data_J1L
#
_chem_comp.id J1L
_chem_comp.name "5'-{[(2R,4R)-1-{2-[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carbonyl)amino]ethyl}-2-carboxypiperidin-4-yl]sulfonyl}-5'-deoxyadenosine"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C27 H36 N12 O9 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-10-09
_chem_comp.pdbx_modified_date 2020-11-27
_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 704.715
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code J1L
_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 7KDR
_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.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
J1L C01 C1 C 0 1 N N N 9.726 10.685 23.351 -1.171 -3.561 2.117 C01 J1L 1
J1L C1 C2 C 0 1 N N S 12.944 4.816 20.938 3.897 0.236 -1.035 C1 J1L 2
J1L C10 C3 C 0 1 N N N 13.681 6.159 20.906 3.159 -1.059 -1.382 C10 J1L 3
J1L C11 C4 C 0 1 N N R 11.336 8.001 21.126 1.584 -3.231 -0.521 C11 J1L 4
J1L C12 C5 C 0 1 N N N 10.458 8.717 22.148 0.759 -3.881 0.593 C12 J1L 5
J1L C13 C6 C 0 1 N N R 10.819 10.192 22.348 -0.345 -2.917 1.034 C13 J1L 6
J1L C14 C7 C 0 1 N N N 11.826 10.280 20.118 -0.443 -1.929 -1.177 C14 J1L 7
J1L C15 C8 C 0 1 N N N 11.577 8.815 19.884 0.657 -2.864 -1.683 C15 J1L 8
J1L C16 C9 C 0 1 N N N 11.025 12.369 21.206 -2.355 -1.784 0.302 C16 J1L 9
J1L C18 C10 C 0 1 N N N 12.085 14.869 22.920 -5.514 -0.652 -1.301 C18 J1L 10
J1L C19 C11 C 0 1 N N N 10.539 20.826 21.777 -9.833 2.878 1.573 C19 J1L 11
J1L C2 C12 C 0 1 N N S 13.492 3.827 19.978 4.494 0.873 -2.310 C2 J1L 12
J1L C20 C13 C 0 1 N N N 11.040 18.805 20.522 -7.567 2.304 1.858 C20 J1L 13
J1L C21 C14 C 0 1 N N N 11.838 16.330 22.967 -6.661 0.158 -0.887 C21 J1L 14
J1L C22 C15 C 0 1 N N N 11.674 17.005 24.278 -7.846 0.287 -1.810 C22 J1L 15
J1L C23 C16 C 0 1 N N N 12.950 17.019 25.025 -8.015 -1.006 -2.610 C23 J1L 16
J1L C24 C17 C 0 1 N N N 10.583 16.373 25.106 -7.624 1.457 -2.769 C24 J1L 17
J1L C25 C18 C 0 1 N N N 11.114 18.960 22.931 -8.933 1.371 0.079 C25 J1L 18
J1L C26 C19 C 0 1 N N N 11.267 18.213 21.804 -7.679 1.463 0.723 C26 J1L 19
J1L C27 C20 C 0 1 N N N 12.367 12.894 21.541 -3.353 -1.687 -0.854 C27 J1L 20
J1L C3 C21 C 0 1 N N R 12.321 3.450 18.971 5.845 1.456 -1.841 C3 J1L 21
J1L C4 C22 C 0 1 N N R 11.154 3.847 19.799 5.905 1.103 -0.338 C4 J1L 22
J1L C5 C23 C 0 1 Y N N 8.690 3.921 19.472 7.802 -0.498 0.115 C5 J1L 23
J1L C6 C24 C 0 1 Y N N 8.483 5.310 17.862 9.393 0.854 0.701 C6 J1L 24
J1L C7 C25 C 0 1 Y N N 8.060 6.150 16.859 10.568 1.508 1.107 C7 J1L 25
J1L C8 C26 C 0 1 Y N N 10.284 6.703 16.463 9.466 3.528 0.921 C8 J1L 26
J1L C9 C27 C 0 1 Y N N 9.856 5.217 18.111 8.262 1.637 0.415 C9 J1L 27
J1L N1 N1 N 0 1 Y N N 9.974 4.308 19.126 7.275 0.757 0.050 N1 J1L 28
