data_J1I
#
_chem_comp.id J1I
_chem_comp.name "5'-S-{2-[{2-[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carbonyl)amino]ethyl}(phosphonomethyl)amino]ethyl}-5'-thioadenosine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C24 H35 N12 O8 P S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "(((2-(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carboxamido)ethyl)(2-((((2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl)thio)ethyl)amino)methyl)phosphonic acid"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-08-17
_chem_comp.pdbx_modified_date 2021-03-13
_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 682.649
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code J1I
_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 6AN6
_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
J1I N N1 N 0 1 N N N -13.529 18.982 85.522 11.495 3.841 1.334 N J1I 1
J1I C C1 C 0 1 N N N -10.102 14.165 82.610 8.959 -1.141 -1.269 C J1I 2
J1I O O1 O 0 1 N N N -6.411 14.821 83.165 5.654 -1.334 -1.903 O J1I 3
J1I P01 P1 P 0 1 N N N -7.477 12.794 78.003 0.839 -3.978 -0.558 P01 J1I 4
J1I C01 C2 C 0 1 Y N N -5.151 16.377 72.017 -10.816 2.751 0.337 C01 J1I 5
J1I N01 N2 N 0 1 Y N N -6.309 16.416 71.270 -10.756 3.646 -0.632 N01 J1I 6
J1I O01 O2 O 0 1 N N N -3.244 12.530 73.779 -5.734 0.053 0.920 O01 J1I 7
J1I OP3 O3 O 0 1 N N N -7.693 11.301 77.938 1.049 -5.493 -0.054 OP3 J1I 8
J1I N02 N3 N 0 1 Y N N -4.330 15.337 72.293 -9.825 1.925 0.599 N02 J1I 9
J1I O02 O4 O 0 1 N N N -1.126 12.443 70.983 -8.966 -1.477 0.580 O02 J1I 10
J1I OP2 O5 O 0 1 N N N -8.391 13.261 79.262 1.762 -3.710 -1.850 OP2 J1I 11
J1I C03 C3 C 0 1 Y N N -5.944 14.070 70.925 -8.592 2.896 -1.160 C03 J1I 12
J1I N03 N4 N 0 1 Y N N -4.253 12.874 71.737 -7.524 1.264 -0.104 N03 J1I 13
J1I O03 O6 O 0 1 N N N 0.147 12.461 73.147 -7.272 -2.764 2.079 O03 J1I 14
J1I OP1 O7 O 0 1 N N N -8.009 13.675 76.896 -0.582 -3.770 -0.915 OP1 J1I 15
J1I C04 C4 C 0 1 Y N N -6.700 15.232 70.717 -9.677 3.756 -1.401 C04 J1I 16
J1I N04 N5 N 0 1 Y N N -6.150 12.767 70.469 -7.371 2.723 -1.720 N04 J1I 17
J1I C05 C5 C 0 1 Y N N -5.128 12.079 70.968 -6.743 1.766 -1.102 C05 J1I 18
J1I N05 N6 N 0 1 N N N -7.830 15.117 69.938 -9.624 4.697 -2.414 N05 J1I 19
J1I C06 C6 C 0 1 N N S -1.001 13.231 73.315 -6.640 -2.169 0.944 C06 J1I 20
J1I N06 N7 N 0 1 N N N -5.408 14.595 78.375 1.095 -1.443 0.320 N06 J1I 21
J1I C07 C7 C 0 1 N N R -1.775 13.126 71.987 -7.609 -1.191 0.235 C07 J1I 22
J1I N07 N8 N 0 1 N N N -7.023 16.036 81.329 4.615 -0.324 -0.218 N07 J1I 23
J1I O07 O8 O 0 1 N N N -10.461 19.562 82.103 7.459 2.189 2.752 O07 J1I 24
J1I C08 C8 C 0 1 N N R -3.068 12.367 72.406 -7.168 0.178 0.813 C08 J1I 25
J1I N08 N9 N 0 1 N N N -11.941 19.252 83.777 9.429 3.006 2.078 N08 J1I 26
