -6.759 2.091 -1.257 -0.671 H9 XL5 42
XL5 H10 H10 H 0 1 N N N N N N 15.932 -6.536 -7.595 0.116 0.490 2.969 H10 XL5 43
XL5 H11 H11 H 0 1 N N N N N N 19.111 -8.944 -9.064 0.075 -0.744 -1.131 H11 XL5 44
XL5 H12 H12 H 0 1 N N N N N N 15.770 -11.742 -8.180 -4.202 -0.532 1.956 H12 XL5 45
XL5 H13 H13 H 0 1 N N N N N N 10.934 -12.075 -8.304 -7.019 0.173 -1.959 H13 XL5 46
XL5 H14 H14 H 0 1 N N N N N N 10.418 -11.173 -6.080 -6.445 -1.857 -3.226 H14 XL5 47
XL5 H15 H15 H 0 1 N N N N N N 12.187 -10.184 -4.683 -4.612 -3.311 -2.469 H15 XL5 48
XL5 H16 H16 H 0 1 N N N N N N 14.323 -12.544 -9.491 -5.133 1.525 0.692 H16 XL5 49
XL5 H17 H17 H 0 1 N N N N N N 12.917 -12.622 -12.703 -7.211 2.397 2.216 H17 XL5 50
XL5 H18 H18 H 0 1 N N N N N N 13.741 -13.716 -11.540 -6.937 3.492 0.840 H18 XL5 51
XL5 H19 H19 H 0 1 N N N N N N 15.361 -12.514 -12.944 -9.248 3.716 1.709 H19 XL5 52
XL5 H20 H20 H 0 1 N N N N N N 14.693 -10.944 -12.382 -9.250 3.076 0.048 H20 XL5 53
XL5 H21 H21 H 0 1 N N N N N N 15.517 -12.037 -11.219 -9.524 1.981 1.424 H21 XL5 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
XL5 C22 C21 SING N N 1
XL5 C21 C20 SING N N 2
XL5 O4 C20 DOUB N N 3
XL5 C20 N4 SING N N 4
XL5 CL1 C2 SING N N 5
XL5 C7 O1 SING N N 6
XL5 N4 C15 SING N N 7
XL5 O1 C1 SING N N 8
XL5 C13 N2 DOUB Y N 9
XL5 C13 C10 SING Y N 10
XL5 C1 C2 DOUB Y N 11
XL5 C1 C6 SING Y N 12
XL5 C2 C3 SING Y N 13
XL5 N2 C12 SING Y N 14
XL5 O3 C10 SING N N 15
XL5 O3 C9 SING N N 16
XL5 C10 C11 DOUB Y N 17
XL5 C15 C16 DOUB Y N 18
XL5 C15 C14 SING Y N 19
XL5 C12 N3 SING N N 20
XL5 C12 N1 DOUB Y N 21
XL5 N3 C14 SING N N 22
XL5 C11 N1 SING Y N 23
XL5 C6 C5 DOUB Y N 24
XL5 C9 C3 SING N N 25
XL5 C3 C4 DOUB Y N 26
XL5 C16 C17 SING Y N 27
XL5 C14 C19 DOUB Y N 28
XL5 C5 C4 SING Y N 29
XL5 C5 O2 SING N N 30
XL5 C4 CL2 SING N N 31
XL5 C8 O2 SING N N 32
XL5 C17 C18 DOUB Y N 33
XL5 C19 C18 SING Y N 34
XL5 C19 F1 SING N N 35
XL5 C6 H1 SING N N 36
XL5 C7 H2 SING N N 37
XL5 C7 H3 SING N N 38
XL5 C7 H4 SING N N 39
XL5 C8 H5 SING N N 40
XL5 C8 H6 SING N N 41
XL5 C8 H7 SING N N 42
XL5 C9 H8 SING N N 43
XL5 C9 H9 SING N N 44
XL5 C11 H10 SING N N 45
XL5 C13 H11 SING N N 46
XL5 N3 H12 SING N N 47
XL5 C16 H13 SING N N 48
XL5 C17 H14 SING N N 49
XL5 C18 H15 SING N N 50
XL5 N4 H16 SING N N 51
XL5 C21 H17 SING N N 52
XL5 C21 H18 SING N N 53
XL5 C22 H19 SING N N 54
XL5 C22 H20 SING N N 55
XL5 C22 H21 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
XL5 SMILES ACDLabs 12.01 "c1(c(c(c(Cl)c(OC)c1)COc3cnc(Nc2c(cccc2NC(CC)=O)F)nc3)Cl)OC"
XL5 InChI InChI 1.03 "InChI=1S/C22H21Cl2FN4O4/c1-4-18(30)28-15-7-5-6-14(25)21(15)29-22-26-9-12(10-27-22)33-11-13-19(23)16(31-2)8-17(32-3)20(13)24/h5-10H,4,11H2,1-3H3,(H,28,30)(H,26,27,29)"
XL5 InChIKey InChI 1.03 QQZLOGCMIZJHHI-UHFFFAOYSA-N
XL5 SMILES_CANONICAL CACTVS 3.385 "CCC(=O)Nc1cccc(F)c1Nc2ncc(OCc3c(Cl)c(OC)cc(OC)c3Cl)cn2"
XL5 SMILES CACTVS 3.385 "CCC(=O)Nc1cccc(F)c1Nc2ncc(OCc3c(Cl)c(OC)cc(OC)c3Cl)cn2"
XL5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CCC(=O)Nc1cccc(c1Nc2ncc(cn2)OCc3c(c(cc(c3Cl)OC)OC)Cl)F"
XL5 SMILES "OpenEye OEToolkits" 2.0.6 "CCC(=O)Nc1cccc(c1Nc2ncc(cn2)OCc3c(c(cc(c3Cl)OC)OC)Cl)F"
#
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
XL5 "SYSTEMATIC NAME" ACDLabs 12.01 "N-[2-({5-[(2,6-dichloro-3,5-dimethoxyphenyl)methoxy]pyrimidin-2-yl}amino)-3-fluorophenyl]propanamide"
XL5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "~{N}-[2-[[5-[[2,6-bis(chloranyl)-3,5-dimethoxy-phenyl]methoxy]pyrimidin-2-yl]amino]-3-fluoranyl-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
XL5 "Create component" 2017-11-05 RCSB
XL5 "Initial release" 2019-07-10 RCSB
XL5 "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id XL5
_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 ?
#