Chemical Components in the PDB

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L9Q : Summary

Code

L9Q

One-letter code

X

Molecule name

(1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate

Synonyms

1-stearoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine

Systematic names

ProgramVersionName
ACDLabs 12.01 (21S,24S)-27-amino-24-hydroxy-24-oxido-18-oxo-19,23,25-trioxa-24lambda~5~-phosphaheptacosan-21-yl (9Z)-octadec-9-enoate
OpenEye OEToolkits 1.7.0 [(2S)-3-[2-azanylethoxy(hydroxy)phosphoryl]oxy-2-[(Z)-octadec-9-enoyl]oxy-propyl] octadecanoate

Formula

C41 H80 N O8 P

Formal charge

0

Molecular weight

746.05 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(OCC(OC(=O)CCCCCCC\C=C/CCCCCCCC)COP(=O)(OCCN)O)CCCCCCCCCCCCCCCCC
SMILES CACTVS 3.370 CCCCCCCCCCCCCCCCCC(=O)OC[CH](CO[P](O)(=O)OCCN)OC(=O)CCCCCCCC=CCCCCCCCC
SMILES OpenEye OEToolkits 1.7.0 CCCCCCCCCCCCCCCCCC(=O)OCC(COP(=O)(O)OCCN)OC(=O)CCCCCCCC=CCCCCCCCC
Canonical SMILES CACTVS 3.370 CCCCCCCCCCCCCCCCCC(=O)OC[C@@H](CO[P](O)(=O)OCCN)OC(=O)CCCCCCC\C=C/CCCCCCCC
Canonical SMILES OpenEye OEToolkits 1.7.0 CCCCCCCCCCCCCCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)CCCCCCC/C=C\CCCCCCCC

IUPAC InChI

InChI=1S/C41H80NO8P/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-40(43)47-37-39(38-49-51(45,46)48-36-35-42)50-41(44)34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h18,20,39H,3-17,19,21-38,42H2,1-2H3,(H,45,46)/b20-18-/t39-/m0/s1

