data_PM8
#
_chem_comp.id PM8
_chem_comp.name "S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C21 H41 N2 O7 P S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2005-12-19
_chem_comp.pdbx_modified_date 2024-09-27
_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 496.598
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PM8
_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 2FAE
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_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
PM8 O23 O23 O 0 1 N N N N N N 7.912 29.635 26.313 8.692 4.323 0.321 O23 PM8 1
PM8 P24 P24 P 0 1 N N S N N N 7.366 29.622 24.894 8.128 2.926 0.891 P24 PM8 2
PM8 O26 O26 O 0 1 N N N N N N 6.145 28.703 24.809 6.831 3.155 1.564 O26 PM8 3
PM8 O27 O27 O 0 1 N N N N N N 6.850 31.040 24.624 7.925 1.893 -0.327 O27 PM8 4
PM8 C28 C28 C 0 1 N N N N N N 5.891 30.885 23.629 7.740 0.489 -0.135 C28 PM8 5
PM8 C29 C29 C 0 1 N N N N N N 5.052 32.173 23.608 7.578 -0.195 -1.494 C29 PM8 6
PM8 C30 C30 C 0 1 N N N N N N 4.167 32.065 22.399 6.361 0.386 -2.216 C30 PM8 7
PM8 C31 C31 C 0 1 N N N N N N 4.156 32.227 24.899 8.833 0.042 -2.336 C31 PM8 8
PM8 C32 C32 C 0 1 N N R N N N 5.951 33.433 23.570 7.379 -1.698 -1.287 C32 PM8 9
PM8 O33 O33 O 0 1 N N N N N N 6.851 33.331 22.459 8.569 -2.264 -0.734 O33 PM8 10
PM8 C34 C34 C 0 1 N N N N N N 5.114 34.745 23.463 6.228 -1.927 -0.343 C34 PM8 11
PM8 O35 O35 O 0 1 N N N N N N 5.317 35.690 24.244 6.432 -2.384 0.763 O35 PM8 12
PM8 N36 N36 N 0 1 N N N N N N 4.181 34.786 22.498 4.971 -1.625 -0.726 N36 PM8 13
PM8 C37 C37 C 0 1 N N N N N N 3.274 35.928 22.198 3.864 -1.757 0.225 C37 PM8 14
PM8 C38 C38 C 0 1 N N N N N N 2.571 35.809 20.725 2.556 -1.355 -0.458 C38 PM8 15
PM8 C39 C39 C 0 1 N N N N N N 3.709 35.645 19.769 1.417 -1.490 0.519 C39 PM8 16
PM8 O40 O40 O 0 1 N N N N N N 3.884 34.611 19.095 1.631 -1.870 1.651 O40 PM8 17
PM8 N41 N41 N 0 1 N N N N N N 4.536 36.716 19.681 0.160 -1.188 0.136 N41 PM8 18
PM8 C42 C42 C 0 1 N N N N N N 5.764 36.649 18.916 -0.947 -1.319 1.086 C42 PM8 19
PM8 C43 C43 C 0 1 N N N N N N 6.042 36.714 17.509 -2.256 -0.917 0.403 C43 PM8 20
PM8 S1 S1 S 0 1 N N N N N N 7.848 36.340 17.139 -3.624 -1.079 1.577 S1 PM8 21
PM8 C1 C1 C 0 1 N N N N N N 8.971 37.505 17.890 -4.927 -0.583 0.585 C1 PM8 22
PM8 O1 O1 O 0 1 N N N N N N 8.747 37.968 19.005 -4.724 -0.257 -0.566 O1 PM8 23
PM8 C2 C2 C 0 1 N N N N N N 10.214 37.908 17.105 -6.328 -0.550 1.141 C2 PM8 24
PM8 C3 C3 C 0 1 N N N N N N 10.264 39.381 16.816 -7.296 -0.074 0.057 C3 PM8 25
