data_E4M
#
_chem_comp.id E4M
_chem_comp.name
"1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C31 H44 N6 O16 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2009-09-08
_chem_comp.pdbx_modified_date 2011-06-04
_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 787.685
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code E4M
_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 3IQF
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
E4M N1 N1 N 0 1 N N N 1.061 26.821 38.876 -12.621 -0.677 -0.213 N1 E4M 1
E4M C2 C2 C 0 1 N N N 1.953 26.258 39.715 -12.943 0.488 0.308 C2 E4M 2
E4M N3 N3 N 0 1 N N N 3.291 26.343 39.444 -12.005 1.418 0.637 N3 E4M 3
E4M C4 C4 C 0 1 N N N 3.752 26.981 38.327 -10.693 1.158 0.436 C4 E4M 4
E4M N5 N5 N 1 1 N N N 3.148 28.230 36.278 -9.037 -0.450 -0.342 N5 E4M 5
E4M C6 C6 C 0 1 N N R 2.306 29.358 35.887 -8.716 -1.512 -1.323 C6 E4M 6
E4M C7 C7 C 0 1 N N S 0.910 28.746 35.713 -9.625 -2.700 -0.991 C7 E4M 7
E4M N8 N8 N 0 1 N N N 0.548 27.994 36.917 -11.017 -2.219 -1.011 N8 E4M 8
E4M C9 C9 C 0 1 N N R 3.001 29.952 34.626 -7.241 -1.829 -1.051 C9 E4M 9
E4M PA PA P 0 1 N N N 8.991 29.648 18.799 8.446 -0.290 -0.888 PA E4M 10
E4M C10 C10 C 0 1 N N N 4.470 28.628 35.865 -7.969 -0.077 0.262 C10 E4M 11
E4M N10 N10 N 0 1 N N N 4.433 29.670 34.864 -6.848 -0.787 -0.084 N10 E4M 12
E4M C11 C11 C 0 1 Y N N 7.679 30.359 32.237 -2.994 -0.115 1.345 C11 E4M 13
E4M C12 C12 C 0 1 Y N N 6.378 30.669 31.841 -3.247 -1.201 0.527 C12 E4M 14
E4M C13 C13 C 0 1 Y N N 5.315 30.430 32.705 -4.524 -1.427 0.052 C13 E4M 15
E4M C14 C14 C 0 1 Y N N 5.527 29.906 33.978 -5.555 -0.562 0.396 C14 E4M 16
E4M C15 C15 C 0 1 Y N N 6.846 29.596 34.390 -5.298 0.528 1.217 C15 E4M 17
E4M C16 C16 C 0 1 Y N N 7.904 29.810 33.511 -4.019 0.748 1.690 C16 E4M 18
E4M O2A O2A O 0 1 N N N 8.623 28.643 17.715 7.804 -1.763 -0.779 O2A E4M 19
E4M C1J C1J C 0 1 N N S 8.160 29.736 24.412 4.637 3.903 0.668 C1J E4M 20
E4M O1A O1A O 0 1 N N N 7.974 30.765 19.066 9.251 -0.157 -2.276 O1A E4M 21
E4M C2J C2J C 0 1 N N R 6.769 29.202 24.074 5.165 5.072 -0.187 C2J E4M 22
E4M O2J O2J O 0 1 N N N 6.049 28.823 25.244 4.199 5.448 -1.171 O2J E4M 23
E4M O3A O3A O 0 1 N N N 10.442 30.078 18.796 9.374 -0.071 0.244 O3A E4M 24
E4M C3J C3J C 0 1 N N S 7.019 28.065 23.098 6.435 4.503 -0.864 C3J E4M 25
E4M O3J O3J O 0 1 N N N 7.247 26.836 23.743 6.518 4.922 -2.228 O3J E4M 26
E4M C4A C4A C 0 1 N N N 2.814 27.547 37.455 -10.341 -0.082 -0.115 C4A E4M 27