J1I C09 C9 C 0 1 N N S -1.964 12.620 74.377 -5.463 -1.279 1.387 C09 J1I 27
J1I N09 N10 N 0 1 N N N -11.988 17.227 85.098 10.193 2.569 -0.096 N09 J1I 28
J1I C10 C10 C 0 1 N N N -2.076 13.467 75.644 -4.161 -1.792 0.769 C10 J1I 29
J1I N10 N11 N 0 1 N N N -10.465 15.467 84.683 8.913 1.287 -1.613 N10 J1I 30
J1I C11 C11 C 0 1 N N N -3.985 15.474 76.633 -1.338 -1.562 0.564 C11 J1I 31
J1I N11 N12 N 0 1 N N N -9.295 16.936 82.606 7.022 0.949 0.344 N11 J1I 32
J1I C12 C12 C 0 1 N N N -5.327 14.784 76.894 -0.061 -0.839 0.995 C12 J1I 33
J1I C13 C13 C 0 1 N N N -6.240 15.655 79.034 2.304 -0.632 0.521 C13 J1I 34
J1I C14 C14 C 0 1 N N N -5.834 15.717 80.522 3.375 -1.055 -0.487 C14 J1I 35
J1I C15 C15 C 0 1 N N N -5.811 13.203 78.670 1.307 -2.824 0.773 C15 J1I 36
J1I C17 C16 C 0 1 N N N -12.436 18.431 84.783 10.358 3.125 1.090 C17 J1I 37
J1I C18 C17 C 0 1 N N N -10.919 16.734 84.344 9.105 1.860 -0.375 C18 J1I 38
J1I C19 C18 C 0 1 N N N -10.363 17.475 83.323 8.109 1.683 0.609 C19 J1I 39
J1I C20 C19 C 0 1 N N N -10.860 18.797 82.989 8.297 2.297 1.873 C20 J1I 40
J1I C21 C20 C 0 1 N N N -9.437 14.818 83.826 8.101 0.061 -1.671 C21 J1I 41
J1I C22 C21 C 0 1 N N N -8.495 15.970 83.377 6.942 0.195 -0.716 C22 J1I 42
J1I C23 C22 C 0 1 N N N -7.220 15.547 82.596 5.702 -0.535 -0.985 C23 J1I 43
J1I C24 C23 C 0 1 N N N -8.743 13.806 84.771 7.575 -0.138 -3.093 C24 J1I 44
J1I S S1 S 0 1 N N N -3.084 14.891 75.161 -2.767 -0.816 1.397 S J1I 45
J1I C02 C24 C 0 1 Y N N -4.769 14.170 71.717 -8.705 1.962 -0.117 C02 J1I 46
J1I HN2 H1 H 0 1 N N N -13.944 18.458 86.266 11.631 4.255 2.201 HN2 J1I 47
J1I HN3 H2 H 0 1 N N N -13.878 19.891 85.295 12.169 3.932 0.642 HN3 J1I 48
J1I HC3 H3 H 0 1 N N N -9.334 13.688 81.983 9.330 -0.999 -0.254 HC3 J1I 49
J1I HC1 H4 H 0 1 N N N -10.821 13.405 82.950 8.356 -2.048 -1.312 HC1 J1I 50
J1I HC2 H5 H 0 1 N N N -10.629 14.933 82.024 9.801 -1.231 -1.954 HC2 J1I 51
J1I H02 H6 H 0 1 N N N -4.853 17.321 72.448 -11.710 2.698 0.941 H02 J1I 52
J1I H1 H7 H 0 1 N N N -8.174 11.084 77.148 0.819 -6.162 -0.713 H1 J1I 53
J1I H021 H8 H 0 0 N N N -1.672 12.427 70.206 -9.260 -2.361 0.319 H021 J1I 54
J1I H031 H10 H 0 0 N N N 0.667 12.489 73.942 -8.056 -3.288 1.863 H031 J1I 55
J1I H051 H12 H 0 0 N N N -4.983 11.022 70.802 -5.748 1.420 -1.344 H051 J1I 56
J1I H053 H13 H 0 0 N N N -8.276 16.009 69.863 -10.379 5.285 -2.570 H053 J1I 57
J1I H052 H14 H 0 0 N N N -7.575 14.794 69.027 -8.831 4.768 -2.968 H052 J1I 58
J1I H061 H15 H 0 0 N N N -0.782 14.282 73.555 -6.300 -2.938 0.251 H061 J1I 59
J1I H071 H17 H 0 0 N N N -2.054 14.138 71.660 -7.470 -1.221 -0.845 H071 J1I 60
J1I H072 H18 H 0 0 N N N -7.719 16.637 80.936 4.654 0.313 0.513 H072 J1I 61
J1I H081 H19 H 0 0 N N N -2.935 11.303 72.161 -7.613 0.345 1.794 H081 J1I 62
J1I H01 H20 H 0 1 N N N -12.344 20.152 83.613 9.583 3.430 2.936 H01 J1I 63