PM8 C4 C4 C 0 1 N N N N N N 11.490 39.740 16.017 -8.718 -0.040 0.622 C4 PM8 26
PM8 C5 C5 C 0 1 N N N N N N 11.430 41.194 15.584 -9.686 0.436 -0.463 C5 PM8 27
PM8 C6 C6 C 0 1 N N N N N N 11.978 42.137 16.631 -11.108 0.470 0.102 C6 PM8 28
PM8 C7 C7 C 0 1 N N N N N N 13.129 42.946 16.058 -12.076 0.946 -0.982 C7 PM8 29
PM8 C8 C8 C 0 1 N N N N N N 13.306 44.260 16.792 -13.498 0.979 -0.418 C8 PM8 30
PM8 C9 C9 C 0 1 N N N N N N 14.767 44.619 16.865 -14.467 1.456 -1.502 C9 PM8 31
PM8 C10 C10 C 0 1 N N N N N N 14.976 46.032 17.168 -15.888 1.489 -0.937 C10 PM8 32
PM8 H23 H23 H 0 1 N N N N N N 8.862 29.638 26.287 8.839 4.994 1.002 H23 PM8 33
PM8 H24 H24 H 0 1 N N N N N N 8.369 29.191 23.986 9.056 2.385 1.820 H24 PM8 34
PM8 H281 1H28 H 0 0 N N N N N N 5.257 30.009 23.830 8.607 0.075 0.380 H281 PM8 35
PM8 H282 2H28 H 0 0 N N N N N N 6.375 30.729 22.654 6.846 0.320 0.466 H282 PM8 36
PM8 H301 1H30 H 0 0 N N N N N N 4.408 31.143 21.850 6.550 1.430 -2.464 H301 PM8 37
PM8 H302 2H30 H 0 0 N N N N N N 4.331 32.935 21.746 6.178 -0.178 -3.131 H302 PM8 38
PM8 H303 3H30 H 0 0 N N N N N N 3.114 32.039 22.716 5.488 0.319 -1.567 H303 PM8 39
PM8 H311 1H31 H 0 0 N N N N N N 3.504 31.342 24.930 9.690 -0.424 -1.851 H311 PM8 40
PM8 H312 2H31 H 0 0 N N N N N N 3.539 33.137 24.879 8.694 -0.393 -3.326 H312 PM8 41
PM8 H313 3H31 H 0 0 N N N N N N 4.799 32.240 25.792 9.009 1.114 -2.433 H313 PM8 42
PM8 H32 H32 H 0 1 N N N N N N 6.515 33.484 24.513 7.163 -2.171 -2.245 H32 PM8 43
PM8 H33 H33 H 0 1 N N N N N N 6.354 33.308 21.650 8.823 -1.890 0.121 H33 PM8 44
PM8 H36 H36 H 0 1 N N N N N N 4.086 33.971 21.926 4.800 -1.321 -1.631 H36 PM8 45
PM8 H371 1H37 H 0 0 N N N N N N 3.880 36.846 22.205 3.795 -2.791 0.562 H371 PM8 46
PM8 H372 2H37 H 0 0 N N N N N N 2.481 35.951 22.960 4.042 -1.107 1.081 H372 PM8 47
PM8 H381 1H38 H 0 0 N N N N N N 1.957 36.691 20.488 2.624 -0.320 -0.795 H381 PM8 48
PM8 H382 2H38 H 0 0 N N N N N N 1.891 34.946 20.681 2.378 -2.005 -1.315 H382 PM8 49
PM8 H41 H41 H 0 1 N N N N N N 4.294 37.565 20.151 -0.011 -0.884 -0.769 H41 PM8 50
PM8 H421 1H42 H 0 0 N N N N N N 5.936 35.569 19.035 -1.016 -2.353 1.423 H421 PM8 51
PM8 H422 2H42 H 0 0 N N N N N N 6.331 37.507 19.307 -0.770 -0.669 1.943 H422 PM8 52
PM8 H431 1H43 H 0 0 N N N N N N 5.824 37.735 17.162 -2.187 0.117 0.066 H431 PM8 53
PM8 H432 2H43 H 0 0 N N N N N N 5.415 35.974 16.990 -2.433 -1.567 -0.454 H432 PM8 54
PM8 H21 1H2 H 0 1 N N N N N N 10.187 37.379 16.141 -6.612 -1.550 1.469 H21 PM8 55
PM8 H22 2H2 H 0 1 N N N N N N 11.101 37.640 17.697 -6.366 0.135 1.989 H22 PM8 56
