data_S12
#
_chem_comp.id S12
_chem_comp.name "O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine"
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C24 H46 N O9 P"
_chem_comp.mon_nstd_parent_comp_id SER
_chem_comp.pdbx_synonyms 1-oleoyl-2-hydroxy-sn-glycero-3-phospho-L-serine
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2012-03-29
_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 523.597
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code S12
_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 4EAX
_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
S12 C C C 0 1 N N N 5.641 9.475 -2.115 12.977 -1.245 1.233 C S12 1
S12 N N N 0 1 N N N 5.256 9.744 -4.478 11.896 0.905 0.896 N S12 2
S12 P P P 0 1 N N N 7.702 6.741 -5.451 8.225 -0.914 -0.711 P S12 3
S12 OG OG O 0 1 N N N 7.043 7.828 -4.450 9.451 -0.506 0.249 O1 S12 4
S12 C2 C2 C 0 1 N N N 6.885 6.025 -7.933 5.622 -0.326 -0.858 C2 S12 5
S12 O2 O2 O 0 1 N N N 6.647 6.678 -6.683 6.905 -0.106 -0.266 O2 S12 6
S12 C3 C3 C 0 1 N N S 5.907 6.589 -8.973 4.595 0.602 -0.206 C3 S12 7
S12 O3 O3 O 0 1 N N N 7.738 5.416 -4.734 7.974 -2.368 -0.601 O3 S12 8
S12 C4 C4 C 0 1 N N N 6.046 5.890 -10.342 3.201 0.282 -0.750 C4 S12 9
S12 O4 O4 O 0 1 N N N 9.146 7.455 -6.055 8.591 -0.546 -2.235 O4 S12 10
S12 C5 C5 C 0 1 N N N 4.785 5.778 -12.548 0.929 0.916 -0.407 C5 S12 11
S12 C6 C6 C 0 1 N N N 4.166 6.481 -13.750 -0.153 1.710 0.278 C6 S12 12
S12 C7 C7 C 0 1 N N N 4.952 6.494 -15.057 -1.513 1.337 -0.316 C7 S12 13
S12 C8 C8 C 0 1 N N N 4.370 7.106 -16.110 -2.611 2.143 0.380 C8 S12 14
S12 C9 C9 C 0 1 N N N 4.995 7.241 -17.498 -3.971 1.770 -0.214 C9 S12 15
S12 CA CA C 0 1 N N S 5.111 8.824 -3.363 11.663 -0.508 1.224 CA S12 16
S12 CB CB C 0 1 N N N 5.868 7.537 -3.684 10.736 -1.129 0.177 CB S12 17
S12 C10 C10 C 0 1 N N N 4.069 7.801 -18.582 -5.070 2.576 0.481 C10 S12 18
S12 C11 C11 C 0 1 N N N 4.613 8.185 -19.743 -6.430 2.203 -0.113 C11 S12 19
S12 O11 O11 O 0 1 N N N 6.138 8.009 -9.062 4.922 1.961 -0.506 O11 S12 20
S12 C12 C12 C 0 1 N N N 6.064 8.007 -19.767 -7.529 3.009 0.583 C12 S12 21
S12 C13 C13 C 0 1 N N N 6.809 8.294 -20.735 -8.868 2.642 -0.002 C13 S12 22
S12 C14 C14 C 0 1 N N N 7.598 8.568 -21.677 -9.833 2.228 0.781 C14 S12 23
S12 O51 O51 O 0 1 N N N 4.832 4.555 -12.525 0.643 0.132 -1.281 O51 S12 24
S12 O52 O52 O 0 1 N N N 5.264 6.523 -11.370 2.212 1.079 -0.047 O52 S12 25
S12 O O O 0 1 N N N 4.872 9.589 -1.128 13.933 -0.783 0.657 OT1 S12 26
S12 OXT OXT O 0 1 N Y N 6.993 9.942 -2.101 13.086 -2.414 1.885 OT2 S12 27
