data_ME8
#
_chem_comp.id ME8
_chem_comp.name
;[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]
(2S)-2-azanyl-4-methylsulfanyl-butanoate
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H23 N6 O8 P S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "L-methionine-AMP; methionyl-adenylate"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2009-10-30
_chem_comp.pdbx_modified_date 2020-06-17
_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 478.417
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code ME8
_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 3KFL
_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
ME8 O O O 0 1 N N N 30.609 45.685 -7.969 4.896 -1.750 -1.197 O ME8 1
ME8 N1 N1 N 0 1 Y N N 38.757 46.833 -0.978 -7.005 2.818 0.282 N1 ME8 2
ME8 O1 O1 O 0 1 N N N 31.305 43.558 -8.553 3.386 -1.164 0.307 O1 ME8 3
ME8 P1 P1 P 0 1 N N N 32.918 43.852 -8.463 2.330 -2.130 -0.430 P1 ME8 4
ME8 C2 C2 C 0 1 Y N N 37.670 46.290 -0.298 -6.963 1.726 1.023 C2 ME8 5
ME8 N2 N2 N 0 1 N N N 29.161 42.838 -9.561 7.001 -0.658 -0.000 N2 ME8 6
ME8 N3 N3 N 0 1 Y N N 36.636 45.706 -1.021 -5.933 0.907 1.016 N3 ME8 7
ME8 C4 C4 C 0 1 Y N N 36.913 45.392 -2.404 -4.877 1.152 0.247 C4 ME8 8
ME8 C5 C5 C 0 1 Y N N 37.899 46.194 -3.126 -4.873 2.302 -0.561 C5 ME8 9
ME8 C6 C6 C 0 1 Y N N 38.902 46.773 -2.359 -5.996 3.146 -0.519 C6 ME8 10
ME8 N6 N6 N 0 1 N N N 39.960 47.333 -2.899 -6.049 4.292 -1.292 N6 ME8 11
ME8 N7 N7 N 0 1 Y N N 37.684 45.879 -4.404 -3.697 2.313 -1.233 N7 ME8 12
ME8 C8 C8 C 0 1 Y N N 36.535 45.184 -4.538 -2.995 1.270 -0.896 C8 ME8 13
ME8 C9 C9 C 0 1 N N N 30.394 44.560 -8.411 4.621 -1.100 -0.216 C9 ME8 14
ME8 N9 N9 N 0 1 Y N N 35.913 45.042 -3.363 -3.680 0.522 0.014 N9 ME8 15
ME8 CA CA C 0 1 N N S 28.999 44.083 -8.763 5.664 -0.217 0.419 CA ME8 16
ME8 CB CB C 0 1 N N N 28.280 43.794 -7.455 5.443 1.231 -0.022 CB ME8 17
ME8 SD SD S 0 1 N N N 26.114 42.906 -6.018 6.161 3.862 0.196 SD ME8 18
ME8 CE CE C 0 1 N N N 24.450 42.466 -6.464 7.391 4.776 1.166 CE ME8 19
ME8 CG CG C 0 1 N N N 26.844 43.337 -7.636 6.422 2.145 0.719 CG ME8 20
ME8 "C1'" "C1'" C 0 1 N N R 34.740 44.240 -3.004 -3.223 -0.725 0.632 "C1'" ME8 21
ME8 O1S O1S O 0 1 N N N 33.493 42.669 -9.108 2.237 -1.760 -1.860 O1S ME8 22
ME8 "C2'" "C2'" C 0 1 N N R 33.692 45.144 -2.383 -3.766 -1.950 -0.146 "C2'" ME8 23
ME8 "O2'" "O2'" O 0 1 N N N 32.704 44.296 -1.800 -5.067 -2.313 0.319 "O2'" ME8 24
ME8 O2S O2S O 0 1 N N N 33.315 45.206 -8.943 2.820 -3.658 -0.302 O2S ME8 25
ME8 "C3'" "C3'" C 0 1 N N S 33.167 45.812 -3.650 -2.728 -3.044 0.207 "C3'" ME8 26
