Chemical Components in the PDB

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9PE : Summary

Code

9PE

One-letter code

X

Molecule name

(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate

Systematic names

ProgramVersionName
ACDLabs 10.04 (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate
OpenEye OEToolkits 1.5.0 [(2R)-1-(2-aminoethoxy-hydroxy-phosphoryl)oxy-3-heptanoyloxy-propan-2-yl] octadecanoate

Formula

C30 H60 N O8 P

Formal charge

0

Molecular weight

593.773 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(OCC(OC(=O)CCCCCCCCCCCCCCCCC)COP(=O)(OCCN)O)CCCCCC
SMILES CACTVS 3.341 CCCCCCCCCCCCCCCCCC(=O)O[CH](COC(=O)CCCCCC)CO[P](O)(=O)OCCN
SMILES OpenEye OEToolkits 1.5.0 CCCCCCCCCCCCCCCCCC(=O)OC(COC(=O)CCCCCC)COP(=O)(O)OCCN
Canonical SMILES CACTVS 3.341 CCCCCCCCCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCC)CO[P@](O)(=O)OCCN
Canonical SMILES OpenEye OEToolkits 1.5.0 CCCCCCCCCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCC)CO[P@@](=O)(O)OCCN

IUPAC InChI

InChI=1S/C30H60NO8P/c1-3-5-7-9-10-11-12-13-14-15-16-17-18-19-21-23-30(33)39-28(27-38-40(34,35)37-25-24-31)26-36-29(32)22-20-8-6-4-2/h28H,3-27,31H2,1-2H3,(H,34,35)/t28-/m1/s1