E4M C4J C4J C 0 1 N N R 8.318 28.474 22.430 6.196 2.974 -0.770 C4J E4M 28
E4M O4J O4J O 0 1 N N N 9.013 29.324 23.345 5.559 2.812 0.516 O4J E4M 29
E4M C5J C5J C 0 1 N N N 8.041 29.271 21.178 7.525 2.217 -0.812 C5J E4M 30
E4M O5J O5J O 0 1 N N N 8.871 28.760 20.148 7.272 0.811 -0.841 O5J E4M 31
E4M C7M C7M C 0 1 N N N -0.174 29.801 35.440 -9.442 -3.801 -2.037 C7M E4M 32
E4M C8A C8A C 0 1 N N N 1.466 27.458 37.753 -11.346 -1.002 -0.445 C8A E4M 33
E4M C9M C9M C 0 1 N N N 2.716 31.457 34.482 -6.417 -1.714 -2.335 C9M E4M 34
E4M NA2 NA2 N 0 1 N N N 1.495 25.639 40.830 -14.265 0.773 0.528 NA2 E4M 35
E4M OH4 OH4 O 0 1 N N N 4.990 27.038 38.074 -9.839 1.981 0.725 OH4 E4M 36
E4M CX1 CX1 C 0 1 N N N 8.844 30.598 31.294 -1.601 0.126 1.867 CX1 E4M 37
E4M CX2 CX2 C 0 1 N N S 8.696 29.867 29.968 -0.834 1.012 0.883 CX2 E4M 38
E4M OX2 OX2 O 0 1 N N N 8.941 28.460 30.145 -0.661 0.314 -0.352 OX2 E4M 39
E4M CX3 CX3 C 0 1 N N S 9.716 30.365 28.948 0.535 1.359 1.470 CX3 E4M 40
E4M OX3 OX3 O 0 1 N N N 9.558 31.748 28.630 0.362 2.057 2.704 OX3 E4M 41
E4M CX4 CX4 C 0 1 N N R 9.605 29.530 27.684 1.302 2.245 0.486 CX4 E4M 42
E4M OX4 OX4 O 0 1 N N N 10.854 29.592 27.006 1.476 1.547 -0.748 OX4 E4M 43
E4M CX5 CX5 C 0 1 N N N 8.491 29.968 26.761 2.672 2.592 1.073 CX5 E4M 44
E4M OX5 OX5 O 0 1 N N N 8.673 29.168 25.598 3.341 3.513 0.209 OX5 E4M 45
E4M HN3 HN3 H 0 1 N N N 3.946 25.929 40.077 -12.278 2.269 1.015 HN3 E4M 46
E4M H6 H6 H 0 1 N N N 2.186 30.199 36.585 -8.875 -1.169 -2.346 H6 E4M 47
E4M H7 H7 H 0 1 N N N 0.959 28.084 34.836 -9.381 -3.086 -0.001 H7 E4M 48
E4M HN8 HN8 H 0 1 N N N 0.024 28.634 37.479 -11.708 -2.760 -1.423 HN8 E4M 49
E4M H9 H9 H 0 1 N N N 2.639 29.515 33.683 -7.135 -2.822 -0.612 H9 E4M 50
E4M H10 H10 H 0 1 N N N 5.380 28.199 36.257 -7.953 0.728 0.982 H10 E4M 51
E4M H12 H12 H 0 1 N N N 6.197 31.094 30.865 -2.445 -1.873 0.260 H12 E4M 52
E4M H13 H13 H 0 1 N N N 4.309 30.654 32.384 -4.720 -2.275 -0.587 H13 E4M 53
E4M H15 H15 H 0 1 N N N 7.029 29.197 35.377 -6.097 1.203 1.487 H15 E4M 54
E4M H16 H16 H 0 1 N N N 8.909 29.551 33.811 -3.818 1.596 2.329 H16 E4M 55
E4M C27 C27 C 0 1 N N S 9.780 28.341 16.931 8.593 -2.951 -0.688 C27 E4M 56
E4M H1J H1J H 0 1 N N N 8.107 30.826 24.547 4.587 4.203 1.715 H1J E4M 57
E4M HO1A HO1A H 0 0 N N N 8.432 31.587 19.193 8.704 -0.289 -3.062 HO1A E4M 58
E4M H2J H2J H 0 1 N N N 6.118 29.962 23.617 5.416 5.924 0.445 H2J E4M 59
E4M HO2J HO2J H 0 0 N N N 5.192 28.497 24.997 3.361 5.758 -0.801 HO2J E4M 60