ME8 "O3'" "O3'" O 0 1 N N N 31.889 46.349 -3.438 -3.209 -3.865 1.273 "O3'" ME8 27
ME8 "C4'" "C4'" C 0 1 N N R 33.022 44.586 -4.566 -1.483 -2.253 0.654 "C4'" ME8 28
ME8 "O4'" "O4'" O 0 1 N N N 34.164 43.758 -4.241 -1.790 -0.856 0.510 "O4'" ME8 29
ME8 "C5'" "C5'" C 0 1 N N N 33.056 44.945 -6.070 -0.290 -2.618 -0.232 "C5'" ME8 30
ME8 "O5'" "O5'" O 0 1 N N N 33.199 43.757 -6.862 0.884 -1.970 0.261 "O5'" ME8 31
ME8 H2 H2 H 0 1 N N N 37.630 46.322 0.781 -7.805 1.497 1.660 H2 ME8 32
ME8 HN2 HN2 H 0 1 N N N 28.261 42.486 -9.817 7.101 -0.607 -1.003 HN2 ME8 33
ME8 HN2A HN2A H 0 0 N N N 29.688 43.038 -10.387 7.720 -0.123 0.463 HN2A ME8 34
ME8 HN6 HN6 H 0 1 N N N 40.526 47.738 -2.181 -5.306 4.521 -1.872 HN6 ME8 35
ME8 HN6A HN6A H 0 0 N N N 40.489 46.641 -3.390 -6.830 4.867 -1.254 HN6A ME8 36
ME8 HA HA H 0 1 N N N 28.422 44.821 -9.339 5.583 -0.283 1.504 HA ME8 37
ME8 HB HB H 0 1 N N N 28.829 42.997 -6.933 5.611 1.314 -1.096 HB ME8 38
ME8 HBA HBA H 0 1 N N N 28.272 44.718 -6.859 4.421 1.530 0.210 HBA ME8 39
ME8 HE HE H 0 1 N N N 23.891 42.180 -5.561 7.199 4.628 2.229 HE ME8 40
ME8 HEA HEA H 0 1 N N N 23.959 43.327 -6.942 8.389 4.411 0.923 HEA ME8 41
ME8 HEB HEB H 0 1 N N N 24.470 41.619 -7.166 7.325 5.838 0.930 HEB ME8 42
ME8 HG HG H 0 1 N N N 26.260 44.149 -8.093 6.254 2.062 1.793 HG ME8 43
ME8 HGA HGA H 0 1 N N N 26.824 42.453 -8.290 7.444 1.846 0.487 HGA ME8 44
ME8 "H1'" "H1'" H 0 1 N N N 35.028 43.432 -2.315 -3.527 -0.768 1.678 "H1'" ME8 45
ME8 "H2'" "H2'" H 0 1 N N N 34.016 45.849 -1.604 -3.778 -1.756 -1.218 "H2'" ME8 46
ME8 "HO2'" "HO2'" H 0 0 N N N 32.027 44.828 -1.399 -5.450 -3.075 -0.137 "HO2'" ME8 47
ME8 HO2S HO2S H 0 0 N N N 33.935 45.120 -9.658 2.903 -3.969 0.610 HO2S ME8 48
ME8 "H3'" "H3'" H 0 1 N N N 33.802 46.630 -4.020 -2.502 -3.652 -0.669 "H3'" ME8 49
ME8 "HO3'" "HO3'" H 0 0 N N N 31.581 46.759 -4.237 -4.025 -4.340 1.066 "HO3'" ME8 50
ME8 "H4'" "H4'" H 0 1 N N N 32.051 44.095 -4.403 -1.256 -2.478 1.696 "H4'" ME8 51
ME8 "H5'" "H5'" H 0 1 N N N 32.118 45.451 -6.343 -0.143 -3.697 -0.217 "H5'" ME8 52
ME8 "H5'A" "H5'A" H 0 0 N N N 33.908 45.613 -6.263 -0.483 -2.291 -1.254 "H5'A" ME8 53
ME8 H8 H8 H 0 1 N N N 36.165 44.793 -5.474 -2.015 1.032 -1.283 H8 ME8 54
# #
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
ME8 N1 C2 SING Y N 1
ME8 O1 P1 SING N N 2
ME8 O1 C9 SING N N 3
ME8 P1 "O5'" SING N N 4
ME8 C2 H2 SING N N 5
ME8 N2 CA SING N N 6
ME8 N2 HN2 SING N N 7
ME8 N2 HN2A SING N N 8
ME8 N3 C2 DOUB Y N 9
ME8 C4 N3 SING Y N 10
ME8 C5 C4 DOUB Y N 11
ME8 C5 C6 SING Y N 12