PM8 H31 1H3 H 0 1 N N N N N N 10.300 39.923 17.773 -7.012 0.926 -0.271 H31 PM8 57
PM8 H32A 2H3 H 0 0 N N N N N N 9.369 39.661 16.240 -7.258 -0.758 -0.790 H32A PM8 58
PM8 H41A 1H4 H 0 0 N N N N N N 11.534 39.101 15.122 -9.002 -1.040 0.949 H41A PM8 59
PM8 H42 2H4 H 0 1 N N N N N N 12.385 39.584 16.638 -8.756 0.645 1.469 H42 PM8 60
PM8 H51 1H5 H 0 1 N N N N N N 10.373 41.451 15.423 -9.402 1.436 -0.790 H51 PM8 61
PM8 H52 2H5 H 0 1 N N N N N N 12.027 41.308 14.667 -9.648 -0.249 -1.310 H52 PM8 62
PM8 H61 1H6 H 0 1 N N N N N N 12.343 41.550 17.487 -11.392 -0.530 0.430 H61 PM8 63
PM8 H62 2H6 H 0 1 N N N N N N 11.180 42.821 16.955 -11.146 1.154 0.949 H62 PM8 64
PM8 H71 1H7 H 0 1 N N N N N N 12.905 43.166 15.004 -11.792 1.946 -1.310 H71 PM8 65
PM8 H72 2H7 H 0 1 N N N N N N 14.055 42.360 16.152 -12.038 0.261 -1.830 H72 PM8 66
PM8 H81 1H8 H 0 1 N N N N N N 12.908 44.159 17.813 -13.782 -0.021 -0.090 H81 PM8 67
PM8 H82 2H8 H 0 1 N N N N N N 12.764 45.052 16.254 -13.536 1.664 0.430 H82 PM8 68
PM8 H91 1H9 H 0 1 N N N N N N 15.215 44.414 15.881 -14.182 2.455 -1.830 H91 PM8 69
PM8 H92 2H9 H 0 1 N N N N N N 15.236 44.018 17.658 -14.428 0.771 -2.349 H92 PM8 70
PM8 H101 1H10 H 0 0 N N N N N N 14.139 46.621 16.764 -15.926 2.174 -0.090 H101 PM8 71
PM8 H102 2H10 H 0 0 N N N N N N 15.917 46.370 16.710 -16.578 1.828 -1.710 H102 PM8 72
PM8 H103 3H10 H 0 0 N N N N N N 15.029 46.170 18.258 -16.173 0.489 -0.609 H103 PM8 73
#
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
PM8 O23 P24 SING N N 1
PM8 O23 H23 SING N N 2
PM8 P24 O26 DOUB N N 3
PM8 P24 O27 SING N N 4
PM8 P24 H24 SING N N 5
PM8 O27 C28 SING N N 6
PM8 C28 C29 SING N N 7
PM8 C28 H281 SING N N 8
PM8 C28 H282 SING N N 9
PM8 C29 C30 SING N N 10
PM8 C29 C31 SING N N 11
PM8 C29 C32 SING N N 12
PM8 C30 H301 SING N N 13
PM8 C30 H302 SING N N 14
PM8 C30 H303 SING N N 15
PM8 C31 H311 SING N N 16
PM8 C31 H312 SING N N 17
PM8 C31 H313 SING N N 18
PM8 C32 O33 SING N N 19
PM8 C32 C34 SING N N 20
PM8 C32 H32 SING N N 21
PM8 O33 H33 SING N N 22
PM8 C34 O35 DOUB N N 23
PM8 C34 N36 SING N N 24
PM8 N36 C37 SING N N 25
PM8 N36 H36 SING N N 26
PM8 C37 C38 SING N N 27
PM8 C37 H371 SING N N 28
PM8 C37 H372 SING N N 29
PM8 C38 C39 SING N N 30
PM8 C38 H381 SING N N 31
PM8 C38 H382 SING N N 32
PM8 C39 O40 DOUB N N 33
PM8 C39 N41 SING N N 34
PM8 N41 C42 SING N N 35
PM8 N41 H41 SING N N 36
PM8 C42 C43 SING N N 37
PM8 C42 H421 SING N N 38
PM8 C42 H422 SING N N 39
PM8 C43 S1 SING N N 40
PM8 C43 H431 SING N N 41
PM8 C43 H432 SING N N 42
PM8 S1 C1 SING N N 43
PM8 C1 O1 DOUB N N 44