IUPAC InChI key

JQKOHRZNEOQNJE-VYCVAHKRSA-N
L9Q

wwPDB Information

Atom count

131 (51 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2010-03-19

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



L9Q : Atoms of Molecule

Total Number of Atoms: 131
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N N N N N N 0 0.865 -0.218 4.097
2 P P P N N N 0 -0.209 -4.227 2.633
3 C1 C C1 N N N 0 -1.384 -5.106 0.4
4 C2 C C2 S N N 0 -1.524 -4.725 -1.075
5 O2 O O2 N N N 0 -2.246 -3.47 -1.185
6 C3 C C3 N N N 0 -0.134 -4.57 -1.696
7 O3 O O3 N N N 0 0.637 -3.614 -0.922
8 C4 C C4 N N N 0 0.99 -2.642 4.42
9 C11 C C11 N N N 0 1.889 -3.362 -1.337
10 C5 C C5 N N N 0 1.757 -1.32 4.481
11 O11 O O11 N N N 0 2.325 -3.922 -2.314
12 C12 C C12 N N N 0 2.75 -2.381 -0.583
13 C13 C C13 N N N 0 4.118 -2.279 -1.26
14 C14 C C14 N N N 0 4.992 -1.283 -0.495
15 C15 C C15 N N N 0 6.361 -1.181 -1.171
16 C16 C C16 N N N 0 7.235 -0.185 -0.406
17 C17 C C17 N N N 0 8.603 -0.083 -1.082
18 C18 C C18 N N N 0 9.477 0.913 -0.318
19 C19 C C19 N N N 0 10.846 1.015 -0.994
20 O1P O O1P N N N 0 -1.458 -4.309 3.422
21 C20 C C20 N N N 0 11.72 2.011 -0.229
22 C24 C C24 N N N 0 16.205 4.207 -0.052
23 C21 C C21 N N N 0 13.088 2.113 -0.905
24 C22 C C22 N N N 0 13.962 3.109 -0.14
25 C23 C C23 N N N 0 15.331 3.211 -0.817
26 C25 C C25 N N N 0 17.573 4.309 -0.728
27 C26 C C26 N N N 0 18.447 5.305 0.037
28 C27 C C27 N N N 0 19.816 5.407 -0.64
29 C28 C C28 N N N 0 20.69 6.403 0.125
30 O2P O O2P N N N 0 0.687 -5.536 2.907
31 C31 C C31 N N N 0 -3.582 -3.543 -1.288
32 O31 O O31 N N N 0 -4.131 -4.619 -1.286
33 C32 C C32 N N N 0 -4.399 -2.282 -1.405
34 C33 C C33 N N N 0 -5.882 -2.642 -1.508
35 C34 C C34 N N N 0 -6.711 -1.362 -1.627
36 C35 C C35 N N N 0 -8.195 -1.722 -1.729
37 C36 C C36 N N N 0 -9.024 -0.442 -1.849
38 C37 C C37 N N N 0 -10.507 -0.802 -1.951
39 C38 C C38 N N N 0 -11.336 0.478 -2.07
40 C39 C C39 N N N 0 -12.797 0.123 -2.171
41 O3P O O3P N N N 0 -0.568 -4.14 1.066
42 C40 C C40 N N N 0 -13.664 0.679 -1.361
43 C41 C C41 N N N 0 -13.231 1.794 -0.445
44 C42 C C42 N N N 0 -14.148 3.003 -0.645
45 C43 C C43 N N N 0 -13.708 4.135 0.285
46 C44 C C44 N N N 0 -14.625 5.344 0.085
47 C45 C C45 N N N 0 -14.186 6.477 1.015
48 C46 C C46 N N N 0 -15.102 7.685 0.815
49 C47 C C47 N N N 0 -14.663 8.818 1.745
50 C48 C C48 N N N 0 -15.58 10.027 1.545
51 O4P O O4P N N N 0 0.615 -2.913 3.068
52 HN H HN N N N 0 0.041 -0.2 4.678
53 HNA H HNA N N N 0 1.349 0.667 4.129
54 H1 H H1 N N N 0 -2.37 -5.129 0.864
55 H1A H H1A N N N 0 -0.922 -6.089 0.479
56 H2 H H2 N N N 0 -2.072 -5.506 -1.602
57 H3 H H3 N N N 0 0.374 -5.534 -1.694
58 H3A H H3A N N N 0 -0.232 -4.213 -2.721
59 H4 H H4 N N N 0 1.624 -3.448 4.79
60 H4A H H4A N N N 0 0.095 -2.572 5.038
61 H5 H H5 N N N 0 2.603 -1.359 3.795
62 H5A H H5A N N N 0 2.12 -1.157 5.496
63 H12 H H12 N N N 0 2.27 -1.402 -0.583
