data_ZX4
#
_chem_comp.id ZX4
_chem_comp.name "5'-S-{(2R,4R)-1-[3-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)propyl]-2-carboxypiperidin-4-yl}-5'-thioadenosine"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C25 H32 N10 O6 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-04-17
_chem_comp.pdbx_modified_date 2024-06-28
_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 600.650
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code ZX4
_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 8SIF
_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.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
ZX4 C1 C1 C 0 1 N N N N N N 18.960 9.777 2.820 2.128 -0.662 1.136 C1 ZX4 1
ZX4 C10 C2 C 0 1 N N N N N N 13.945 5.717 6.272 -4.543 -0.121 -0.414 C10 ZX4 2
ZX4 C11 C3 C 0 1 N N N N N N 12.722 6.083 7.142 -5.473 -0.416 -1.592 C11 ZX4 3
ZX4 C12 C4 C 0 1 N N S N N N 20.458 9.947 2.915 3.168 -1.220 0.163 C12 ZX4 4
ZX4 C13 C5 C 0 1 Y N N N N N 12.314 4.832 7.955 -6.643 -1.237 -1.115 C13 ZX4 5
ZX4 C14 C6 C 0 1 Y N N N N N 13.132 3.761 8.166 -6.753 -2.576 -1.156 C14 ZX4 6
ZX4 C15 C7 C 0 1 Y N N N N N 11.107 3.334 9.229 -8.666 -1.856 -0.232 C15 ZX4 7
ZX4 C16 C8 C 0 1 Y N N N N N 10.967 4.651 8.611 -7.876 -0.733 -0.513 C16 ZX4 8
ZX4 C17 C9 C 0 1 N N N N N N 9.713 5.298 8.802 -8.370 0.551 -0.194 C17 ZX4 9
ZX4 C18 C10 C 0 1 N N N N N N 8.995 3.325 10.120 -10.319 -0.485 0.625 C18 ZX4 10
ZX4 C19 C11 C 0 1 N N S N N N 21.388 8.988 2.226 3.868 -2.442 0.788 C19 ZX4 11
ZX4 C2 C12 C 0 1 Y N N N N N 23.020 6.822 8.161 9.960 0.911 -0.284 C2 ZX4 12
ZX4 C20 C13 C 0 1 N N R N N N 22.580 8.853 3.121 5.367 -2.052 0.805 C20 ZX4 13
ZX4 C21 C14 C 0 1 N N R N N N 22.290 9.662 4.352 5.425 -0.938 -0.271 C21 ZX4 14
ZX4 C22 C15 C 0 1 Y N N N N N 23.109 10.011 6.593 6.534 1.132 0.651 C22 ZX4 15
ZX4 C23 C16 C 0 1 Y N N N N N 22.535 7.888 6.104 7.854 -0.249 -0.451 C23 ZX4 16
ZX4 C24 C17 C 0 1 Y N N N N N 22.199 5.702 6.329 9.767 -1.101 -1.397 C24 ZX4 17
ZX4 C25 C18 C 0 1 Y N N N N N 23.003 7.978 7.432 8.587 0.858 0.009 C25 ZX4 18
ZX4 C3 C19 C 0 1 N N R N N N 18.732 7.406 4.788 0.056 1.216 1.631 C3 ZX4 19
ZX4 C4 C20 C 0 1 N N N N N N 18.174 5.997 4.856 -0.933 0.082 1.915 C4 ZX4 20
ZX4 C5 C21 C 0 1 N N N N N N 18.144 8.221 5.864 -0.717 2.448 1.153 C5 ZX4 21
ZX4 C6 C22 C 0 1 N N R N N N 16.633 8.274 5.911 -1.530 2.084 -0.091 C6 ZX4 22
ZX4 C7 C23 C 0 1 N N N N N N 16.238 9.056 7.187 -2.308 3.289 -0.553 C7 ZX4 23
ZX4 C8 C24 C 0 1 N N N N N N 16.591 6.000 4.930 -1.740 -0.214 0.649 C8 ZX4 24