J1L N10 N2 N 0 1 N N N 10.664 20.186 20.607 -8.659 2.998 2.250 N10 J1L 29
J1L N11 N3 N 0 1 N N N 11.650 16.888 21.820 -6.637 0.754 0.271 N11 J1L 30
J1L N12 N4 N 0 1 N N N 11.331 18.403 24.166 -9.054 0.529 -1.004 N12 J1L 31
J1L N2 N5 N 0 1 Y N N 7.777 4.493 18.729 9.044 -0.440 0.500 N2 J1L 32
J1L N28 N6 N 0 1 N N N 12.164 14.300 21.703 -4.501 -0.876 -0.440 N28 J1L 33
J1L N3 N7 N 0 1 N N N 6.736 6.304 16.552 11.713 0.789 1.403 N3 J1L 34
J1L N4 N8 N 0 1 Y N N 8.975 6.871 16.126 10.554 2.834 1.201 N4 J1L 35
J1L N5 N9 N 0 1 Y N N 10.812 5.900 17.434 8.344 2.958 0.537 N5 J1L 36
J1L N6 N10 N 0 1 N N N 10.805 10.912 21.025 -1.204 -2.598 -0.113 N6 J1L 37
J1L N8 N11 N 0 1 N N N 10.751 20.283 22.957 -9.960 2.086 0.525 N8 J1L 38
J1L N9 N12 N 0 1 N N N 10.172 22.140 21.737 -10.917 3.596 1.995 N9 J1L 39
J1L O01 O1 O 0 1 N N N 8.789 11.379 22.831 -2.234 -4.069 1.845 O01 J1L 40
J1L O02 O2 O 0 1 N N N 14.026 8.895 21.886 3.407 -2.114 1.022 O02 J1L 41
J1L O03 O3 O 0 1 N N N 9.858 10.374 24.550 -0.725 -3.576 3.383 O03 J1L 42
J1L O04 O4 O 0 1 N N N 12.705 6.982 23.428 1.374 -0.828 0.545 O04 J1L 43
J1L O1 O5 O 0 1 N N N 11.549 4.904 20.649 5.036 -0.044 -0.192 O1 J1L 44
J1L O2 O6 O 0 1 N N N 13.884 2.756 20.827 3.642 1.911 -2.797 O2 J1L 45
J1L O3 O7 O 0 1 N N N 12.252 2.068 18.833 5.869 2.873 -2.024 O3 J1L 46
J1L O4 O8 O 0 1 N N N 12.203 14.233 23.988 -5.474 -1.124 -2.422 O4 J1L 47
J1L O5 O9 O 0 1 N N N 11.128 18.330 19.401 -6.515 2.399 2.465 O5 J1L 48
J1L S1 S1 S 0 1 N N N 12.952 7.532 21.847 2.383 -1.731 0.114 S1 J1L 49
J1L H1 H1 H 0 1 N N N 13.065 4.403 21.950 3.223 0.936 -0.542 H1 J1L 50
J1L H10 H2 H 0 1 N N N 14.694 5.990 21.300 2.392 -0.851 -2.128 H10 J1L 51
J1L H10A H3 H 0 0 N N N 13.745 6.476 19.855 3.868 -1.785 -1.781 H10A J1L 52
J1L H11 H4 H 0 1 N N N 10.852 7.054 20.846 2.345 -3.930 -0.867 H11 J1L 53
J1L H12A H5 H 0 0 N N N 9.413 8.659 21.809 0.310 -4.803 0.223 H12A J1L 54
J1L H12 H6 H 0 1 N N N 10.559 8.201 23.114 1.406 -4.106 1.441 H12 J1L 55
J1L H02 H7 H 0 1 N N N 11.811 10.275 22.816 0.105 -2.001 1.417 H02 J1L 56
J1L H14 H8 H 0 1 N N N 12.820 10.398 20.573 0.007 -1.018 -0.783 H14 J1L 57
J1L H14A H9 H 0 0 N N N 11.803 10.799 19.148 -1.113 -1.677 -1.999 H14A J1L 58
J1L H15A H10 H 0 0 N N N 10.693 8.719 19.237 1.231 -2.362 -2.462 H15A J1L 59
J1L H15 H11 H 0 1 N N N 12.455 8.398 19.369 0.207 -3.770 -2.089 H15 J1L 60
J1L H16A H12 H 0 0 N N N 10.725 12.852 20.264 -2.015 -0.785 0.573 H16A J1L 61
J1L H16 H13 H 0 1 N N N 10.351 12.691 22.014 -2.838 -2.250 1.161 H16 J1L 62
J1L H2 H14 H 0 1 N N N 14.342 4.245 19.419 4.648 0.115 -3.079 H2 J1L 63
J1L H23B H15 H 0 0 N N N 12.804 17.523 25.992 -8.001 -1.859 -1.930 H23B J1L 64
J1L H23A H16 H 0 0 N N N 13.285 15.986 25.198 -8.966 -0.982 -3.143 H23A J1L 65