64 H12A H H12A N N N 0 2.876 -2.723 0.444
65 H13 H H13 N N N 0 4.597 -3.258 -1.259
66 H13A H H13A N N N 0 3.991 -1.937 -2.287
67 H14 H H14 N N N 0 4.513 -0.304 -0.495
68 H14A H H14A N N N 0 5.119 -1.625 0.533
69 H15 H H15 N N N 0 6.84 -2.16 -1.171
70 H15A H H15A N N N 0 6.234 -0.839 -2.198
71 H16 H H16 N N N 0 6.755 0.794 -0.406
72 H16A H H16A N N N 0 7.362 -0.527 0.621
73 H17 H H17 N N N 0 9.083 -1.062 -1.082
74 H19 H H19 N N N 0 11.325 0.036 -0.994
75 H17A H H17A N N N 0 8.476 0.259 -2.11
76 H18 H H18 N N N 0 8.998 1.892 -0.318
77 H18A H H18A N N N 0 9.604 0.571 0.71
78 H19A H H19A N N N 0 10.719 1.357 -2.021
79 H20 H H20 N N N 0 11.24 2.99 -0.229
80 H20A H H20A N N N 0 11.847 1.669 0.798
81 H21 H H21 N N N 0 13.568 1.134 -0.905
82 H21A H H21A N N N 0 12.961 2.455 -1.933
83 H22 H H22 N N N 0 13.483 4.088 -0.141
84 H22A H H22A N N N 0 14.089 2.767 0.887
85 H23 H H23 N N N 0 15.81 2.232 -0.817
86 H23A H H23A N N N 0 15.204 3.553 -1.844
87 H24 H H24 N N N 0 15.725 5.186 -0.052
88 H24A H H24A N N N 0 16.332 3.865 0.975
89 H25 H H25 N N N 0 18.052 3.33 -0.728
90 H25A H H25A N N N 0 17.446 4.651 -1.755
91 H26 H H26 N N N 0 17.968 6.284 0.036
92 H26A H H26A N N N 0 18.574 4.963 1.064
93 H27 H H27 N N N 0 20.295 4.428 -0.64
94 H27A H H27A N N N 0 19.689 5.749 -1.667
95 H28 H H28 N N N 0 20.21 7.382 0.125
96 H28A H H28A N N N 0 20.817 6.061 1.152
97 H28B H H28B N N N 0 21.665 6.476 -0.357
98 HO2P H HO2P N N N 0 1.523 -5.55 2.421
99 H32 H H32 N N N 0 -4.236 -1.66 -0.525
100 H32A H H32A N N N 0 -4.096 -1.734 -2.298
101 H33 H H33 N N N 0 -6.045 -3.264 -2.388
102 H33A H H33A N N N 0 -6.186 -3.19 -0.615
103 H34 H H34 N N N 0 -6.549 -0.74 -0.747
104 H34A H H34A N N N 0 -6.408 -0.814 -2.519
105 H35 H H35 N N N 0 -8.358 -2.344 -2.61
106 H35A H H35A N N N 0 -8.498 -2.27 -0.837
107 H36 H H36 N N N 0 -8.861 0.18 -0.968
108 H36A H H36A N N N 0 -8.72 0.106 -2.741
109 H37 H H37 N N N 0 -10.67 -1.424 -2.832
110 H37A H H37A N N N 0 -10.811 -1.35 -1.059
111 H38 H H38 N N N 0 -11.173 1.1 -1.19
112 H38A H H38A N N N 0 -11.033 1.026 -2.963
113 H39 H H39 N N N 0 -13.13 -0.589 -2.912
114 H40 H H40 N N N 0 -14.688 0.337 -1.349
115 H41 H H41 N N N 0 -13.293 1.459 0.59
116 H41A H H41A N N N 0 -12.203 2.076 -0.675
117 H42 H H42 N N N 0 -14.086 3.338 -1.68
118 H42A H H42A N N N 0 -15.175 2.721 -0.415
119 H43 H H43 N N N 0 -13.77 3.8 1.321
120 H43A H H43A N N N 0 -12.681 4.417 0.055
121 H44 H H44 N N N 0 -14.563 5.68 -0.95
122 H44A H H44A N N N 0 -15.653 5.063 0.315
123 H45 H H45 N N N 0 -14.247 6.141 2.05
124 H45A H H45A N N N 0 -13.158 6.758 0.785
125 H46 H H46 N N N 0 -15.041 8.021 -0.22
126 H46A H H46A N N N 0 -16.13 7.404 1.046
127 H47 H H47 N N N 0 -14.725 8.483 2.781
128 H47A H H47A N N N 0 -13.635 9.099 1.515
129 H48 H H48 N N N 0 -15.518 10.362 0.51
130 H48A H H48A N N N 0 -16.607 9.745 1.776
131 H48B H H48B N N N 0 -15.267 10.834 2.208