E4M H3J H3J H 0 1 N N N 6.157 27.919 22.431 7.331 4.791 -0.315 H3J E4M 61
E4M HO3J HO3J H 0 0 N N N 7.397 26.160 23.093 6.577 5.881 -2.341 HO3J E4M 62
E4M H4J H4J H 0 1 N N N 8.899 27.578 22.166 5.537 2.638 -1.570 H4J E4M 63
E4M H5J H5J H 0 1 N N N 6.983 29.172 20.894 8.079 2.505 -1.706 H5J E4M 64
E4M H5JA H5JA H 0 0 N N N 8.265 30.334 21.350 8.111 2.463 0.074 H5JA E4M 65
E4M H7M H7M H 0 1 N N N -1.149 29.305 35.325 -8.404 -4.132 -2.039 H7M E4M 66
E4M H7MA H7MA H 0 0 N N N -0.219 30.506 36.283 -10.091 -4.643 -1.795 H7MA E4M 67
E4M H7MB H7MB H 0 0 N N N 0.070 30.347 34.517 -9.702 -3.414 -3.022 H7MB E4M 68
E4M H9M H9M H 0 1 N N N 3.221 31.842 33.584 -6.397 -0.675 -2.662 H9M E4M 69
E4M H9MA H9MA H 0 0 N N N 1.632 31.618 34.390 -5.400 -2.056 -2.146 H9MA E4M 70
E4M H9MB H9MB H 0 0 N N N 3.092 31.988 35.369 -6.869 -2.331 -3.113 H9MB E4M 71
E4M HNA2 HNA2 H 0 0 N N N 0.513 25.607 41.016 -14.947 0.122 0.300 HNA2 E4M 72
E4M HNAA HNAA H 0 0 N N N 2.139 25.214 41.466 -14.520 1.627 0.912 HNAA E4M 73
E4M HX1 HX1 H 0 1 N N N 8.906 31.677 31.089 -1.656 0.622 2.836 HX1 E4M 74
E4M HX1A HX1A H 0 0 N N N 9.763 30.243 31.783 -1.084 -0.828 1.975 HX1A E4M 75
E4M HX2 HX2 H 0 1 N N N 7.672 30.054 29.611 -1.396 1.929 0.706 HX2 E4M 76
E4M HOX2 HOX2 H 0 0 N N N 8.846 28.014 29.311 -0.168 -0.514 -0.269 HOX2 E4M 77
E4M HX3 HX3 H 0 1 N N N 10.713 30.257 29.400 1.097 0.442 1.647 HX3 E4M 78
E4M HOX3 HOX3 H 0 0 N N N 10.215 32.004 27.994 -0.131 2.885 2.622 HOX3 E4M 79
E4M HX4 HX4 H 0 1 N N N 9.355 28.501 27.981 0.740 3.162 0.309 HX4 E4M 80
E4M HOX4 HOX4 H 0 0 N N N 10.809 29.076 26.210 1.969 0.719 -0.666 HOX4 E4M 81
E4M HX5 HX5 H 0 1 N N N 7.504 29.796 27.215 2.542 3.045 2.056 HX5 E4M 82
E4M HX5A HX5A H 0 0 N N N 8.565 31.040 26.525 3.267 1.684 1.168 HX5A E4M 83
E4M C28 C28 C 0 1 N N N 9.679 27.344 15.761 8.271 -3.678 0.618 C28 E4M 84
E4M C29 C29 C 0 1 N N N 10.925 27.018 14.917 8.703 -2.814 1.804 C29 E4M 85
E4M C30 C30 C 0 1 N N N 10.823 26.022 13.747 8.386 -3.530 3.091 C30 E4M 86
E4M O13 O13 O 0 1 N N N 9.731 25.627 13.375 7.867 -4.621 3.063 O13 E4M 87
E4M O14 O14 O 0 1 N N N 12.010 25.559 13.097 8.680 -2.957 4.269 O14 E4M 88
E4M C31 C31 C 0 1 N N N 10.132 29.702 16.303 8.281 -3.852 -1.855 C31 E4M 89
E4M O15 O15 O 0 1 N N N 11.295 29.976 16.054 7.466 -3.511 -2.680 O15 E4M 90
E4M O16 O16 O 0 1 N N N 9.097 30.644 16.011 8.908 -5.032 -1.979 O16 E4M 91
E4M H38 H38 H 0 1 N N N 10.490 27.849 17.612 9.651 -2.687 -0.706 H38 E4M 92