J1L H23 H17 H 0 1 N N N 13.711 17.558 24.441 -7.199 -1.099 -3.327 H23 J1L 66
J1L H24B H18 H 0 0 N N N 10.497 16.903 26.066 -6.724 1.279 -3.358 H24B J1L 67
J1L H24 H19 H 0 1 N N N 9.628 16.437 24.564 -8.481 1.549 -3.436 H24 J1L 68
J1L H24A H20 H 0 0 N N N 10.829 15.317 25.292 -7.507 2.378 -2.198 H24A J1L 69
J1L H27 H21 H 0 1 N N N 12.740 12.444 22.473 -2.870 -1.221 -1.713 H27 J1L 70
J1L H27A H22 H 0 0 N N N 13.079 12.694 20.726 -3.694 -2.686 -1.125 H27A J1L 71
J1L H3 H23 H 0 1 N N N 12.398 4.010 18.027 6.670 0.987 -2.377 H3 J1L 72
J1L H4 H24 H 0 1 N N N 10.879 2.983 20.421 5.539 1.936 0.262 H4 J1L 73
J1L H5 H25 H 0 1 N N N 8.467 3.225 20.267 7.267 -1.408 -0.116 H5 J1L 74
J1L H8 H26 H 0 1 N N N 10.996 7.278 15.889 9.499 4.604 1.010 H8 J1L 75
J1L HN10 H27 H 0 0 N N N 10.489 20.690 19.761 -8.605 3.586 3.020 HN10 J1L 76
J1L HN12 H28 H 0 0 N N N 12.077 18.918 24.588 -9.901 0.113 -1.228 HN12 J1L 77
J1L HN28 H29 H 0 0 N N N 12.078 14.876 20.890 -4.532 -0.500 0.454 HN28 J1L 78
J1L HN3 H30 H 0 1 N N N 6.641 6.955 15.799 11.711 -0.178 1.330 HN3 J1L 79
J1L HN3A H31 H 0 0 N N N 6.352 5.422 16.280 12.518 1.253 1.682 HN3A J1L 80
J1L HN9 H33 H 0 1 N N N 10.072 22.657 22.587 -11.762 3.519 1.526 HN9 J1L 81
J1L HN9A H34 H 0 0 N N N 10.003 22.585 20.858 -10.840 4.182 2.764 HN9A J1L 82
J1L H7 H35 H 0 1 N N N 9.138 10.736 25.053 -1.290 -4.001 4.042 H7 J1L 83
J1L HO2 H36 H 0 1 N N N 14.583 3.046 21.401 3.969 2.346 -3.597 HO2 J1L 84
J1L HO3 H37 H 0 1 N N N 12.983 1.765 18.307 5.834 3.151 -2.949 HO3 J1L 85
# #
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
J1L N4 C8 SING Y N 1
J1L N4 C7 DOUB Y N 2
J1L C8 N5 DOUB Y N 3
J1L N3 C7 SING N N 4
J1L C7 C6 SING Y N 5
J1L N5 C9 SING Y N 6
J1L C6 C9 DOUB Y N 7
J1L C6 N2 SING Y N 8
J1L C9 N1 SING Y N 9
J1L N2 C5 DOUB Y N 10
J1L O3 C3 SING N N 11
J1L C3 C4 SING N N 12
J1L C3 C2 SING N N 13
J1L N1 C5 SING Y N 14
J1L N1 C4 SING N N 15
J1L O5 C20 DOUB N N 16
J1L C4 O1 SING N N 17
J1L C15 C14 SING N N 18
J1L C15 C11 SING N N 19
J1L C2 O2 SING N N 20
J1L C2 C1 SING N N 21
J1L C14 N6 SING N N 22
J1L C20 N10 SING N N 23
J1L C20 C26 SING N N 24
J1L N10 C19 SING N N 25
J1L O1 C1 SING N N 26
J1L C10 C1 SING N N 27
J1L C10 S1 SING N N 28
J1L N6 C16 SING N N 29
J1L N6 C13 SING N N 30
J1L C11 S1 SING N N 31
J1L C11 C12 SING N N 32
J1L C16 C27 SING N N 33
J1L C27 N28 SING N N 34
J1L N28 C18 SING N N 35
J1L N9 C19 SING N N 36
J1L C19 N8 DOUB N N 37
J1L C26 N11 SING N N 38
J1L C26 C25 DOUB N N 39
J1L N11 C21 DOUB N N 40
J1L S1 O02 DOUB N N 41
J1L S1 O04 DOUB N N 42
J1L C12 C13 SING N N 43
J1L C13 C01 SING N N 44
J1L O01 C01 DOUB N N 45
J1L C18 C21 SING N N 46
J1L C18 O4 DOUB N N 47
J1L C25 N8 SING N N 48
J1L C25 N12 SING N N 49
J1L C21 C22 SING N N 50