S12 H H H 0 1 N N N 4.905 9.317 -5.311 12.325 0.998 -0.013 HN S12 28
S12 H2 H2 H 0 1 N Y N 4.740 10.580 -4.290 11.039 1.435 0.947 HNA S12 29
S12 H2B H2B H 0 1 N N N 7.919 6.211 -8.258 5.674 -0.117 -1.926 H2 S12 30
S12 H2A H2A H 0 1 N N N 6.725 4.942 -7.822 5.324 -1.363 -0.704 H2A S12 31
S12 H3 H3 H 0 1 N N N 4.885 6.412 -8.607 4.606 0.456 0.874 H3 S12 32
S12 H4 H4 H 0 1 N N N 7.104 5.910 -10.642 3.164 0.513 -1.814 H4 S12 33
S12 H4A H4A H 0 1 N N N 5.714 4.846 -10.240 2.987 -0.777 -0.600 H4A S12 34
S12 H6 H6 H 0 1 N N N 3.202 5.992 -13.953 -0.148 1.485 1.345 H6 S12 35
S12 H6A H6A H 0 1 N N N 3.993 7.529 -13.462 0.029 2.774 0.130 H6A S12 36
S12 H7 H7 H 0 1 N N N 5.909 7.001 -14.865 -1.517 1.562 -1.383 H7 S12 37
S12 H8 H8 H 0 1 N N N 3.418 6.578 -16.267 -2.607 1.918 1.446 H8 S12 38
S12 H9 H9 H 0 1 N N N 5.865 7.910 -17.415 -3.976 1.995 -1.281 H9 S12 39
S12 H9A H9A H 0 1 N N N 5.329 6.243 -17.819 -4.153 0.705 -0.067 H9A S12 40
S12 HA HA H 0 1 N N N 4.048 8.582 -3.217 11.199 -0.580 2.208 HA S12 41
S12 HB2 HB2 H 0 1 N N N 5.215 6.867 -4.262 10.633 -2.197 0.370 HB S12 42
S12 HB3 HB3 H 0 1 N N N 6.160 7.044 -2.745 11.158 -0.978 -0.816 HBA S12 43
S12 H10 H10 H 0 1 N N N 3.327 7.022 -18.811 -5.065 2.351 1.548 H10 S12 44
S12 H11 H11 H 0 1 N N N 4.171 7.588 -20.554 -6.434 2.428 -1.179 H11 S12 45
S12 HO11 HO11 H 0 0 N N N 5.545 8.387 -9.700 4.931 2.164 -1.451 HO11 S12 46
S12 H12 H12 H 0 1 N N N 6.445 8.595 -18.919 -7.524 2.784 1.650 H12 S12 47
S12 H14 H14 H 0 1 N N N 8.047 9.548 -21.738 -9.670 2.151 1.845 H14 S12 48
S12 C15 C15 C 0 1 N N N 7.826 7.823 -22.424 -11.173 1.861 0.196 C17 S12 49
S12 C16 C16 C 0 1 N N N 8.977 7.799 -23.826 -11.540 0.437 0.617 C18 S12 50
S12 C17 C17 C 0 1 N N N 9.303 6.736 -24.892 -12.900 0.064 0.022 C19 S12 51
S12 C18 C18 C 0 1 N N N 10.357 7.029 -25.976 -13.267 -1.360 0.443 C20 S12 52
S12 C19 C19 C 0 1 N N N 10.682 5.966 -27.042 -14.627 -1.733 -0.151 C21 S12 53
S12 C20 C20 C 0 1 N N N 11.737 6.260 -28.125 -14.994 -3.158 0.270 C22 S12 54
S12 C21 C21 C 0 1 N N N 12.062 5.197 -29.191 -16.354 -3.530 -0.324 C23 S12 55
S12 C22 C22 C 0 1 N N N 13.116 5.490 -30.274 -16.721 -4.955 0.097 C24 S12 56
S12 H22 H22 H 0 1 N N N 9.885 6.892 -5.858 8.768 0.393 -2.381 H22 S12 57
S12 H23 H23 H 0 1 N N N 5.141 5.449 -15.342 -1.694 0.272 -0.169 H23 S12 58
S12 H24 H24 H 0 1 N N N 4.169 8.135 -15.777 -2.430 3.207 0.232 H24 S12 59
S12 H25 H25 H 0 1 N N N 3.560 8.678 -18.155 -4.889 3.640 0.334 H25 S12 60