ZX4 C9 C25 C 0 1 N N N N N N 14.638 7.043 5.845 -3.355 0.713 -0.898 C9 ZX4 25
ZX4 N1 N1 N 0 1 Y N N N N N 22.638 9.174 5.665 6.563 -0.048 -0.031 N1 ZX4 26
ZX4 N10 N2 N 0 1 N N N N N N 10.203 2.648 9.967 -9.870 -1.684 0.333 N10 ZX4 27
ZX4 N2 N3 N 0 1 N N N N N N 7.944 2.717 10.888 -11.558 -0.363 1.203 N2 ZX4 28
ZX4 N3 N4 N 0 1 Y N N N N N 23.370 9.362 7.761 7.723 1.661 0.674 N3 ZX4 29
ZX4 N4 N5 N 0 1 Y N N N N N 22.133 6.787 5.507 8.479 -1.196 -1.142 N4 ZX4 30
ZX4 N5 N6 N 0 1 Y N N N N N 22.622 5.673 7.613 10.498 -0.082 -0.985 N5 ZX4 31
ZX4 N6 N7 N 0 1 N N N N N N 23.502 6.928 9.523 10.734 1.976 0.142 N6 ZX4 32
ZX4 N7 N8 N 0 1 N N N N N N 16.059 6.951 6.009 -2.461 0.995 0.233 N7 ZX4 33
ZX4 N8 N9 N 0 1 Y N N N N N 12.384 2.953 8.901 -7.962 -2.955 -0.631 N8 ZX4 34
ZX4 N9 N10 N 0 1 N N N N N N 8.733 4.662 9.547 -9.594 0.642 0.374 N9 ZX4 35
ZX4 O1 O1 O 0 1 N N N N N N 20.813 9.843 4.340 4.179 -0.231 -0.091 O1 ZX4 36
ZX4 O2 O2 O 0 1 N N N N N N 21.784 9.550 0.953 3.663 -3.603 -0.019 O2 ZX4 37
ZX4 O3 O3 O 0 1 N N N N N N 23.780 9.399 2.498 6.187 -3.162 0.434 O3 ZX4 38
ZX4 O4 O4 O 0 1 N N N N N N 16.042 8.435 8.274 -1.754 4.155 -1.417 O4 ZX4 39
ZX4 O5 O5 O 0 1 N N N N N N 16.123 10.308 7.159 -3.430 3.476 -0.146 O5 ZX4 40
ZX4 O6 O6 O 0 1 N N N N N N 9.486 6.388 8.339 -7.711 1.551 -0.424 O6 ZX4 41
ZX4 S1 S1 S 0 1 N N N N N N 18.312 8.077 3.093 1.222 0.695 0.343 S1 ZX4 42
ZX4 H1 H1 H 0 1 N N N N N N 18.500 10.435 3.572 1.429 -1.452 1.413 H1 ZX4 43
ZX4 H2 H2 H 0 1 N N N N N N 18.650 10.096 1.814 2.629 -0.291 2.030 H2 ZX4 44
ZX4 H3 H3 H 0 1 N N N N N N 13.618 5.162 5.381 -5.088 0.433 0.350 H3 ZX4 45
ZX4 H4 H4 H 0 1 N N N N N N 14.646 5.099 6.852 -4.180 -1.060 0.006 H4 ZX4 46
ZX4 H5 H5 H 0 1 N N N N N N 12.984 6.903 7.827 -5.835 0.522 -2.013 H5 ZX4 47
ZX4 H6 H6 H 0 1 N N N N N N 11.887 6.397 6.498 -4.928 -0.970 -2.356 H6 ZX4 48
ZX4 H7 H7 H 0 1 N N N N N N 20.704 10.963 2.571 2.685 -1.505 -0.772 H7 ZX4 49
ZX4 H8 H8 H 0 1 N N N N N N 14.143 3.609 7.818 -6.003 -3.250 -1.543 H8 ZX4 50
ZX4 H9 H9 H 0 1 N N N N N N 20.898 8.012 2.092 3.507 -2.612 1.802 H9 ZX4 51
ZX4 H10 H10 H 0 1 N N N N N N 22.731 7.798 3.392 5.657 -1.665 1.781 H10 ZX4 52
ZX4 H11 H11 H 0 1 N N N N N N 22.751 10.652 4.217 5.482 -1.372 -1.270 H11 ZX4 53
ZX4 H12 H12 H 0 1 N N N N N N 23.263 11.068 6.437 5.655 1.564 1.106 H12 ZX4 54
ZX4 H13 H13 H 0 1 N N N N N N 21.878 4.761 5.908 10.244 -1.887 -1.964 H13 ZX4 55
ZX4 H14 H14 H 0 1 N N N N N N 19.830 7.390 4.855 0.603 1.459 2.542 H14 ZX4 56
