data_J1F
#
_chem_comp.id J1F
_chem_comp.name "((2-(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carboxamido)-N-(2-((((2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl)amino)-2-oxoethyl)acetamido)methyl)phosphonic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C24 H32 N13 O10 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "5'-{[N-(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carbonyl)glycyl-N-(phosphonomethyl)glycyl]amino}-5'-deoxyadenosine"
_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 693.566
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code J1F
_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 6AN4
_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
J1F C01 C1 C 0 1 N N N 3.664 -2.384 5.105 -0.557 2.841 0.515 C01 J1F 1
J1F C1 C2 C 0 1 N N R 3.404 2.748 4.120 4.326 -1.875 0.153 C1 J1F 2
J1F C10 C3 C 0 1 N N N 4.757 2.186 3.631 3.053 -1.319 0.795 C10 J1F 3
J1F C11 C4 C 0 1 N N N 4.209 -0.031 2.657 1.173 0.095 0.164 C11 J1F 4
J1F C12 C5 C 0 1 N N N 4.241 -1.539 2.834 0.429 0.937 -0.841 C12 J1F 5
J1F C13 C6 C 0 1 N N N 6.066 -2.041 4.488 -1.934 0.981 -0.248 C13 J1F 6
J1F C14 C7 C 0 1 N N N 7.130 -1.565 3.447 -3.118 1.631 0.420 C14 J1F 7
J1F C15 C8 C 0 1 N N N 7.959 -3.609 2.386 -5.494 1.188 0.730 C15 J1F 8
J1F C16 C9 C 0 1 N N N 13.852 -5.474 1.055 -9.820 -3.095 -0.788 C16 J1F 9
J1F C17 C10 C 0 1 N N N 12.615 -3.446 1.710 -7.473 -2.923 -0.720 C17 J1F 10
J1F C18 C11 C 0 1 N N N 9.206 -4.406 2.059 -6.683 0.359 0.529 C18 J1F 11
J1F C19 C12 C 0 1 N N N 9.055 -5.806 1.470 -8.023 0.861 1.006 C19 J1F 12
J1F C2 C13 C 0 1 N N S 3.428 4.286 4.129 5.040 -2.842 1.124 C2 J1F 13
J1F C20 C14 C 0 1 N N N 8.391 -5.659 0.081 -8.070 2.386 0.886 C20 J1F 14
J1F C21 C15 C 0 1 N N N 8.296 -6.763 2.389 -8.231 0.456 2.466 C21 J1F 15
J1F C22 C16 C 0 1 N N N 11.549 -5.638 1.255 -8.931 -1.054 -0.191 C22 J1F 16
J1F C23 C17 C 0 1 N N N 11.458 -4.294 1.615 -7.624 -1.571 -0.319 C23 J1F 17
J1F C3 C18 C 0 1 N N R 2.519 4.655 5.319 6.542 -2.570 0.888 C3 J1F 18
J1F C4 C19 C 0 1 N N R 2.476 3.328 6.139 6.558 -1.471 -0.198 C4 J1F 19
J1F C5 C20 C 0 1 Y N N 4.456 3.892 7.729 7.543 0.662 0.723 C5 J1F 20
J1F C6 C21 C 0 1 Y N N 3.695 2.936 9.527 9.620 0.484 0.127 C6 J1F 21
J1F C7 C22 C 0 1 Y N N 3.428 2.397 10.783 10.994 0.605 -0.141 C7 J1F 22
J1F C8 C23 C 0 1 Y N N 1.400 1.600 9.949 10.924 -1.423 -1.240 C8 J1F 23
J1F C9 C24 C 0 1 Y N N 2.711 2.730 8.535 8.952 -0.660 -0.340 C9 J1F 24
J1F N02 N1 N 0 1 N N N 4.762 0.756 3.670 2.331 -0.501 -0.182 N02 J1F 25
J1F N1 N2 N 0 1 Y N N 3.192 3.354 7.412 7.645 -0.521 0.054 N1 J1F 26