E4M H39 H39 H 0 1 N N N 9.350 26.391 16.200 7.198 -3.864 0.676 H39 E4M 93
E4M H40 H40 H 0 1 N N N 8.940 27.766 15.064 8.806 -4.628 0.647 H40 E4M 94
E4M H41 H41 H 0 1 N N N 11.254 27.971 14.478 9.776 -2.628 1.746 H41 E4M 95
E4M H42 H42 H 0 1 N N N 11.664 26.595 15.614 8.169 -1.864 1.775 H42 E4M 96
E4M H43 H43 H 0 1 N N N 11.776 24.954 12.403 8.457 -3.455 5.067 H43 E4M 97
E4M H44 H44 H 0 1 N N N 9.478 31.426 15.630 8.675 -5.575 -2.744 H44 E4M 98
#
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
E4M N1 C2 DOUB N N 1
E4M N1 C8A SING N N 2
E4M C2 N3 SING N N 3
E4M C2 NA2 SING N N 4
E4M N3 C4 SING N N 5
E4M N3 HN3 SING N N 6
E4M C4 C4A SING N N 7
E4M C4 OH4 DOUB N N 8
E4M N5 C6 SING N N 9
E4M N5 C10 DOUB N N 10
E4M N5 C4A SING N N 11
E4M C6 C7 SING N N 12
E4M C6 C9 SING N N 13
E4M C6 H6 SING N N 14
E4M C7 N8 SING N N 15
E4M C7 C7M SING N N 16
E4M C7 H7 SING N N 17
E4M N8 C8A SING N N 18
E4M N8 HN8 SING N N 19
E4M C9 N10 SING N N 20
E4M C9 C9M SING N N 21
E4M C9 H9 SING N N 22
E4M PA O2A SING N N 23
E4M PA O1A SING N N 24
E4M PA O3A DOUB N N 25
E4M PA O5J SING N N 26
E4M C10 N10 SING N N 27
E4M C10 H10 SING N N 28
E4M N10 C14 SING N N 29
E4M C11 C12 DOUB Y N 30
E4M C11 C16 SING Y N 31
E4M C11 CX1 SING N N 32
E4M C12 C13 SING Y N 33
E4M C12 H12 SING N N 34
E4M C13 C14 DOUB Y N 35
E4M C13 H13 SING N N 36
E4M C14 C15 SING Y N 37
E4M C15 C16 DOUB Y N 38
E4M C15 H15 SING N N 39
E4M C16 H16 SING N N 40
E4M O2A C27 SING N N 41
E4M C1J C2J SING N N 42
E4M C1J O4J SING N N 43
E4M C1J OX5 SING N N 44
E4M C1J H1J SING N N 45
E4M O1A HO1A SING N N 46
E4M C2J O2J SING N N 47
E4M C2J C3J SING N N 48
E4M C2J H2J SING N N 49
E4M O2J HO2J SING N N 50
E4M C3J O3J SING N N 51
E4M C3J C4J SING N N 52
E4M C3J H3J SING N N 53
E4M O3J HO3J SING N N 54
E4M C4A C8A DOUB N N 55
E4M C4J O4J SING N N 56
E4M C4J C5J SING N N 57
E4M C4J H4J SING N N 58
E4M C5J O5J SING N N 59
E4M C5J H5J SING N N 60
E4M C5J H5JA SING N N 61
E4M C7M H7M SING N N 62
E4M C7M H7MA SING N N 63
E4M C7M H7MB SING N N 64
E4M C9M H9M SING N N 65
E4M C9M H9MA SING N N 66
E4M C9M H9MB SING N N 67
E4M NA2 HNA2 SING N N 68
E4M NA2 HNAA SING N N 69
E4M CX1 CX2 SING N N 70
E4M CX1 HX1 SING N N 71
E4M CX1 HX1A SING N N 72
E4M CX2 OX2 SING N N 73
E4M CX2 CX3 SING N N 74
E4M CX2 HX2 SING N N 75
E4M OX2 HOX2 SING N N 76
E4M CX3 OX3 SING N N 77
E4M CX3 CX4 SING N N 78
E4M CX3 HX3 SING N N 79
E4M OX3 HOX3 SING N N 80
E4M CX4 OX4 SING N N 81
E4M CX4 CX5 SING N N 82