L9Q : Chemical Bonds

Total Number of Bonds: 130
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C5 N C N sing 1.47 N N
2 N HN N H sing 1.01 N N
3 N HNA N H sing 1.01 N N
4 O3P P O P sing 1.61 N N
5 O1P P O P doub 1.48 N N
6 P O2P P O sing 1.61 N N
7 P O4P P O sing 1.61 N N
8 C2 C1 C C sing 1.53 N N
9 O3P C1 O C sing 1.43 N N
10 C1 H1 C H sing 1.09 N N
11 C1 H1A C H sing 1.09 N N
12 C3 C2 C C sing 1.53 N N
13 C2 O2 C O sing 1.45 N N
14 C2 H2 C H sing 1.09 N N
15 C31 O2 C O sing 1.34 N N
16 O3 C3 O C sing 1.45 N N
17 C3 H3 C H sing 1.09 N N
18 C3 H3A C H sing 1.09 N N
19 C11 O3 C O sing 1.34 N N
20 O4P C4 O C sing 1.43 N N
21 C4 C5 C C sing 1.53 N N
22 C4 H4 C H sing 1.09 N N
23 C4 H4A C H sing 1.09 N N
24 C5 H5 C H sing 1.09 N N
25 C5 H5A C H sing 1.09 N N
26 C12 C11 C C sing 1.51 N N
27 O11 C11 O C doub 1.21 N N
28 C12 C13 C C sing 1.53 N N
29 C12 H12 C H sing 1.09 N N
30 C12 H12A C H sing 1.09 N N
31 C14 C13 C C sing 1.53 N N
32 C13 H13 C H sing 1.09 N N
33 C13 H13A C H sing 1.09 N N
34 C15 C14 C C sing 1.53 N N
35 C14 H14 C H sing 1.09 N N
36 C14 H14A C H sing 1.09 N N
37 C16 C15 C C sing 1.53 N N
38 C15 H15 C H sing 1.09 N N
39 C15 H15A C H sing 1.09 N N
40 C16 C17 C C sing 1.53 N N
41 C16 H16 C H sing 1.09 N N
42 C16 H16A C H sing 1.09 N N
43 C17 C18 C C sing 1.53 N N
44 C17 H17 C H sing 1.09 N N
45 C17 H17A C H sing 1.09 N N
46 C19 C18 C C sing 1.53 N N
47 C18 H18 C H sing 1.09 N N
48 C18 H18A C H sing 1.09 N N
49 C19 C20 C C sing 1.53 N N
50 C19 H19 C H sing 1.09 N N
51 C19 H19A C H sing 1.09 N N
52 C21 C20 C C sing 1.53 N N
53 C20 H20 C H sing 1.09 N N
54 C20 H20A C H sing 1.09 N N
55 C21 C22 C C sing 1.53 N N
56 C21 H21 C H sing 1.09 N N
57 C21 H21A C H sing 1.09 N N
58 C23 C22 C C sing 1.53 N N
59 C22 H22 C H sing 1.09 N N
60 C22 H22A C H sing 1.09 N N
61 C23 C24 C C sing 1.53 N N
62 C23 H23 C H sing 1.09 N N
63 C23 H23A C H sing 1.09 N N
64 C25 C24 C C sing 1.53 N N
65 C24 H24 C H sing 1.09 N N
66 C24 H24A C H sing 1.09 N N
67 C25 C26 C C sing 1.53 N N
68 C25 H25 C H sing 1.09 N N
69 C25 H25A C H sing 1.09 N N
70 C27 C26 C C sing 1.53 N N
71 C26 H26 C H sing 1.09 N N
72 C26 H26A C H sing 1.09 N N
73 C28 C27 C C sing 1.53 N N
74 C27 H27 C H sing 1.09 N N
75 C27 H27A C H sing 1.09 N N
76 C28 H28 C H sing 1.09 N N
77 C28 H28A C H sing 1.09 N N
78 C28 H28B C H sing 1.09 N N
79 O2P HO2P O H sing 0.97 N N
80 C32 C31 C C sing 1.51 N N
81 C31 O31 C O doub 1.21 N N
82 C32 C33 C C sing 1.53 N N
83 C32 H32 C H sing 1.09 N N
84 C32 H32A C H sing 1.09 N N
85 C34 C33 C C sing 1.53 N N
86 C33 H33 C H sing 1.09 N N
87 C33 H33A C H sing 1.09 N N
88 C34 C35 C C sing 1.53 N N
89 C34 H34 C H sing 1.09 N N
90 C34 H34A C H sing 1.09 N N
91 C36 C35 C C sing 1.53 N N
92 C35 H35 C H sing 1.09 N N
93 C35 H35A C H sing 1.09 N N
94 C36 C37 C C sing 1.53 N N
95 C36 H36 C H sing 1.09 N N
96 C36 H36A C H sing 1.09 N N
97 C38 C37 C C sing 1.53 N N
98 C37 H37 C H sing 1.09 N N
99 C37 H37A C H sing 1.09 N N
100 C39 C38 C C sing 1.51 Z N
101 C38 H38 C H sing 1.09 N N
102 C38 H38A C H sing 1.09 N N
103 C39 C40 C C doub 1.31 N N
104 C39 H39 C H sing 1.08 N N
105 C40 C41 C C sing 1.51 N N
106 C40 H40 C H sing 1.08 N N
107 C41 C42 C C sing 1.53 N N
108 C41 H41 C H sing 1.09 N N
109 C41 H41A C H sing 1.09 N N
110 C42 C43 C C sing 1.53 N N
111 C42 H42 C H sing 1.09 N N
112 C42 H42A C H sing 1.09 N N
113 C43 C44 C C sing 1.53 N N
114 C43 H43 C H sing 1.09 N N
115 C43 H43A C H sing 1.09 N N
116 C44 C45 C C sing 1.53 N N
117 C44 H44 C H sing 1.09 N N
118 C44 H44A C H sing 1.09 N N
119 C45 C46 C C sing 1.53 N N
120 C45 H45 C H sing 1.09 N N
121 C45 H45A C H sing 1.09 N N
122 C46 C47 C C sing 1.53 N N
123 C46 H46 C H sing 1.09 N N
124 C46 H46A C H sing 1.09 N N
125 C47 C48 C C sing 1.53 N N
126 C47 H47 C H sing 1.09 N N
127 C47 H47A C H sing 1.09 N N
128 C48 H48 C H sing 1.09 N N
129 C48 H48A C H sing 1.09 N N
130 C48 H48B C H sing 1.09 N N



L9Q : Used in PDB Entries

Total Number of PDB Entries: 8
Ligand Code PDB Entry ID Type Total Distinct
L9Q 3l9r Open in New Window Bound ligand 2 1
L9Q 6or2 Open in New Window Bound ligand 1 1
L9Q 6w2x Open in New Window Bound ligand 2 1
L9Q 6w2y Open in New Window Bound ligand 2 1
L9Q 8glg Open in New Window Bound ligand 1 1
L9Q 8hsi Open in New Window Bound ligand 1 1
L9Q 8ifu Open in New Window Bound ligand 6 1
L9Q 8k1m Open in New Window Bound ligand 1 1