ZX4 H15 H15 H 0 1 N N N N N N 18.488 5.445 3.958 -0.385 -0.812 2.214 H15 ZX4 57
ZX4 H16 H16 H 0 1 N N N N N N 18.572 5.498 5.752 -1.609 0.380 2.716 H16 ZX4 58
ZX4 H17 H17 H 0 1 N N N N N N 18.496 7.814 6.824 -1.390 2.784 1.942 H17 ZX4 59
ZX4 H18 H18 H 0 1 N N N N N N 18.513 9.251 5.745 -0.015 3.245 0.908 H18 ZX4 60
ZX4 H19 H19 H 0 1 N N N N N N 16.250 8.802 5.025 -0.856 1.761 -0.884 H19 ZX4 61
ZX4 H20 H20 H 0 1 N N N N N N 16.192 6.314 3.954 -1.065 -0.526 -0.148 H20 ZX4 62
ZX4 H21 H21 H 0 1 N N N N N N 16.246 4.980 5.156 -2.455 -1.012 0.852 H21 ZX4 63
ZX4 H22 H22 H 0 1 N N N N N N 14.256 7.866 6.467 -2.809 0.159 -1.663 H22 ZX4 64
ZX4 H23 H23 H 0 1 N N N N N N 14.409 7.245 4.788 -3.717 1.651 -1.319 H23 ZX4 65
ZX4 H24 H24 H 0 1 N N N N N N 8.085 1.819 11.305 -12.087 -1.155 1.389 H24 ZX4 66
ZX4 H25 H25 H 0 1 N N N N N N 7.072 3.192 11.006 -11.905 0.515 1.425 H25 ZX4 67
ZX4 H26 H26 H 0 1 N N N N N N 23.482 6.026 9.955 10.330 2.697 0.650 H26 ZX4 68
ZX4 H27 H27 H 0 1 N N N N N N 24.440 7.275 9.519 11.681 2.002 -0.066 H27 ZX4 69
ZX4 H29 H29 H 0 1 N N N N N N 12.746 2.075 9.214 -8.271 -3.871 -0.552 H29 ZX4 70
ZX4 H30 H30 H 0 1 N N N N N N 7.850 5.107 9.697 -9.957 1.512 0.603 H30 ZX4 71
ZX4 H31 H31 H 0 1 N N N N N N 22.372 8.950 0.511 4.083 -4.402 0.328 H31 ZX4 72
ZX4 H32 H32 H 0 1 N N N N N N 24.517 9.299 3.089 6.114 -3.921 1.030 H32 ZX4 73
ZX4 H33 H33 H 0 1 N N N N N N 15.820 9.056 8.958 -2.292 4.912 -1.684 H33 ZX4 74
#
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
ZX4 O2 C19 SING N N 1
ZX4 C19 C12 SING N N 2
ZX4 C19 C20 SING N N 3
ZX4 O3 C20 SING N N 4
ZX4 C1 C12 SING N N 5
ZX4 C1 S1 SING N N 6
ZX4 C12 O1 SING N N 7
ZX4 S1 C3 SING N N 8
ZX4 C20 C21 SING N N 9
ZX4 O1 C21 SING N N 10
ZX4 C21 N1 SING N N 11
ZX4 C3 C4 SING N N 12
ZX4 C3 C5 SING N N 13
ZX4 C4 C8 SING N N 14
ZX4 C8 N7 SING N N 15
ZX4 N4 C23 DOUB Y N 16
ZX4 N4 C24 SING Y N 17
ZX4 N1 C23 SING Y N 18
ZX4 N1 C22 SING Y N 19
ZX4 C9 N7 SING N N 20
ZX4 C9 C10 SING N N 21
ZX4 C5 C6 SING N N 22
ZX4 C6 N7 SING N N 23
ZX4 C6 C7 SING N N 24
ZX4 C23 C25 SING Y N 25
ZX4 C10 C11 SING N N 26
ZX4 C24 N5 DOUB Y N 27
ZX4 C22 N3 DOUB Y N 28
ZX4 C11 C13 SING N N 29
ZX4 O5 C7 DOUB N N 30
ZX4 C7 O4 SING N N 31
ZX4 C25 N3 SING Y N 32
ZX4 C25 C2 DOUB Y N 33
ZX4 N5 C2 SING Y N 34
ZX4 C13 C14 DOUB Y N 35
ZX4 C13 C16 SING Y N 36
ZX4 C2 N6 SING N N 37
ZX4 C14 N8 SING Y N 38
ZX4 O6 C17 DOUB N N 39
ZX4 C16 C17 SING N N 40
ZX4 C16 C15 DOUB Y N 41
ZX4 C17 N9 SING N N 42
ZX4 N8 C15 SING Y N 43
ZX4 C15 N10 SING N N 44
