data_SDO
#
_chem_comp.id SDO
_chem_comp.name "N~3~-{(2S)-4-[(dihydroxyphosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-N-{2-[(3,7-dioxooctyl)sulfanyl]ethyl}-beta-alaninamide"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C19 H35 N2 O8 P S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2014-10-16
_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 482.529
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SDO
_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 2MVU
_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
SDO P24 P24 P 0 1 N N N N N N -11.348 9.561 -2.752 -8.152 2.740 0.938 P24 SDO 1
SDO O26 O26 O 0 1 N N N N N N -12.261 10.314 -1.748 -6.695 3.351 1.244 O26 SDO 2
SDO O23 O23 O 0 1 N N N N N N -12.026 8.855 -3.959 -8.861 3.945 0.141 O23 SDO 3
SDO O27 O27 O 0 1 N N N N N N -10.316 10.571 -3.317 -7.836 1.696 -0.246 O27 SDO 4
SDO C28 C28 C 0 1 N N N N N N -9.469 11.301 -2.372 -7.486 0.331 -0.008 C28 SDO 5
SDO C29 C29 C 0 1 N N N N N N -8.385 12.106 -3.106 -7.253 -0.376 -1.345 C29 SDO 6
SDO C30 C30 C 0 1 N N N N N N -7.596 12.857 -2.056 -8.530 -0.316 -2.184 C30 SDO 7
SDO C31 C31 C 0 1 N N N N N N -7.455 11.138 -3.844 -6.115 0.318 -2.097 C31 SDO 8
SDO C32 C32 C 0 1 N N S N N N -8.986 13.133 -4.166 -6.879 -1.838 -1.090 C32 SDO 9
SDO O33 O33 O 0 1 N N N N N N -7.917 13.820 -4.817 -7.990 -2.519 -0.503 O33 SDO 10
SDO C34 C34 C 0 1 N N N N N N -9.879 14.213 -3.521 -5.701 -1.899 -0.152 C34 SDO 11
SDO O35 O35 O 0 1 N N N N N N -9.518 15.395 -3.549 -5.855 -2.268 0.993 O35 SDO 12
SDO N36 N36 N 0 1 N N N N N N -10.996 13.837 -2.949 -4.475 -1.543 -0.586 N36 SDO 13
SDO C37 C37 C 0 1 N N N N N N -11.937 14.753 -2.304 -3.312 -1.708 0.289 C37 SDO 14
SDO C38 C38 C 0 1 N N N N N N -12.437 14.252 -0.941 -2.053 -1.232 -0.439 C38 SDO 15
SDO C39 C39 C 0 1 N N N N N N -11.438 14.422 0.214 -0.857 -1.403 0.461 C39 SDO 16
SDO O40 O40 O 0 1 N N N N N N -11.706 14.030 1.348 -0.997 -1.860 1.576 O40 SDO 17
SDO N41 N41 N 0 1 N N N N N N -10.287 15.009 -0.092 0.369 -1.047 0.027 N41 SDO 18
SDO C42 C42 C 0 1 N N N N N N -9.225 15.253 0.869 1.532 -1.212 0.902 C42 SDO 19
SDO C43 C43 C 0 1 N N N N N N -8.105 16.086 0.291 2.790 -0.736 0.174 C43 SDO 20
SDO S1 S1 S 0 1 N N N N N N -6.521 16.186 1.181 4.230 -0.941 1.257 S1 SDO 21
SDO C1 C1 C 0 1 N N N N N N -6.401 15.248 2.737 5.600 -0.333 0.235 C1 SDO 22
SDO C2 C2 C 0 1 N N N N N N -7.602 14.446 3.207 6.909 -0.441 1.019 C2 SDO 23
SDO C3 C3 C 0 1 N N N N N N -7.524 13.618 4.558 8.047 0.063 0.170 C3 SDO 24
SDO O3 O3 O 0 1 N N N N N N -8.535 12.983 4.863 7.833 0.468 -0.948 O3 SDO 25
SDO C4 C4 C 0 1 N N N N N N -6.285 13.502 5.546 9.452 0.064 0.715 C4 SDO 26
SDO C5 C5 C 0 1 N N N N N N -4.982 14.245 5.226 10.408 0.622 -0.340 C5 SDO 27
SDO C6 C6 C 0 1 N N N N N N -3.816 13.836 6.150 11.835 0.622 0.213 C6 SDO 28
SDO C7 C7 C 0 1 N N N N N N -3.867 14.339 7.612 12.777 1.171 -0.827 C7 SDO 29
SDO O7 O7 O 0 1 N N N N N N -2.965 14.035 8.395 12.352 1.526 -1.900 O7 SDO 30