S12 H26 H26 H 0 1 N N N 4.385 9.249 -19.905 -6.611 1.138 0.035 H26 S12 61
S12 H27 H27 H 0 1 N N N 6.231 6.937 -19.576 -7.347 4.074 0.435 H27 S12 62
S12 H28 H28 H 0 1 N N N 5.958 8.580 -21.335 -9.031 2.719 -1.067 H28 S12 63
S12 HXT HXT H 0 1 N Y N 7.186 10.330 -1.256 13.949 -2.850 1.862 H29 S12 64
S12 H30 H30 H 0 1 N N N 8.132 6.950 -21.828 -11.931 2.555 0.560 H30 S12 65
S12 H31 H31 H 0 1 N N N 6.850 7.624 -22.892 -11.122 1.917 -0.892 H31 S12 66
S12 H32 H32 H 0 1 N N N 8.671 8.672 -24.422 -10.782 -0.257 0.252 H32 S12 67
S12 H33 H33 H 0 1 N N N 9.952 7.998 -23.358 -11.591 0.381 1.704 H33 S12 68
S12 H34 H34 H 0 1 N N N 9.643 5.840 -24.353 -13.658 0.757 0.387 H34 S12 69
S12 H35 H35 H 0 1 N N N 8.362 6.513 -25.416 -12.849 0.120 -1.065 H35 S12 70
S12 H36 H36 H 0 1 N N N 10.017 7.926 -26.515 -12.509 -2.054 0.079 H36 S12 71
S12 H37 H37 H 0 1 N N N 11.298 7.251 -25.452 -13.318 -1.416 1.531 H37 S12 72
S12 H38 H38 H 0 1 N N N 11.021 5.069 -26.503 -15.385 -1.040 0.213 H38 S12 73
S12 H39 H39 H 0 1 N N N 9.741 5.744 -27.567 -14.576 -1.677 -1.238 H39 S12 74
S12 H40 H40 H 0 1 N N N 11.398 7.157 -28.664 -14.236 -3.851 -0.094 H40 S12 75
S12 H41 H41 H 0 1 N N N 12.678 6.482 -27.600 -15.045 -3.213 1.357 H41 S12 76
S12 H42 H42 H 0 1 N N N 12.401 4.300 -28.652 -17.112 -2.837 0.040 H42 S12 77
S12 H43 H43 H 0 1 N N N 11.121 4.975 -29.716 -16.303 -3.474 -1.411 H43 S12 78
S12 H44 H44 H 0 1 N N N 13.210 4.619 -30.940 -17.690 -5.220 -0.326 H44 S12 79
S12 H45 H45 H 0 1 N N N 12.805 6.368 -30.860 -15.963 -5.648 -0.267 H45 S12 80
S12 H46 H46 H 0 1 N N N 14.086 5.693 -29.796 -16.772 -5.011 1.184 H46 S12 81
# #
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
S12 C CA SING N N 1
S12 C O DOUB N N 2
S12 C OXT SING N N 3
S12 N CA SING N N 4
S12 N H SING N N 5
S12 N H2 SING N N 6
S12 P OG SING N N 7
S12 P O2 SING N N 8
S12 P O3 DOUB N N 9
S12 P O4 SING N N 10
S12 OG CB SING N N 11
S12 C2 O2 SING N N 12
S12 C2 C3 SING N N 13
S12 C2 H2B SING N N 14
S12 C2 H2A SING N N 15
S12 C3 C4 SING N N 16
S12 C3 O11 SING N N 17
S12 C3 H3 SING N N 18
S12 C4 O52 SING N N 19
S12 C4 H4 SING N N 20
S12 C4 H4A SING N N 21
S12 C5 C6 SING N N 22
S12 C5 O51 DOUB N N 23
S12 C5 O52 SING N N 24
S12 C6 C7 SING N N 25
S12 C6 H6 SING N N 26
S12 C6 H6A SING N N 27
S12 C7 C8 SING N N 28
S12 C7 H7 SING N N 29
S12 C8 C9 SING N N 30
S12 C8 H8 SING N N 31
S12 C9 C10 SING N N 32
S12 C9 H9 SING N N 33
S12 C9 H9A SING N N 34
S12 CA CB SING N N 35
S12 CA HA SING N N 36
S12 CB HB2 SING N N 37
S12 CB HB3 SING N N 38
