data_A1EKR
#
_chem_comp.id A1EKR
_chem_comp.name "4-[5-chloranyl-2-[[3-[(dimethylamino)methyl]phenyl]amino]pyrimidin-4-yl]-~{N}-morpholin-4-yl-thiophene-2-carboxamide"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C22 H25 Cl N6 O2 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2025-01-25
_chem_comp.pdbx_modified_date 2025-03-28
_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 472.991
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code A1EKR
_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 9LNR
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBC
_chem_comp.pdbx_pcm ?
#
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_n_terminal_atom_flag
_chem_comp_atom.pdbx_backbone_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
A1EKR C10 C1 C 0 1 Y N N N N N 18.164 -1.083 14.804 2.316 -0.745 -0.062 C10 A1EKR 1
A1EKR N12 N1 N 0 1 N N N N N N 19.372 -1.348 15.540 3.139 0.347 -0.288 N12 A1EKR 2
A1EKR C13 C2 C 0 1 Y N N N N N 19.448 -2.237 16.689 4.528 0.198 -0.235 C13 A1EKR 3
A1EKR C15 C3 C 0 1 Y N N N N N 18.608 -3.317 18.653 6.498 -1.090 -0.697 C15 A1EKR 4
A1EKR C17 C4 C 0 1 Y N N N N N 20.883 -3.701 17.955 6.686 1.044 0.378 C17 A1EKR 5
A1EKR C21 C5 C 0 1 N N N N N N 21.977 -6.606 18.777 8.565 4.272 0.556 C21 A1EKR 6
A1EKR C22 C6 C 0 1 N N N N N N 21.380 -5.932 16.610 8.824 2.460 -1.030 C22 A1EKR 7
A1EKR C24 C7 C 0 1 N N N N N N 11.046 -2.803 15.230 -4.234 0.701 0.095 C24 A1EKR 8
A1EKR C28 C8 C 0 1 N N N N N N 9.937 -5.449 16.892 -7.110 1.911 -1.210 C28 A1EKR 9
A1EKR C01 C9 C 0 1 Y N N N N N 12.547 -2.645 15.277 -3.279 -0.388 -0.135 C01 A1EKR 10
A1EKR C02 C10 C 0 1 Y N N N N N 13.468 -1.859 14.603 -1.951 -0.320 0.104 C02 A1EKR 11
A1EKR C03 C11 C 0 1 Y N N N N N 14.782 -2.075 15.000 -1.271 -1.490 -0.199 C03 A1EKR 12
A1EKR C04 C12 C 0 1 Y N N N N N 14.927 -2.998 16.037 -2.063 -2.488 -0.681 C04 A1EKR 13
A1EKR C06 C13 C 0 1 Y N N N N N 15.908 -1.409 14.493 0.191 -1.641 -0.016 C06 A1EKR 14
A1EKR C07 C14 C 0 1 Y N N N N N 15.963 -0.537 13.396 0.734 -2.869 0.379 C07 A1EKR 15
A1EKR C08 C15 C 0 1 Y N N N N N 17.183 0.037 13.074 2.104 -2.959 0.547 C08 A1EKR 16
A1EKR C14 C16 C 0 1 Y N N N N N 18.403 -2.455 17.585 5.126 -0.945 -0.751 C14 A1EKR 17
A1EKR C16 C17 C 0 1 Y N N N N N 19.849 -3.932 18.849 7.277 -0.097 -0.131 C16 A1EKR 18
A1EKR C18 C18 C 0 1 Y N N N N N 20.668 -2.847 16.890 5.314 1.195 0.328 C18 A1EKR 19
A1EKR C19 C19 C 0 1 N N N N N N 22.281 -4.338 18.102 7.540 2.123 0.995 C19 A1EKR 20
A1EKR C29 C20 C 0 1 N N N N N N 10.846 -5.920 18.036 -8.051 3.087 -0.937 C29 A1EKR 21
A1EKR C31 C21 C 0 1 N N N N N N 10.430 -4.046 19.232 -8.348 2.349 1.323 C31 A1EKR 22
A1EKR C32 C22 C 0 1 N N N N N N 9.579 -3.494 18.077 -7.410 1.165 1.072 C32 A1EKR 23
A1EKR N09 N2 N 0 1 Y N N N N N 18.249 -0.251 13.786 2.857 -1.893 0.316 N09 A1EKR 24