ZX4 N9 C18 SING N N 45
ZX4 N10 C18 DOUB N N 46
ZX4 C18 N2 SING N N 47
ZX4 C1 H1 SING N N 48
ZX4 C1 H2 SING N N 49
ZX4 C10 H3 SING N N 50
ZX4 C10 H4 SING N N 51
ZX4 C11 H5 SING N N 52
ZX4 C11 H6 SING N N 53
ZX4 C12 H7 SING N N 54
ZX4 C14 H8 SING N N 55
ZX4 C19 H9 SING N N 56
ZX4 C20 H10 SING N N 57
ZX4 C21 H11 SING N N 58
ZX4 C22 H12 SING N N 59
ZX4 C24 H13 SING N N 60
ZX4 C3 H14 SING N N 61
ZX4 C4 H15 SING N N 62
ZX4 C4 H16 SING N N 63
ZX4 C5 H17 SING N N 64
ZX4 C5 H18 SING N N 65
ZX4 C6 H19 SING N N 66
ZX4 C8 H20 SING N N 67
ZX4 C8 H21 SING N N 68
ZX4 C9 H22 SING N N 69
ZX4 C9 H23 SING N N 70
ZX4 N2 H24 SING N N 71
ZX4 N2 H25 SING N N 72
ZX4 N6 H26 SING N N 73
ZX4 N6 H27 SING N N 74
ZX4 N8 H29 SING N N 75
ZX4 N9 H30 SING N N 76
ZX4 O2 H31 SING N N 77
ZX4 O3 H32 SING N N 78
ZX4 O4 H33 SING N N 79
#
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
ZX4 SMILES ACDLabs 12.01 "O=C(O)C1CC(CCN1CCCc1c[NH]c2N=C(N)NC(=O)c21)SCC1OC(n2cnc3c(N)ncnc32)C(O)C1O"
ZX4 InChI InChI 1.06 "InChI=1S/C25H32N10O6S/c26-19-16-21(30-9-29-19)35(10-31-16)23-18(37)17(36)14(41-23)8-42-12-3-5-34(13(6-12)24(39)40)4-1-2-11-7-28-20-15(11)22(38)33-25(27)32-20/h7,9-10,12-14,17-18,23,36-37H,1-6,8H2,(H,39,40)(H2,26,29,30)(H4,27,28,32,33,38)/t12-,13-,14-,17-,18-,23-/m1/s1"
ZX4 InChIKey InChI 1.06 AOZGSZXCWJDLPF-LVEUASCASA-N
ZX4 SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2[nH]cc(CCCN3CC[C@H](C[C@@H]3C(O)=O)SC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2C(=O)N1"
ZX4 SMILES CACTVS 3.385 "NC1=Nc2[nH]cc(CCCN3CC[CH](C[CH]3C(O)=O)SC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2C(=O)N1"
ZX4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1c(c2c([nH]1)N=C(NC2=O)N)CCCN3CC[C@H](C[C@@H]3C(=O)O)SC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O"
ZX4 SMILES "OpenEye OEToolkits" 2.0.7 "c1c(c2c([nH]1)N=C(NC2=O)N)CCCN3CCC(CC3C(=O)O)SCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O"
#
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
ZX4 "SYSTEMATIC NAME" ACDLabs 12.01 "5'-S-{(2R,4R)-1-[3-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)propyl]-2-carboxypiperidin-4-yl}-5'-thioadenosine"
ZX4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{R},4~{R})-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]-1-[3-(2-azanyl-4-oxidanylidene-3,7-dihydropyrrolo[2,3-d]pyrimidin-5-yl)propyl]piperidine-2-carboxylic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
ZX4 "Create component" 2023-04-17 RCSB
ZX4 "Initial release" 2024-07-03 RCSB
#