J1F N10 N3 N 0 1 N N N 13.835 -4.134 1.406 -8.589 -3.651 -0.943 N10 J1F 27
J1F N11 N4 N 0 1 N N N 10.258 -3.666 1.913 -6.563 -0.798 -0.059 N11 J1F 28
J1F N12 N5 N 0 1 N N N 10.411 -6.386 1.187 -9.081 0.266 0.173 N12 J1F 29
J1F N2 N6 N 0 1 Y N N 4.779 3.667 9.011 8.702 1.252 0.762 N2 J1F 30
J1F N3 N7 N 0 1 N N N 4.330 2.558 11.788 11.706 1.710 0.294 N3 J1F 31
J1F N4 N8 N 0 1 Y N N 2.259 1.718 11.009 11.595 -0.365 -0.822 N4 J1F 32
J1F N5 N9 N 0 1 Y N N 1.532 2.059 8.695 9.637 -1.579 -1.013 N5 J1F 33
J1F N6 N10 N 0 1 N N N 4.716 -1.992 4.154 -0.722 1.569 -0.193 N6 J1F 34
J1F N7 N11 N 0 1 N N N 8.204 -2.464 3.095 -4.308 0.802 0.218 N7 J1F 35
J1F N8 N12 N 0 1 N N N 12.765 -6.269 0.957 -9.979 -1.835 -0.425 N8 J1F 36
J1F N9 N13 N 0 1 N N N 15.087 -6.025 0.779 -10.927 -3.862 -1.019 N9 J1F 37
J1F O01 O1 O 0 1 N N N 3.706 0.525 1.661 0.728 -0.046 1.283 O01 J1F 38
J1F OP2 O2 O 0 1 N N N 4.281 -5.027 5.156 -2.128 4.253 -1.331 OP2 J1F 39
J1F OP3 O3 O 0 1 N N N 1.921 -4.211 5.838 -0.375 5.607 0.085 OP3 J1F 40
J1F OP1 O4 O 0 1 N N N 2.613 -4.227 3.375 0.352 4.023 -1.740 OP1 J1F 41
J1F O1 O5 O 0 1 N N N 3.171 2.333 5.442 5.278 -0.814 -0.077 O1 J1F 42
J1F O2 O6 O 0 1 N N N 2.909 4.831 2.960 4.720 -4.198 0.806 O2 J1F 43
J1F O3 O7 O 0 1 N N N 1.238 4.984 4.886 7.196 -3.750 0.416 O3 J1F 44
J1F O4 O8 O 0 1 N N N 6.836 -3.965 2.046 -5.575 2.226 1.361 O4 J1F 45
J1F O5 O9 O 0 1 N N N 12.728 -2.275 2.011 -6.366 -3.414 -0.860 O5 J1F 46
J1F O6 O10 O 0 1 N N N 6.505 -2.399 5.576 -2.070 -0.072 -0.834 O6 J1F 47
J1F P01 P1 P 0 1 N N N 3.057 -4.210 4.831 -0.658 4.217 -0.676 P01 J1F 48
J1F H23 H1 H 0 1 N N N 4.061 -2.294 6.127 -1.345 2.947 1.261 H23 J1F 49
J1F H05 H2 H 0 1 N N N 2.807 -1.705 4.983 0.415 2.858 1.009 H05 J1F 50
J1F H06 H3 H 0 1 N N N 2.605 2.402 3.448 4.089 -2.383 -0.782 H06 J1F 51
J1F H26 H4 H 0 1 N N N 5.560 2.566 4.279 2.419 -2.145 1.118 H26 J1F 52
J1F H17 H5 H 0 1 N N N 4.932 2.518 2.597 3.319 -0.707 1.657 H17 J1F 53
J1F H27 H6 H 0 1 N N N 3.221 -1.924 2.686 1.094 1.707 -1.233 H27 J1F 54
J1F H18 H7 H 0 1 N N N 4.907 -1.960 2.067 0.083 0.305 -1.660 H18 J1F 55
J1F H20 H8 H 0 1 N N N 7.591 -0.651 3.850 -2.922 1.733 1.487 H20 J1F 56
J1F H28 H9 H 0 1 N N N 6.591 -1.325 2.519 -3.284 2.617 -0.015 H28 J1F 57
J1F H07 H11 H 0 1 N N N 4.452 4.638 4.324 4.769 -2.617 2.156 H07 J1F 58
J1F H29 H12 H 0 1 N N N 7.382 -5.236 0.199 -7.737 2.683 -0.108 H29 J1F 59
J1F H31 H13 H 0 1 N N N 8.998 -4.990 -0.546 -9.092 2.731 1.045 H31 J1F 60
J1F H21 H14 H 0 1 N N N 8.320 -6.647 -0.398 -7.416 2.830 1.636 H21 J1F 61
J1F H22 H15 H 0 1 N N N 8.812 -6.828 3.358 -7.442 0.889 3.080 H22 J1F 62
J1F H30 H16 H 0 1 N N N 7.273 -6.389 2.543 -9.200 0.819 2.809 H30 J1F 63