A1EKR N11 N3 N 0 1 Y N N N N N 17.022 -1.652 15.150 1.009 -0.611 -0.225 N11 A1EKR 25
A1EKR N20 N4 N 0 1 N N N N N N 22.333 -5.727 17.673 7.936 3.086 -0.041 N20 A1EKR 26
A1EKR N26 N5 N 0 1 N N N N N N 10.769 -3.649 16.378 -5.542 0.519 -0.176 N26 A1EKR 27
A1EKR N27 N6 N 0 1 N N N N N N 9.734 -4.075 16.811 -6.431 1.533 0.038 N27 A1EKR 28
A1EKR O25 O1 O 0 1 N N N N N N 10.340 -2.352 14.406 -3.846 1.769 0.530 O25 A1EKR 29
A1EKR O30 O2 O 0 1 N N N N N N 10.454 -5.430 19.277 -8.975 2.723 0.093 O30 A1EKR 30
A1EKR S05 S1 S 0 1 Y N N N N N 13.343 -3.581 16.472 -3.690 -1.979 -0.757 S05 A1EKR 31
A1EKR CL23 CL1 CL 0 0 N N N N N N 14.614 -0.087 12.316 -0.288 -4.242 0.666 CL23 A1EKR 32
A1EKR H121 H1 H 0 0 N N N N N N 20.211 -0.893 15.243 2.751 1.215 -0.483 H121 A1EKR 33
A1EKR H151 H2 H 0 0 N N N N N N 17.800 -3.515 19.341 6.963 -1.980 -1.094 H151 A1EKR 34
A1EKR H213 H3 H 0 0 N N N N N N 22.691 -6.467 19.602 8.849 4.968 -0.233 H213 A1EKR 35
A1EKR H212 H4 H 0 0 N N N N N N 20.962 -6.364 19.126 7.860 4.756 1.232 H212 A1EKR 36
A1EKR H211 H5 H 0 0 N N N N N N 22.008 -7.652 18.437 9.453 3.971 1.112 H211 A1EKR 37
A1EKR H221 H6 H 0 0 N N N N N N 21.416 -6.981 16.282 8.308 1.627 -1.506 H221 A1EKR 38
A1EKR H223 H7 H 0 0 N N N N N N 20.369 -5.696 16.973 9.102 3.195 -1.785 H223 A1EKR 39
A1EKR H222 H8 H 0 0 N N N N N N 21.628 -5.275 15.763 9.722 2.094 -0.531 H222 A1EKR 40
A1EKR H282 H9 H 0 0 N N N N N N 8.956 -5.929 17.020 -7.685 1.064 -1.583 H282 A1EKR 41
A1EKR H281 H10 H 0 0 N N N N N N 10.386 -5.781 15.944 -6.369 2.204 -1.954 H281 A1EKR 42
A1EKR H021 H11 H 0 0 N N N N N N 13.191 -1.146 13.841 -1.464 0.562 0.494 H021 A1EKR 43
A1EKR H041 H12 H 0 0 N N N N N N 15.859 -3.299 16.491 -1.711 -3.467 -0.971 H041 A1EKR 44
A1EKR H081 H13 H 0 0 N N N N N N 17.257 0.719 12.240 2.557 -3.891 0.851 H081 A1EKR 45
A1EKR H141 H14 H 0 0 N N N N N N 17.451 -1.962 17.451 4.517 -1.721 -1.193 H141 A1EKR 46
A1EKR H161 H15 H 0 0 N N N N N N 20.001 -4.586 19.695 8.350 -0.215 -0.086 H161 A1EKR 47
A1EKR H181 H16 H 0 0 N N N N N N 21.475 -2.653 16.199 4.853 2.087 0.725 H181 A1EKR 48
A1EKR H191 H17 H 0 0 N N N N N N 22.577 -4.289 19.160 6.971 2.636 1.770 H191 A1EKR 49
A1EKR H192 H18 H 0 0 N N N N N N 22.993 -3.759 17.495 8.431 1.674 1.434 H192 A1EKR 50
A1EKR H292 H19 H 0 0 N N N N N N 10.825 -7.019 18.070 -7.470 3.951 -0.615 H292 A1EKR 51
A1EKR H291 H20 H 0 0 N N N N N N 11.872 -5.579 17.832 -8.599 3.334 -1.846 H291 A1EKR 52
A1EKR H312 H21 H 0 0 N N N N N N 11.461 -3.682 19.112 -9.111 2.062 2.047 H312 A1EKR 53
A1EKR H311 H22 H 0 0 N N N N N N 10.017 -3.672 20.181 -7.777 3.192 1.711 H311 A1EKR 54
A1EKR H322 H23 H 0 0 N N N N N N 9.816 -2.425 17.978 -6.887 0.914 1.995 H322 A1EKR 55
A1EKR H321 H24 H 0 0 N N N N N N 8.523 -3.610 18.364 -7.990 0.306 0.736 H321 A1EKR 56