IUPAC InChI key

RWBMCOYSJCETON-MUUNZHRXSA-N
9PE

wwPDB Information

Atom count

100 (40 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2008-04-28

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



9PE : Atoms of Molecule

Total Number of Atoms: 100
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 P P P S N N 0 -5.574 2.729 -0.696
2 N N N N N N 0 -8.658 0.669 -3.064
3 O11 O O11 N N N 0 -4.967 1.706 0.389
4 O12 O O12 N N N 0 -6.527 3.645 -0.032
5 O13 O O13 N N N 0 -6.338 1.901 -1.846
6 O14 O O14 N N N 0 -4.378 3.584 -1.355
7 C11 C C11 N N N 0 -7.072 2.528 -2.899
8 C12 C C12 N N N 0 -7.669 1.455 -3.813
9 C1 C C1 N N N 0 -4.321 2.137 1.589
10 C2 C C2 R N N 0 -3.866 0.916 2.39
11 C3 C C3 N N N 0 -5.062 -0.005 2.639
12 O31 O O31 N N N 0 -5.685 -0.343 1.371
13 O32 O O32 N N N 0 -7.161 -1.561 2.477
14 C31 C C31 N N N 0 -6.756 -1.15 1.415
15 C32 C C32 N N N 0 -7.455 -1.545 0.139
16 C33 C C33 N N N 0 -8.635 -2.461 0.466
17 C34 C C34 N N N 0 -9.344 -2.862 -0.83
18 C35 C C35 N N N 0 -10.525 -3.779 -0.502
19 C36 C C36 N N N 0 -11.234 -4.179 -1.798
20 C37 C C37 N N N 0 -12.414 -5.096 -1.471
21 O21 O O21 N N N 0 -2.849 0.197 1.643
22 O22 O O22 N N N 0 -1.313 1.439 2.633
23 C24 C C24 N N N 0 2.01 -0.263 0.777
24 C21 C C21 N N N 0 -1.573 0.555 1.852
25 C22 C C22 N N N 0 -0.463 -0.146 1.111
26 C23 C C23 N N N 0 0.883 0.448 1.529
27 C25 C C25 N N N 0 3.357 0.331 1.195
28 C26 C C26 N N N 0 4.484 -0.381 0.444
29 C27 C C27 N N N 0 5.83 0.213 0.861
30 C28 C C28 N N N 0 6.957 -0.498 0.11
31 C2C C C2C N N N 0 11.903 -0.733 -0.558
32 C29 C C29 N N N 0 8.303 0.096 0.528
33 C2A C C2A N N N 0 9.43 -0.616 -0.224
34 C2B C C2B N N N 0 10.777 -0.022 0.194
35 C2D C C2D N N N 0 13.25 -0.139 -0.14
36 C2E C C2E N N N 0 14.377 -0.851 -0.891
37 C2F C C2F N N N 0 15.723 -0.257 -0.474
38 C2G C C2G N N N 0 16.85 -0.969 -1.225
39 C2H C C2H N N N 0 18.197 -0.374 -0.808
40 C2I C C2I N N N 0 19.323 -1.086 -1.559
41 HN H HN N N N 0 -9.37 1.265 -2.67
42 HNA H HNA N N N 0 -9.067 -0.047 -3.646
43 HO14 H HO14 N N N 0 -3.714 3.046 -1.808
44 H11 H H11 N N N 0 -7.875 3.13 -2.474
45 H11A H H11A N N N 0 -6.405 3.167 -3.477
46 H12 H H12 N N N 0 -6.876 0.798 -4.168
47 H12A H H12A N N N 0 -8.154 1.933 -4.665
48 H1 H H1 N N N 0 -3.455 2.748 1.335
49 H1A H H1A N N N 0 -5.018 2.725 2.186
50 H2 H H2 N N N 0 -3.453 1.241 3.345
51 H3 H H3 N N N 0 -4.723 -0.916 3.132
52 H3A H H3A N N N 0 -5.787 0.504 3.275
53 H32 H H32 N N N 0 -7.819 -0.65 -0.368
54 H35 H H35 N N N 0 -10.161 -4.673 0.004
55 H32A H H32A N N N 0 -6.755 -2.071 -0.511
56 H33 H H33 N N N 0 -8.271 -3.356 0.972
57 H33A H H33A N N N 0 -9.335 -1.935 1.115
58 H34 H H34 N N N 0 -9.708 -1.968 -1.336
59 H34A H H34A N N N 0 -8.645 -3.388 -1.479
60 H35A H H35A N N N 0 -11.224 -3.253 0.147
61 H36 H H36 N N N 0 -11.597 -3.285 -2.304
62 H36A H H36A N N N 0 -10.534 -4.705 -2.447
63 H37 H H37 N N N 0 -13.114 -4.57 -0.821
64 H37A H H37A N N N 0 -12.919 -5.381 -2.393
65 H37B H H37B N N N 0 -12.05 -5.99 -0.964
66 H22 H H22 N N N 0 -0.481 -1.209 1.351
67 H24 H H24 N N N 0 1.992 -1.326 1.017
68 H22A H H22A N N N 0 -0.601 -0.013 0.038
69 H23 H H23 N N N 0 0.902 1.512 1.289
70 H23A H H23A N N N 0 1.022 0.316 2.602
71 H24A H H24A N N N 0 1.872 -0.131 -0.296
72 H25 H H25 N N N 0 3.375 1.394 0.955
73 H25A H H25A N N N 0 3.495 0.198 2.268
74 H26 H H26 N N N 0 4.465 -1.444 0.684
75 H26A H H26A N N N 0 4.345 -0.248 -0.629
76 H27 H H27 N N N 0 5.848 1.276 0.622
77 H27A H H27A N N N 0 5.969 0.081 1.934
78 H28 H H28 N N N 0 6.939 -1.561 0.35
79 H28A H H28A N N N 0 6.818 -0.366 -0.963
80 H29 H H29 N N N 0 8.322 1.159 0.288
81 H29A H H29A N N N 0 8.442 -0.037 1.601
82 H2A H H2A N N N 0 9.412 -1.679 0.016
83 H2AA H H2AA N N N 0 9.292 -0.483 -1.297
84 H2B H H2B N N N 0 10.795 1.041 -0.046
85 H2BA H H2BA N N N 0 10.915 -0.154 1.267
86 H2C H H2C N N N 0 11.885 -1.797 -0.318
87 H2CA H H2CA N N N 0 11.765 -0.601 -1.631
88 H2D H H2D N N N 0 13.268 0.924 -0.38
89 H2DA H H2DA N N N 0 13.389 -0.272 0.933
90 H2E H H2E N N N 0 14.359 -1.914 -0.651
91 H2EA H H2EA N N N 0 14.238 -0.718 -1.964
92 H2F H H2F N N N 0 15.741 0.806 -0.714
93 H2FA H H2FA N N N 0 15.862 -0.389 0.599
94 H2G H H2G N N N 0 16.832 -2.032 -0.985
95 H2GA H H2GA N N N 0 16.712 -0.836 -2.298
96 H2H H H2H N N N 0 18.215 0.689 -1.047
97 H2HA H H2HA N N N 0 18.335 -0.507 0.266
98 H2I H H2I N N N 0 19.305 -2.149 -1.319
99 H2IA H H2IA N N N 0 19.185 -0.953 -2.632
100 H2IB H H2IB N N N 0 20.283 -0.663 -1.261