E4M CX4 HX4 SING N N 83
E4M OX4 HOX4 SING N N 84
E4M CX5 OX5 SING N N 85
E4M CX5 HX5 SING N N 86
E4M CX5 HX5A SING N N 87
E4M C27 C28 SING N N 88
E4M C28 C29 SING N N 89
E4M C29 C30 SING N N 90
E4M C30 O13 DOUB N N 91
E4M C30 O14 SING N N 92
E4M C27 C31 SING N N 93
E4M C31 O15 DOUB N N 94
E4M C31 O16 SING N N 95
E4M C27 H38 SING N N 96
E4M C28 H39 SING N N 97
E4M C28 H40 SING N N 98
E4M C29 H41 SING N N 99
E4M C29 H42 SING N N 100
E4M O14 H43 SING N N 101
E4M O16 H44 SING N N 102
#
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
E4M SMILES ACDLabs 11.02 "O=C4C=5[N+]3=CN(c1ccc(cc1)CC(O)C(O)C(O)COC2OC(C(O)C2O)COP(=O)(OC(C(=O)O)CCC(=O)O)O)C(C)C3C(NC=5N=C(N)N4)C"
E4M SMILES_CANONICAL CACTVS 3.352 "C[C@@H]1NC2=C(C(=O)NC(=N2)N)[N+]3=CN([C@H](C)[C@@H]13)c4ccc(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]5O[C@H](CO[P](O)(=O)O[C@@H](CCC(O)=O)C(O)=O)[C@@H](O)[C@H]5O)cc4"
E4M SMILES CACTVS 3.352 "C[CH]1NC2=C(C(=O)NC(=N2)N)[N+]3=CN([CH](C)[CH]13)c4ccc(C[CH](O)[CH](O)[CH](O)CO[CH]5O[CH](CO[P](O)(=O)O[CH](CCC(O)=O)C(O)=O)[CH](O)[CH]5O)cc4"
E4M SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C[C@H]1[C@@H]2[C@H](N(C=[N+]2C3=C(N1)N=C(NC3=O)N)c4ccc(cc4)C[C@@H]([C@@H]([C@@H](CO[C@@H]5[C@@H]([C@@H]([C@H](O5)CO[P@](=O)(O)O[C@@H](CCC(=O)O)C(=O)O)O)O)O)O)O)C"
E4M SMILES "OpenEye OEToolkits" 1.7.0 "CC1C2C(N(C=[N+]2C3=C(N1)N=C(NC3=O)N)c4ccc(cc4)CC(C(C(COC5C(C(C(O5)COP(=O)(O)OC(CCC(=O)O)C(=O)O)O)O)O)O)O)C"
E4M InChI InChI 1.03
;InChI=1S/C31H43N6O16P/c1-13-22-14(2)36(12-37(22)23-27(33-13)34-31(32)35-28(23)45)16-5-3-15(4-6-16)9-17(38)24(42)18(39)10-50-30-26(44)25(43)20(52-30)11-51-54(48,49)53-19(29(46)47)7-8-21(40)41/h3-6,12-14,17-20,22,24-26,30,38-39,42-44H,7-11H2,1-2H3,(H6-,32,33,34,35,40,41,45,46,47,48,49)/p+1/t13-,14+,17-,18+,19-,20+,22+,24-,25+,26+,30-/m0/s1
;
E4M InChIKey InChI 1.03 RANKJVUGLXUXOL-CAFBYHECSA-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
E4M "SYSTEMATIC NAME" ACDLabs 11.02
"1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol"
E4M "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1
"(2S)-2-[[(2R,3S,4R,5S)-5-[(2R,3S,4S)-5-[4-[(6S,6aR,7R)-3-azanyl-6,7-dimethyl-1-oxo-5,6,6a,7-tetrahydro-2H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl]-2,3,4-trihydroxy-pentoxy]-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxypentanedioic 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
E4M "Create component" 2009-09-08 PDBJ
E4M "Modify descriptor" 2011-06-04 RCSB
#