J1I H091 H21 H 0 0 N N N -1.595 11.620 74.649 -5.385 -1.281 2.475 H091 J1I 64
J1I H102 H22 H 0 0 N N N -2.568 12.899 76.448 -4.021 -2.840 1.035 H102 J1I 65
J1I H101 H23 H 0 0 N N N -1.081 13.793 75.981 -4.212 -1.697 -0.316 H101 J1I 66
J1I H103 H24 H 0 0 N N N -10.082 15.530 85.605 9.298 1.676 -2.414 H103 J1I 67
J1I H112 H25 H 0 0 N N N -4.174 16.551 76.511 -1.460 -1.473 -0.516 H112 J1I 68
J1I H122 H28 H 0 0 N N N -5.364 13.811 76.381 0.060 -0.928 2.075 H122 J1I 69
J1I H121 H29 H 0 0 N N N -6.157 15.415 76.543 -0.131 0.215 0.723 H121 J1I 70
J1I H132 H30 H 0 0 N N N -6.055 16.628 78.555 2.064 0.421 0.375 H132 J1I 71
J1I H131 H31 H 0 0 N N N -7.307 15.401 78.948 2.679 -0.783 1.533 H131 J1I 72
J1I H142 H32 H 0 0 N N N -5.071 16.497 80.664 3.032 -0.830 -1.497 H142 J1I 73
J1I H141 H33 H 0 0 N N N -5.426 14.744 80.834 3.557 -2.126 -0.396 H141 J1I 74
J1I H152 H34 H 0 0 N N N -5.824 13.063 79.761 0.692 -3.016 1.653 H152 J1I 75
J1I H151 H35 H 0 0 N N N -5.074 12.520 78.222 2.357 -2.967 1.026 H151 J1I 76
J1I H243 H37 H 0 0 N N N -8.290 14.344 85.617 7.130 -1.130 -3.181 H243 J1I 77
J1I H241 H38 H 0 0 N N N -9.486 13.088 85.149 6.821 0.619 -3.311 H241 J1I 78
J1I H242 H39 H 0 0 N N N -7.960 13.266 84.219 8.399 -0.046 -3.802 H242 J1I 79
J1I HP2 H40 H 0 1 N N N -8.995 13.938 78.981 2.711 -3.756 -1.671 HP2 J1I 80
J1I H111 H41 H 0 0 N N N -3.343 15.312 77.511 -1.269 -2.616 0.835 H111 J1I 81
# #
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
J1I N C17 SING N N 1
J1I C C21 SING N N 2
J1I O C23 DOUB N N 3
J1I P01 OP3 SING N N 4
J1I P01 OP2 SING N N 5
J1I P01 OP1 DOUB N N 6
J1I P01 C15 SING N N 7
J1I C01 N01 DOUB Y N 8
J1I C01 N02 SING Y N 9
J1I N01 C04 SING Y N 10
J1I O01 C08 SING N N 11
J1I O01 C09 SING N N 12
J1I N02 C02 DOUB Y N 13
J1I O02 C07 SING N N 14
J1I C03 C04 DOUB Y N 15
J1I C03 N04 SING Y N 16
J1I C03 C02 SING Y N 17
J1I N03 C05 SING Y N 18
J1I N03 C08 SING N N 19
J1I N03 C02 SING Y N 20
J1I O03 C06 SING N N 21
J1I C04 N05 SING N N 22
J1I N04 C05 DOUB Y N 23
J1I C06 C07 SING N N 24
J1I C06 C09 SING N N 25
J1I N06 C12 SING N N 26
J1I N06 C13 SING N N 27
J1I N06 C15 SING N N 28
J1I C07 C08 SING N N 29
J1I N07 C14 SING N N 30
J1I N07 C23 SING N N 31
J1I O07 C20 DOUB N N 32
J1I N08 C17 SING N N 33
J1I N08 C20 SING N N 34
J1I C09 C10 SING N N 35
J1I N09 C17 DOUB N N 36
J1I N09 C18 SING N N 37
J1I C10 S SING N N 38
J1I N10 C18 SING N N 39
J1I N10 C21 SING N N 40
J1I C11 C12 SING N N 41
J1I C11 S SING N N 42
J1I N11 C19 SING N N 43
J1I N11 C22 DOUB N N 44
J1I C13 C14 SING N N 45
J1I C18 C19 DOUB N N 46
J1I C19 C20 SING N N 47
J1I C21 C22 SING N N 48
J1I C21 C24 SING N N 49
J1I C22 C23 SING N N 50
J1I N HN2 SING N N 51
J1I N HN3 SING N N 52
J1I C HC3 SING N N 53
J1I C HC1 SING N N 54
J1I C HC2 SING N N 55
J1I C01 H02 SING N N 56
J1I OP3 H1 SING N N 57
J1I O02 H021 SING N N 58