SDO C8 C8 C 0 1 N N N N N N -5.027 15.203 8.089 14.250 1.278 -0.527 C8 SDO 31
SDO H1 H1 H 0 1 N N N N N N -11.728 10.699 -1.062 -6.111 2.753 1.730 H1 SDO 32
SDO H2 H2 H 0 1 N N N N N N -11.363 8.434 -4.494 -9.129 4.685 0.704 H2 SDO 33
SDO H28A H28A H 0 0 N N N N N N -10.095 11.991 -1.788 -6.576 0.288 0.590 H28A SDO 34
SDO H28B H28B H 0 0 N N N N N N -8.985 10.582 -1.694 -8.297 -0.163 0.527 H28B SDO 35
SDO H30A H30A H 0 0 N N N N N N -6.807 13.448 -2.543 -8.826 0.725 -2.322 H30A SDO 36
SDO H30B H30B H 0 0 N N N N N N -8.269 13.529 -1.503 -8.348 -0.773 -3.157 H30B SDO 37
SDO H30C H30C H 0 0 N N N N N N -7.139 12.140 -1.358 -9.327 -0.855 -1.672 H30C SDO 38
SDO H31A H31A H 0 0 N N N N N N -6.676 11.708 -4.372 -5.241 0.388 -1.449 H31A SDO 39
SDO H31B H31B H 0 0 N N N N N N -6.984 10.458 -3.119 -5.863 -0.259 -2.986 H31B SDO 40
SDO H31C H31C H 0 0 N N N N N N -8.037 10.553 -4.571 -6.431 1.319 -2.390 H31C SDO 41
SDO H32A H32A H 0 0 N N N N N N -9.582 12.566 -4.897 -6.617 -2.316 -2.034 H32A SDO 42
SDO H33A H33A H 0 0 N N N N N N -7.996 14.753 -4.658 -8.278 -2.146 0.341 H33A SDO 43
SDO H36A H36A H 0 0 N N N N N N -11.220 12.862 -2.954 -4.363 -1.178 -1.477 H36A SDO 44
SDO H37A H37A H 0 0 N N N N N N -11.436 15.721 -2.157 -3.452 -1.119 1.195 H37A SDO 45
SDO H37B H37B H 0 0 N N N N N N -12.805 14.885 -2.967 -3.203 -2.760 0.554 H37B SDO 46
SDO H38A H38A H 0 0 N N N N N N -13.352 14.808 -0.687 -1.913 -1.822 -1.345 H38A SDO 47
SDO H38B H38B H 0 0 N N N N N N -12.672 13.182 -1.035 -2.163 -0.181 -0.704 H38B SDO 48
SDO H41A H41A H 0 0 N N N N N N -10.143 15.300 -1.038 0.480 -0.682 -0.864 H41A SDO 49
SDO H42A H42A H 0 0 N N N N N N -9.648 15.782 1.736 1.392 -0.623 1.808 H42A SDO 50
SDO H42B H42B H 0 0 N N N N N N -8.814 14.286 1.195 1.641 -2.264 1.167 H42B SDO 51
SDO H43A H43A H 0 0 N N N N N N -7.887 15.682 -0.708 2.930 -1.326 -0.732 H43A SDO 52
SDO H43B H43B H 0 0 N N N N N N -8.485 17.114 0.196 2.681 0.315 -0.091 H43B SDO 53
SDO H1A H1A H 0 1 N N N N N N -5.566 14.541 2.624 5.670 -0.933 -0.673 H1A SDO 54
SDO H1B H1B H 0 1 N N N N N N -6.165 15.971 3.532 5.420 0.708 -0.031 H1B SDO 55
SDO H2A H2A H 0 1 N N N N N N -8.435 15.156 3.318 6.839 0.158 1.927 H2A SDO 56
SDO H2B H2B H 0 1 N N N N N N -7.837 13.728 2.408 7.089 -1.483 1.285 H2B SDO 57
SDO H4A H4A H 0 1 N N N N N N -6.625 13.864 6.527 9.494 0.686 1.609 H4A SDO 58
SDO H4B H4B H 0 1 N N N N N N -6.033 12.434 5.617 9.744 -0.956 0.968 H4B SDO 59
SDO H5A H5A H 0 1 N N N N N N -4.699 14.026 4.186 10.366 -0.001 -1.235 H5A SDO 60
SDO H5B H5B H 0 1 N N N N N N -5.157 15.325 5.339 10.116 1.641 -0.593 H5B SDO 61
SDO H6A H6A H 0 1 N N N N N N -3.785 12.737 6.178 11.877 1.244 1.107 H6A SDO 62
SDO H6B H6B H 0 1 N N N N N N -2.887 14.217 5.700 12.127 -0.398 0.465 H6B SDO 63
SDO H8A H8A H 0 1 N N N N N N -4.885 15.454 9.150 14.749 0.356 -0.826 H8A SDO 64
SDO H8B H8B H 0 1 N N N N N N -5.064 16.128 7.495 14.674 2.116 -1.081 H8B SDO 65
SDO H8C H8C H 0 1 N N N N N N -5.970 14.651 7.966 14.393 1.439 0.541 H8C SDO 66