S12 C10 C11 SING N N 39
S12 C10 H10 SING N N 40
S12 C11 C12 SING N N 41
S12 C11 H11 SING N N 42
S12 O11 HO11 SING N N 43
S12 C12 C13 SING N N 44
S12 C12 H12 SING N N 45
S12 C13 C14 DOUB N E 46
S12 C14 H14 SING N N 47
S12 C14 C15 SING N N 48
S12 C15 C16 SING N N 49
S12 C16 C17 SING N N 50
S12 C17 C18 SING N N 51
S12 C18 C19 SING N N 52
S12 C19 C20 SING N N 53
S12 C20 C21 SING N N 54
S12 C21 C22 SING N N 55
S12 O4 H22 SING N N 56
S12 C7 H23 SING N N 57
S12 C8 H24 SING N N 58
S12 C10 H25 SING N N 59
S12 C11 H26 SING N N 60
S12 C12 H27 SING N N 61
S12 C13 H28 SING N N 62
S12 OXT HXT SING N N 63
S12 C15 H30 SING N N 64
S12 C15 H31 SING N N 65
S12 C16 H32 SING N N 66
S12 C16 H33 SING N N 67
S12 C17 H34 SING N N 68
S12 C17 H35 SING N N 69
S12 C18 H36 SING N N 70
S12 C18 H37 SING N N 71
S12 C19 H38 SING N N 72
S12 C19 H39 SING N N 73
S12 C20 H40 SING N N 74
S12 C20 H41 SING N N 75
S12 C21 H42 SING N N 76
S12 C21 H43 SING N N 77
S12 C22 H44 SING N N 78
S12 C22 H45 SING N N 79
S12 C22 H46 SING N N 80
# #
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
S12 SMILES ACDLabs 12.01 "O=C(O)C(N)COP(=O)(OCC(O)COC(=O)CCCCCCC/C=C/CCCCCCCC)O"
S12 InChI InChI 1.03 "InChI=1S/C24H46NO9P/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-23(27)32-18-21(26)19-33-35(30,31)34-20-22(25)24(28)29/h9-10,21-22,26H,2-8,11-20,25H2,1H3,(H,28,29)(H,30,31)/t21-,22-/m0/s1"
S12 InChIKey InChI 1.03 JZWNYZVVZXZRRH-VXKWHMMOSA-N
S12 SMILES_CANONICAL CACTVS 3.370 "CCCCCCCC/C=C/CCCCCCCC(=O)OC[C@H](O)CO[P](O)(=O)OC[C@H](N)C(O)=O"
S12 SMILES CACTVS 3.370 "CCCCCCCCC=CCCCCCCCC(=O)OC[CH](O)CO[P](O)(=O)OC[CH](N)C(O)=O"
S12 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CCCCCCCCC=CCCCCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OC[C@@H](C(=O)O)N)O"
S12 SMILES "OpenEye OEToolkits" 1.7.6 "CCCCCCCCC=CCCCCCCCC(=O)OCC(COP(=O)(O)OCC(C(=O)O)N)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
S12 "SYSTEMATIC NAME" ACDLabs 12.01 "O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine"
S12 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2S)-2-azanyl-3-[[(2S)-3-octadec-9-enoyloxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-propanoic 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
S12 "Create component" 2012-03-29 PDBJ
S12 "Initial release" 2012-09-07 RCSB
S12 "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id S12
_pdbx_chem_comp_synonyms.name 1-oleoyl-2-hydroxy-sn-glycero-3-phospho-L-serine
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##