J1L C01 O03 SING N N 51
J1L N12 C22 SING N N 52
J1L C22 C23 SING N N 53
J1L C22 C24 SING N N 54
J1L C1 H1 SING N N 55
J1L C10 H10 SING N N 56
J1L C10 H10A SING N N 57
J1L C11 H11 SING N N 58
J1L C12 H12A SING N N 59
J1L C12 H12 SING N N 60
J1L C13 H02 SING N N 61
J1L C14 H14 SING N N 62
J1L C14 H14A SING N N 63
J1L C15 H15A SING N N 64
J1L C15 H15 SING N N 65
J1L C16 H16A SING N N 66
J1L C16 H16 SING N N 67
J1L C2 H2 SING N N 68
J1L C23 H23B SING N N 69
J1L C23 H23A SING N N 70
J1L C23 H23 SING N N 71
J1L C24 H24B SING N N 72
J1L C24 H24 SING N N 73
J1L C24 H24A SING N N 74
J1L C27 H27 SING N N 75
J1L C27 H27A SING N N 76
J1L C3 H3 SING N N 77
J1L C4 H4 SING N N 78
J1L C5 H5 SING N N 79
J1L C8 H8 SING N N 80
J1L N10 HN10 SING N N 81
J1L N12 HN12 SING N N 82
J1L N28 HN28 SING N N 83
J1L N3 HN3 SING N N 84
J1L N3 HN3A SING N N 85
J1L N9 HN9 SING N N 86
J1L N9 HN9A SING N N 87
J1L O03 H7 SING N N 88
J1L O2 HO2 SING N N 89
J1L O3 HO3 SING N N 90
# #
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
J1L SMILES ACDLabs 12.01 "C(O)(C4CC(S(CC1C(O)C(C(O1)n2cnc3c2ncnc3N)O)(=O)=O)CCN4CCNC(C=6C(C)(C)NC=5N=C(NC(C=5N=6)=O)N)=O)=O"
J1L InChI InChI 1.03 "InChI=1S/C27H36N12O9S/c1-27(2)18(34-15-20(37-27)35-26(29)36-22(15)42)23(43)30-4-6-38-5-3-11(7-12(38)25(44)45)49(46,47)8-13-16(40)17(41)24(48-13)39-10-33-14-19(28)31-9-32-21(14)39/h9-13,16-17,24,40-41H,3-8H2,1-2H3,(H,30,43)(H,44,45)(H2,28,31,32)(H4,29,35,36,37,42)/t11-,12-,13-,16-,17-,24-/m1/s1"
J1L InChIKey InChI 1.03 LIEKVCRXNQELKW-NERDUYAPSA-N
J1L SMILES_CANONICAL CACTVS 3.385 "CC1(C)NC2=C(N=C1C(=O)NCCN3CC[C@H](C[C@@H]3C(O)=O)[S](=O)(=O)C[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)C(=O)NC(=N2)N"
J1L SMILES CACTVS 3.385 "CC1(C)NC2=C(N=C1C(=O)NCCN3CC[CH](C[CH]3C(O)=O)[S](=O)(=O)C[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)C(=O)NC(=N2)N"
J1L SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1(C(=NC2=C(N1)N=C(NC2=O)N)C(=O)NCCN3CC[C@H](C[C@@H]3C(=O)O)S(=O)(=O)C[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)C"
J1L SMILES "OpenEye OEToolkits" 2.0.7 "CC1(C(=NC2=C(N1)N=C(NC2=O)N)C(=O)NCCN3CCC(CC3C(=O)O)S(=O)(=O)CC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)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
J1L "SYSTEMATIC NAME" ACDLabs 12.01 "5'-{[(2R,4R)-1-{2-[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carbonyl)amino]ethyl}-2-carboxypiperidin-4-yl]sulfonyl}-5'-deoxyadenosine"
J1L "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]methylsulfonyl]-1-[2-[(2-azanyl-7,7-dimethyl-4-oxidanylidene-3,8-dihydropteridin-6-yl)carbonylamino]ethyl]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
J1L "Create component" 2020-10-09 RCSB
J1L "Initial release" 2020-12-02 RCSB
##