J1F H04 H17 H 0 1 N N N 8.257 -7.761 1.927 -8.201 -0.631 2.549 H04 J1F 64
J1F H11 H18 H 0 1 N N N 2.981 5.454 5.918 7.014 -2.211 1.802 H11 J1F 65
J1F H14 H19 H 0 1 N N N 1.426 3.042 6.299 6.666 -1.917 -1.187 H14 J1F 66
J1F H02 H20 H 0 1 N N N 5.085 4.419 7.027 6.633 1.054 1.154 H02 J1F 67
J1F H03 H21 H 0 1 N N N 0.486 1.061 10.151 11.451 -2.189 -1.790 H03 J1F 68
J1F H08 H22 H 0 1 N N N 5.179 0.300 4.456 2.686 -0.388 -1.077 H08 J1F 69
J1F H01 H23 H 0 1 N N N 14.699 -3.632 1.448 -8.511 -4.579 -1.217 H01 J1F 70
J1F H19 H25 H 0 1 N N N 10.371 -6.749 0.256 -9.852 0.783 -0.108 H19 J1F 71
J1F H12 H26 H 0 1 N N N 3.985 2.122 12.619 11.256 2.412 0.790 H12 J1F 72
J1F H24 H27 H 0 1 N N N 5.199 2.137 11.527 12.654 1.782 0.103 H24 J1F 73
J1F H15 H28 H 0 1 N N N 9.140 -2.247 3.373 -4.244 -0.026 -0.284 H15 J1F 74
J1F H16 H29 H 0 1 N N N 15.158 -6.987 0.515 -10.828 -4.788 -1.290 H16 J1F 75
J1F H25 H30 H 0 1 N N N 15.911 -5.462 0.843 -11.813 -3.480 -0.913 H25 J1F 76
J1F HP2 H31 H 0 1 N N N 4.602 -5.446 4.366 -2.841 4.378 -0.689 HP2 J1F 77
J1F HP3 H32 H 0 1 N N N 1.090 -4.222 5.378 -0.413 6.385 -0.488 HP3 J1F 78
J1F H10 H33 H 0 1 N N N 2.944 5.779 3.010 5.142 -4.848 1.385 H10 J1F 79
J1F H13 H34 H 0 1 N N N 0.698 5.207 5.635 7.163 -4.492 1.035 H13 J1F 80
# #
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
J1F C20 C19 SING N N 1
J1F N9 C16 SING N N 2
J1F N8 C16 DOUB N N 3
J1F N8 C22 SING N N 4
J1F C16 N10 SING N N 5
J1F N12 C22 SING N N 6
J1F N12 C19 SING N N 7
J1F C22 C23 DOUB N N 8
J1F N10 C17 SING N N 9
J1F C19 C18 SING N N 10
J1F C19 C21 SING N N 11
J1F C23 C17 SING N N 12
J1F C23 N11 SING N N 13
J1F O01 C11 DOUB N N 14
J1F C17 O5 DOUB N N 15
J1F N11 C18 DOUB N N 16
J1F O4 C15 DOUB N N 17
J1F C18 C15 SING N N 18
J1F C15 N7 SING N N 19
J1F C11 C12 SING N N 20
J1F C11 N02 SING N N 21
J1F C12 N6 SING N N 22
J1F O2 C2 SING N N 23
J1F N7 C14 SING N N 24
J1F OP1 P01 DOUB N N 25
J1F C14 C13 SING N N 26
J1F C10 N02 SING N N 27
J1F C10 C1 SING N N 28
J1F C1 C2 SING N N 29
J1F C1 O1 SING N N 30
J1F C2 C3 SING N N 31
J1F N6 C13 SING N N 32
J1F N6 C01 SING N N 33
J1F C13 O6 DOUB N N 34
J1F P01 C01 SING N N 35
J1F P01 OP2 SING N N 36
J1F P01 OP3 SING N N 37
J1F O3 C3 SING N N 38
J1F C3 C4 SING N N 39
J1F O1 C4 SING N N 40
J1F C4 N1 SING N N 41
J1F N1 C5 SING Y N 42
J1F N1 C9 SING Y N 43
J1F C5 N2 DOUB Y N 44
J1F C9 N5 DOUB Y N 45
J1F C9 C6 SING Y N 46
J1F N5 C8 SING Y N 47
J1F N2 C6 SING Y N 48
J1F C6 C7 DOUB Y N 49
J1F C8 N4 DOUB Y N 50
J1F C7 N4 SING Y N 51
J1F C7 N3 SING N N 52
J1F C01 H23 SING N N 53
J1F C01 H05 SING N N 54
J1F C1 H06 SING N N 55
J1F C10 H26 SING N N 56