9PE : Chemical Bonds

Total Number of Bonds: 99
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O12 P O P doub 1.48 N N
2 P O11 P O sing 1.61 N N
3 P O14 P O sing 1.61 N N
4 P O13 P O sing 1.61 N N
5 C12 N C N sing 1.47 N N
6 N HN N H sing 1.01 N N
7 N HNA N H sing 1.01 N N
8 O11 C1 O C sing 1.43 N N
9 O13 C11 O C sing 1.43 N N
10 O14 HO14 O H sing 0.97 N N
11 C11 C12 C C sing 1.53 N N
12 C11 H11 C H sing 1.09 N N
13 C11 H11A C H sing 1.09 N N
14 C12 H12 C H sing 1.09 N N
15 C12 H12A C H sing 1.09 N N
16 C2 C1 C C sing 1.53 N N
17 C1 H1 C H sing 1.09 N N
18 C1 H1A C H sing 1.09 N N
19 O21 C2 O C sing 1.45 N N
20 C2 C3 C C sing 1.53 N N
21 C2 H2 C H sing 1.09 N N
22 O31 C3 O C sing 1.45 N N
23 C3 H3 C H sing 1.09 N N
24 C3 H3A C H sing 1.09 N N
25 O31 C31 O C sing 1.34 N N
26 C31 O32 C O doub 1.21 N N
27 C32 C31 C C sing 1.51 N N
28 C33 C32 C C sing 1.53 N N
29 C32 H32 C H sing 1.09 N N
30 C32 H32A C H sing 1.09 N N
31 C34 C33 C C sing 1.53 N N
32 C33 H33 C H sing 1.09 N N
33 C33 H33A C H sing 1.09 N N
34 C35 C34 C C sing 1.53 N N
35 C34 H34 C H sing 1.09 N N
36 C34 H34A C H sing 1.09 N N
37 C36 C35 C C sing 1.53 N N
38 C35 H35 C H sing 1.09 N N
39 C35 H35A C H sing 1.09 N N
40 C37 C36 C C sing 1.53 N N
41 C36 H36 C H sing 1.09 N N
42 C36 H36A C H sing 1.09 N N
43 C37 H37 C H sing 1.09 N N
44 C37 H37A C H sing 1.09 N N
45 C37 H37B C H sing 1.09 N N
46 C21 O21 C O sing 1.34 N N
47 O22 C21 O C doub 1.21 N N
48 C22 C21 C C sing 1.51 N N
49 C23 C22 C C sing 1.53 N N
50 C22 H22 C H sing 1.09 N N
51 C22 H22A C H sing 1.09 N N
52 C23 C24 C C sing 1.53 N N
53 C23 H23 C H sing 1.09 N N
54 C23 H23A C H sing 1.09 N N
55 C25 C24 C C sing 1.53 N N
56 C24 H24 C H sing 1.09 N N
57 C24 H24A C H sing 1.09 N N
58 C26 C25 C C sing 1.53 N N
59 C25 H25 C H sing 1.09 N N
60 C25 H25A C H sing 1.09 N N
61 C27 C26 C C sing 1.53 N N
62 C26 H26 C H sing 1.09 N N
63 C26 H26A C H sing 1.09 N N
64 C28 C27 C C sing 1.53 N N
65 C27 H27 C H sing 1.09 N N
66 C27 H27A C H sing 1.09 N N
67 C28 C29 C C sing 1.53 N N
68 C28 H28 C H sing 1.09 N N
69 C28 H28A C H sing 1.09 N N
70 C2A C29 C C sing 1.53 N N
71 C29 H29 C H sing 1.09 N N
72 C29 H29A C H sing 1.09 N N
73 C2A C2B C C sing 1.53 N N
74 C2A H2A C H sing 1.09 N N
75 C2A H2AA C H sing 1.09 N N
76 C2C C2B C C sing 1.53 N N
77 C2B H2B C H sing 1.09 N N
78 C2B H2BA C H sing 1.09 N N
79 C2C C2D C C sing 1.53 N N
80 C2C H2C C H sing 1.09 N N
81 C2C H2CA C H sing 1.09 N N
82 C2E C2D C C sing 1.53 N N
83 C2D H2D C H sing 1.09 N N
84 C2D H2DA C H sing 1.09 N N
85 C2E C2F C C sing 1.53 N N
86 C2E H2E C H sing 1.09 N N
87 C2E H2EA C H sing 1.09 N N
88 C2G C2F C C sing 1.53 N N
89 C2F H2F C H sing 1.09 N N
90 C2F H2FA C H sing 1.09 N N
91 C2H C2G C C sing 1.53 N N
92 C2G H2G C H sing 1.09 N N
93 C2G H2GA C H sing 1.09 N N
94 C2I C2H C C sing 1.53 N N
95 C2H H2H C H sing 1.09 N N
96 C2H H2HA C H sing 1.09 N N
97 C2I H2I C H sing 1.09 N N
98 C2I H2IA C H sing 1.09 N N
99 C2I H2IB C H sing 1.09 N N



9PE : Used in PDB Entries

Total Number of PDB Entries: 6
Ligand Code PDB Entry ID Type Total Distinct
9PE 3cx5 Open in New Window Bound ligand 2 1
9PE 3cxh Open in New Window Bound ligand 2 1
9PE 6giq Open in New Window Bound ligand 2 1
9PE 6o6r Open in New Window Bound ligand 4 1
9PE 6o72 Open in New Window Bound ligand 4 1
9PE 6ymx Open in New Window Bound ligand 2 1