J1I OP2 HP2 SING N N 59
J1I O03 H031 SING N N 60
J1I C05 H051 SING N N 61
J1I N05 H053 SING N N 62
J1I N05 H052 SING N N 63
J1I C06 H061 SING N N 64
J1I C07 H071 SING N N 65
J1I N07 H072 SING N N 66
J1I C08 H081 SING N N 67
J1I N08 H01 SING N N 68
J1I C09 H091 SING N N 69
J1I C10 H102 SING N N 70
J1I C10 H101 SING N N 71
J1I N10 H103 SING N N 72
J1I C11 H112 SING N N 73
J1I C11 H111 SING N N 74
J1I C12 H122 SING N N 75
J1I C12 H121 SING N N 76
J1I C13 H132 SING N N 77
J1I C13 H131 SING N N 78
J1I C14 H142 SING N N 79
J1I C14 H141 SING N N 80
J1I C15 H152 SING N N 81
J1I C15 H151 SING N N 82
J1I C24 H243 SING N N 83
J1I C24 H241 SING N N 84
J1I C24 H242 SING N N 85
# #
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
J1I SMILES ACDLabs 12.01 "NC=1NC(=O)C=2N=C(C(C)(NC=2N=1)C)C(=O)NCCN(CCSCC5OC(n4cnc3c(ncnc34)N)C(O)C5O)CP(O)(O)=O"
J1I InChI InChI 1.03 "InChI=1S/C24H35N12O8PS/c1-24(2)16(31-13-18(34-24)32-23(26)33-20(13)39)21(40)27-3-4-35(10-45(41,42)43)5-6-46-7-11-14(37)15(38)22(44-11)36-9-30-12-17(25)28-8-29-19(12)36/h8-9,11,14-15,22,37-38H,3-7,10H2,1-2H3,(H,27,40)(H2,25,28,29)(H2,41,42,43)(H4,26,32,33,34,39)/t11-,14-,15-,22-/m1/s1"
J1I InChIKey InChI 1.03 LNONYTMYGAJODO-HUYKWJOFSA-N
J1I SMILES_CANONICAL CACTVS 3.385 "CC1(C)NC2=C(N=C1C(=O)NCCN(CCSC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)C[P](O)(O)=O)C(=O)NC(=N2)N"
J1I SMILES CACTVS 3.385 "CC1(C)NC2=C(N=C1C(=O)NCCN(CCSC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)C[P](O)(O)=O)C(=O)NC(=N2)N"
J1I SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC1(C(=NC2=C(N1)N=C(NC2=O)N)C(=O)NCCN(CCSC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)CP(=O)(O)O)C"
J1I SMILES "OpenEye OEToolkits" 2.0.6 "CC1(C(=NC2=C(N1)N=C(NC2=O)N)C(=O)NCCN(CCSCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)CP(=O)(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
J1I "SYSTEMATIC NAME" ACDLabs 12.01 "5'-S-{2-[{2-[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carbonyl)amino]ethyl}(phosphonomethyl)amino]ethyl}-5'-thioadenosine"
J1I "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[2-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]ethyl-[2-[(2-azanyl-7,7-dimethyl-4-oxidanylidene-3,8-dihydropteridin-6-yl)carbonylamino]ethyl]amino]methylphosphonic 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
J1I "Create component" 2017-08-17 RCSB
J1I "Modify synonyms" 2017-08-17 RCSB
J1I "Initial release" 2018-08-15 RCSB
J1I "Modify synonyms" 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id J1I
_pdbx_chem_comp_synonyms.name "(((2-(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carboxamido)ethyl)(2-((((2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl)thio)ethyl)amino)methyl)phosphonic acid"
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
##