A1EKR H261 H26 H 0 0 N N N N N N 11.579 -3.923 16.896 -5.851 -0.333 -0.523 H261 A1EKR 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
A1EKR CL23 C07 SING N N 1
A1EKR C08 C07 DOUB Y N 2
A1EKR C08 N09 SING Y N 3
A1EKR C07 C06 SING Y N 4
A1EKR N09 C10 DOUB Y N 5
A1EKR O25 C24 DOUB N N 6
A1EKR C06 C03 SING N N 7
A1EKR C06 N11 DOUB Y N 8
A1EKR C02 C03 SING Y N 9
A1EKR C02 C01 DOUB Y N 10
A1EKR C10 N11 SING Y N 11
A1EKR C10 N12 SING N N 12
A1EKR C03 C04 DOUB Y N 13
A1EKR C24 C01 SING N N 14
A1EKR C24 N26 SING N N 15
A1EKR C01 S05 SING Y N 16
A1EKR N12 C13 SING N N 17
A1EKR C04 S05 SING Y N 18
A1EKR N26 N27 SING N N 19
A1EKR C22 N20 SING N N 20
A1EKR C13 C18 DOUB Y N 21
A1EKR C13 C14 SING Y N 22
A1EKR N27 C28 SING N N 23
A1EKR N27 C32 SING N N 24
A1EKR C18 C17 SING Y N 25
A1EKR C28 C29 SING N N 26
A1EKR C14 C15 DOUB Y N 27
A1EKR N20 C19 SING N N 28
A1EKR N20 C21 SING N N 29
A1EKR C17 C19 SING N N 30
A1EKR C17 C16 DOUB Y N 31
A1EKR C29 O30 SING N N 32
A1EKR C32 C31 SING N N 33
A1EKR C15 C16 SING Y N 34
A1EKR C31 O30 SING N N 35
A1EKR N12 H121 SING N N 36
A1EKR C15 H151 SING N N 37
A1EKR C21 H213 SING N N 38
A1EKR C21 H212 SING N N 39
A1EKR C21 H211 SING N N 40
A1EKR C22 H221 SING N N 41
A1EKR C22 H223 SING N N 42
A1EKR C22 H222 SING N N 43
A1EKR C28 H282 SING N N 44
A1EKR C28 H281 SING N N 45
A1EKR C02 H021 SING N N 46
A1EKR C04 H041 SING N N 47
A1EKR C08 H081 SING N N 48
A1EKR C14 H141 SING N N 49
A1EKR C16 H161 SING N N 50
A1EKR C18 H181 SING N N 51
A1EKR C19 H191 SING N N 52
A1EKR C19 H192 SING N N 53
A1EKR C29 H292 SING N N 54
A1EKR C29 H291 SING N N 55
A1EKR C31 H312 SING N N 56
A1EKR C31 H311 SING N N 57
A1EKR C32 H322 SING N N 58
A1EKR C32 H321 SING N N 59
A1EKR N26 H261 SING N N 60
#
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
A1EKR InChI InChI 1.06 "InChI=1S/C22H25ClN6O2S/c1-28(2)13-15-4-3-5-17(10-15)25-22-24-12-18(23)20(26-22)16-11-19(32-14-16)21(30)27-29-6-8-31-9-7-29/h3-5,10-12,14H,6-9,13H2,1-2H3,(H,27,30)(H,24,25,26)"
A1EKR InChIKey InChI 1.06 JXVORTVTLKOYIT-UHFFFAOYSA-N
A1EKR SMILES_CANONICAL CACTVS 3.385 "CN(C)Cc1cccc(Nc2ncc(Cl)c(n2)c3csc(c3)C(=O)NN4CCOCC4)c1"
A1EKR SMILES CACTVS 3.385 "CN(C)Cc1cccc(Nc2ncc(Cl)c(n2)c3csc(c3)C(=O)NN4CCOCC4)c1"
A1EKR SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN(C)Cc1cccc(c1)Nc2ncc(c(n2)c3cc(sc3)C(=O)NN4CCOCC4)Cl"
A1EKR SMILES "OpenEye OEToolkits" 2.0.7 "CN(C)Cc1cccc(c1)Nc2ncc(c(n2)c3cc(sc3)C(=O)NN4CCOCC4)Cl"
#
_pdbx_chem_comp_identifier.comp_id A1EKR
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier "4-[5-chloranyl-2-[[3-[(dimethylamino)methyl]phenyl]amino]pyrimidin-4-yl]-~{N}-morpholin-4-yl-thiophene-2-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
A1EKR "Create component" 2025-01-25 PDBC
A1EKR "Initial release" 2025-04-02 RCSB
#