J1F C10 H17 SING N N 57
J1F C12 H27 SING N N 58
J1F C12 H18 SING N N 59
J1F C14 H20 SING N N 60
J1F C14 H28 SING N N 61
J1F C2 H07 SING N N 62
J1F C20 H29 SING N N 63
J1F C20 H31 SING N N 64
J1F C20 H21 SING N N 65
J1F C21 H22 SING N N 66
J1F C21 H30 SING N N 67
J1F C21 H04 SING N N 68
J1F C3 H11 SING N N 69
J1F C4 H14 SING N N 70
J1F C5 H02 SING N N 71
J1F C8 H03 SING N N 72
J1F N02 H08 SING N N 73
J1F N10 H01 SING N N 74
J1F N12 H19 SING N N 75
J1F N3 H12 SING N N 76
J1F N3 H24 SING N N 77
J1F N7 H15 SING N N 78
J1F N9 H16 SING N N 79
J1F N9 H25 SING N N 80
J1F OP2 HP2 SING N N 81
J1F OP3 HP3 SING N N 82
J1F O2 H10 SING N N 83
J1F O3 H13 SING N N 84
# #
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
J1F SMILES ACDLabs 12.01 "C(N(CC(NCC3C(C(C(n2cnc1c(ncnc12)N)O3)O)O)=O)C(=O)CNC(C=5C(C)(C)NC4=C(C(=O)NC(=N4)N)N=5)=O)P(O)(O)=O"
J1F InChI InChI 1.03 "InChI=1S/C24H32N13O10P/c1-24(2)16(32-13-18(35-24)33-23(26)34-20(13)42)21(43)28-4-11(39)36(8-48(44,45)46)5-10(38)27-3-9-14(40)15(41)22(47-9)37-7-31-12-17(25)29-6-30-19(12)37/h6-7,9,14-15,22,40-41H,3-5,8H2,1-2H3,(H,27,38)(H,28,43)(H2,25,29,30)(H2,44,45,46)(H4,26,33,34,35,42)/t9-,14-,15-,22-/m1/s1"
J1F InChIKey InChI 1.03 IHZBIHWJVSGIOO-MDNHXVGFSA-N
J1F SMILES_CANONICAL CACTVS 3.385 "CC1(C)NC2=C(N=C1C(=O)NCC(=O)N(CC(=O)NC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)C[P](O)(O)=O)C(=O)NC(=N2)N"
J1F SMILES CACTVS 3.385 "CC1(C)NC2=C(N=C1C(=O)NCC(=O)N(CC(=O)NC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)C[P](O)(O)=O)C(=O)NC(=N2)N"
J1F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC1(C(=NC2=C(N1)N=C(NC2=O)N)C(=O)NCC(=O)N(CC(=O)NC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)CP(=O)(O)O)C"
J1F SMILES "OpenEye OEToolkits" 2.0.6 "CC1(C(=NC2=C(N1)N=C(NC2=O)N)C(=O)NCC(=O)N(CC(=O)NCC3C(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
J1F "SYSTEMATIC NAME" ACDLabs 12.01 "5'-{[N-(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carbonyl)glycyl-N-(phosphonomethyl)glycyl]amino}-5'-deoxyadenosine"
J1F "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-2-oxidanylidene-ethyl]-[2-[(2-azanyl-7,7-dimethyl-4-oxidanylidene-3,8-dihydropteridin-6-yl)carbonylamino]ethanoyl]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
J1F "Create component" 2017-08-17 RCSB
J1F "Initial release" 2018-08-15 RCSB
J1F "Modify synonyms" 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id J1F
_pdbx_chem_comp_synonyms.name "5'-{[N-(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carbonyl)glycyl-N-(phosphonomethyl)glycyl]amino}-5'-deoxyadenosine"
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
##