ME8 C6 N1 DOUB Y N 13
ME8 N6 C6 SING N N 14
ME8 N6 HN6 SING N N 15
ME8 N6 HN6A SING N N 16
ME8 N7 C5 SING Y N 17
ME8 C8 N7 DOUB Y N 18
ME8 C8 N9 SING Y N 19
ME8 C9 O DOUB N N 20
ME8 N9 C4 SING Y N 21
ME8 N9 "C1'" SING N N 22
ME8 CA C9 SING N N 23
ME8 CA CB SING N N 24
ME8 CA HA SING N N 25
ME8 CB HB SING N N 26
ME8 CB HBA SING N N 27
ME8 CE SD SING N N 28
ME8 CE HE SING N N 29
ME8 CE HEA SING N N 30
ME8 CE HEB SING N N 31
ME8 CG CB SING N N 32
ME8 CG SD SING N N 33
ME8 CG HG SING N N 34
ME8 CG HGA SING N N 35
ME8 "C1'" "C2'" SING N N 36
ME8 "C1'" "H1'" SING N N 37
ME8 O1S P1 DOUB N N 38
ME8 "C2'" "O2'" SING N N 39
ME8 "C2'" "H2'" SING N N 40
ME8 "O2'" "HO2'" SING N N 41
ME8 O2S P1 SING N N 42
ME8 O2S HO2S SING N N 43
ME8 "C3'" "C2'" SING N N 44
ME8 "C3'" "O3'" SING N N 45
ME8 "C3'" "H3'" SING N N 46
ME8 "O3'" "HO3'" SING N N 47
ME8 "C4'" "C3'" SING N N 48
ME8 "C4'" "O4'" SING N N 49
ME8 "C4'" "H4'" SING N N 50
ME8 "O4'" "C1'" SING N N 51
ME8 "C5'" "C4'" SING N N 52
ME8 "C5'" "H5'" SING N N 53
ME8 "C5'" "H5'A" SING N N 54
ME8 "O5'" "C5'" SING N N 55
ME8 C8 H8 SING N N 56
# #
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
ME8 SMILES ACDLabs 11.02 "O=P(OC(=O)C(N)CCSC)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O"
ME8 SMILES_CANONICAL CACTVS 3.352 "CSCC[C@H](N)C(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23"
ME8 SMILES CACTVS 3.352 "CSCC[CH](N)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23"
ME8 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CSCC[C@@H](C(=O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N"
ME8 SMILES "OpenEye OEToolkits" 1.7.0 "CSCCC(C(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N"
ME8 InChI InChI 1.03 "InChI=1S/C15H23N6O8PS/c1-31-3-2-7(16)15(24)29-30(25,26)27-4-8-10(22)11(23)14(28-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H,25,26)(H2,17,18,19)/t7-,8+,10+,11+,14+/m0/s1"
ME8 InChIKey InChI 1.03 RZQLXQQLNKBFRX-TWBCTODHSA-N
# #
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
ME8 "SYSTEMATIC NAME" ACDLabs 11.02 "5'-O-[(S)-{[(2S)-2-amino-4-(methylsulfanyl)butanoyl]oxy}(hydroxy)phosphoryl]adenosine"
ME8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] (2S)-2-azanyl-4-methylsulfanyl-butanoate"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
ME8 "Create component" 2009-10-30 RCSB
ME8 "Modify aromatic_flag" 2011-06-04 RCSB
ME8 "Modify descriptor" 2011-06-04 RCSB
ME8 "Modify synonyms" 2020-06-05 PDBE
# #
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 ME8 L-methionine-AMP ? ?
2 ME8 methionyl-adenylate ? ?
##