PM8 C1 C2 SING N N 45
PM8 C2 C3 SING N N 46
PM8 C2 H21 SING N N 47
PM8 C2 H22 SING N N 48
PM8 C3 C4 SING N N 49
PM8 C3 H31 SING N N 50
PM8 C3 H32A SING N N 51
PM8 C4 C5 SING N N 52
PM8 C4 H41A SING N N 53
PM8 C4 H42 SING N N 54
PM8 C5 C6 SING N N 55
PM8 C5 H51 SING N N 56
PM8 C5 H52 SING N N 57
PM8 C6 C7 SING N N 58
PM8 C6 H61 SING N N 59
PM8 C6 H62 SING N N 60
PM8 C7 C8 SING N N 61
PM8 C7 H71 SING N N 62
PM8 C7 H72 SING N N 63
PM8 C8 C9 SING N N 64
PM8 C8 H81 SING N N 65
PM8 C8 H82 SING N N 66
PM8 C9 C10 SING N N 67
PM8 C9 H91 SING N N 68
PM8 C9 H92 SING N N 69
PM8 C10 H101 SING N N 70
PM8 C10 H102 SING N N 71
PM8 C10 H103 SING N N 72
#
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
PM8 SMILES ACDLabs 10.04 "O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)O)CCCCCCCCC"
PM8 InChI InChI 1.03 "InChI=1S/C21H41N2O7PS/c1-4-5-6-7-8-9-10-11-18(25)32-15-14-22-17(24)12-13-23-20(27)19(26)21(2,3)16-30-31(28)29/h19,26,31H,4-16H2,1-3H3,(H,22,24)(H,23,27)(H,28,29)/t19-/m0/s1"
PM8 InChIKey InChI 1.03 BPRKYNVKIAROET-IBGZPJMESA-N
PM8 SMILES_CANONICAL CACTVS 3.385 "CCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[PH](O)=O"
PM8 SMILES CACTVS 3.385 "CCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[PH](O)=O"
PM8 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 "CCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@H](=O)O)O"
PM8 SMILES "OpenEye OEToolkits" 1.7.5 "CCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)O)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
PM8 "SYSTEMATIC NAME" ACDLabs 10.04 "S-[2-({N-[(2R)-2-hydroxy-4-{[(R)-hydroxy(oxido)phosphanyl]oxy}-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl] decanethioate"
PM8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(3R)-4-[[3-(2-decanoylsulfanylethylamino)-3-oxo-propyl]amino]-3-hydroxy-2,2-dimethyl-4-oxo-butoxy]phosphinic 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
PM8 "Create component" 2005-12-19 RCSB
PM8 "Modify descriptor" 2011-06-04 RCSB
PM8 "Modify descriptor" 2012-01-05 RCSB
PM8 "Modify coordinates" 2012-01-05 RCSB
PM8 "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id PM8
_pdbx_chem_comp_pcm.modified_residue_id SER
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category Lipid/lipid-like
_pdbx_chem_comp_pcm.position "Amino-acid side chain"
_pdbx_chem_comp_pcm.polypeptide_position "Any position"
_pdbx_chem_comp_pcm.comp_id_linking_atom P24
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom OG
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#