#
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
SDO P24 O26 SING N N 1
SDO P24 O23 SING N N 2
SDO P24 O27 SING N N 3
SDO O27 C28 SING N N 4
SDO C28 C29 SING N N 5
SDO C29 C30 SING N N 6
SDO C29 C31 SING N N 7
SDO C29 C32 SING N N 8
SDO C32 O33 SING N N 9
SDO C32 C34 SING N N 10
SDO C34 O35 DOUB N N 11
SDO C34 N36 SING N N 12
SDO N36 C37 SING N N 13
SDO C37 C38 SING N N 14
SDO C38 C39 SING N N 15
SDO C39 O40 DOUB N N 16
SDO C39 N41 SING N N 17
SDO N41 C42 SING N N 18
SDO C42 C43 SING N N 19
SDO C43 S1 SING N N 20
SDO S1 C1 SING N N 21
SDO C1 C2 SING N N 22
SDO C2 C3 SING N N 23
SDO C3 O3 DOUB N N 24
SDO C3 C4 SING N N 25
SDO C4 C5 SING N N 26
SDO C5 C6 SING N N 27
SDO C6 C7 SING N N 28
SDO C7 O7 DOUB N N 29
SDO C7 C8 SING N N 30
SDO O26 H1 SING N N 31
SDO O23 H2 SING N N 32
SDO C28 H28A SING N N 33
SDO C28 H28B SING N N 34
SDO C30 H30A SING N N 35
SDO C30 H30B SING N N 36
SDO C30 H30C SING N N 37
SDO C31 H31A SING N N 38
SDO C31 H31B SING N N 39
SDO C31 H31C SING N N 40
SDO C32 H32A SING N N 41
SDO O33 H33A SING N N 42
SDO N36 H36A SING N N 43
SDO C37 H37A SING N N 44
SDO C37 H37B SING N N 45
SDO C38 H38A SING N N 46
SDO C38 H38B SING N N 47
SDO N41 H41A SING N N 48
SDO C42 H42A SING N N 49
SDO C42 H42B SING N N 50
SDO C43 H43A SING N N 51
SDO C43 H43B SING N N 52
SDO C1 H1A SING N N 53
SDO C1 H1B SING N N 54
SDO C2 H2A SING N N 55
SDO C2 H2B SING N N 56
SDO C4 H4A SING N N 57
SDO C4 H4B SING N N 58
SDO C5 H5A SING N N 59
SDO C5 H5B SING N N 60
SDO C6 H6A SING N N 61
SDO C6 H6B SING N N 62
SDO C8 H8A SING N N 63
SDO C8 H8B SING N N 64
SDO C8 H8C SING N N 65
#
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
SDO SMILES ACDLabs 12.01 "O=C(NCCSCCC(=O)CCCC(=O)C)CCNC(=O)C(O)C(C)(C)COP(O)O"
SDO InChI InChI 1.03 "InChI=1S/C19H35N2O8PS/c1-14(22)5-4-6-15(23)8-11-31-12-10-20-16(24)7-9-21-18(26)17(25)19(2,3)13-29-30(27)28/h17,25,27-28H,4-13H2,1-3H3,(H,20,24)(H,21,26)/t17-/m1/s1"
SDO InChIKey InChI 1.03 TUVOCCHXVSLSRA-QGZVFWFLSA-N
SDO SMILES_CANONICAL CACTVS 3.385 "CC(=O)CCCC(=O)CCSCCNC(=O)CCNC(=O)[C@@H](O)C(C)(C)COP(O)O"
SDO SMILES CACTVS 3.385 "CC(=O)CCCC(=O)CCSCCNC(=O)CCNC(=O)[CH](O)C(C)(C)COP(O)O"
SDO SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC(=O)CCCC(=O)CCSCCNC(=O)CCNC(=O)[C@H](C(C)(C)COP(O)O)O"
SDO SMILES "OpenEye OEToolkits" 1.7.6 "CC(=O)CCCC(=O)CCSCCNC(=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
SDO "SYSTEMATIC NAME" ACDLabs 12.01 "N~3~-{(2S)-4-[(dihydroxyphosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-N-{2-[(3,7-dioxooctyl)sulfanyl]ethyl}-beta-alaninamide"
SDO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(3S)-4-[[3-[2-[3,7-bis(oxidanylidene)octylsulfanyl]ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphite"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
SDO "Create component" 2014-10-16 RCSB
SDO "Initial release" 2015-10-21 RCSB
SDO "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id SDO
_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 ?
#