Chemical Components in the PDB

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PS1 : Summary

Code

PS1

One-letter code

X

Molecule name

1,2-DIDECANOYL-SN-GLYCERO-3-[PHOSPHO-L-SERINE]

Systematic names

ProgramVersionName
ACDLabs 10.04 O-({[(2R)-2,3-bis(decanoyloxy)propyl]oxy}phosphinato)-L-serine
OpenEye OEToolkits 1.5.0 [(2S)-2-amino-3-hydroxy-3-oxo-propyl] [(2R)-2,3-di(decanoyloxy)propyl] phosphate

Formula

C26 H49 N O10 P

Formal charge

-1

Molecular weight

566.642 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(OCC(OC(=O)CCCCCCCCC)COP([O-])(=O)OCC(N)C(=O)O)CCCCCCCCC
SMILES CACTVS 3.341 CCCCCCCCCC(=O)OC[CH](CO[P]([O-])(=O)OC[CH](N)C(O)=O)OC(=O)CCCCCCCCC
SMILES OpenEye OEToolkits 1.5.0 CCCCCCCCCC(=O)OCC(COP(=O)([O-])OCC(C(=O)O)N)OC(=O)CCCCCCCCC
Canonical SMILES CACTVS 3.341 CCCCCCCCCC(=O)OC[C@H](CO[P]([O-])(=O)OC[C@H](N)C(O)=O)OC(=O)CCCCCCCCC
Canonical SMILES OpenEye OEToolkits 1.5.0 CCCCCCCCCC(=O)OC[C@H](CO[P@](=O)([O-])OC[C@@H](C(=O)O)N)OC(=O)CCCCCCCCC

IUPAC InChI

InChI=1S/C26H50NO10P/c1-3-5-7-9-11-13-15-17-24(28)34-19-22(20-35-38(32,33)36-21-23(27)26(30)31)37-25(29)18-16-14-12-10-8-6-4-2/h22-23H,3-21,27H2,1-2H3,(H,30,31)(H,32,33)/p-1/t22-,23+/m1/s1

IUPAC InChI key

LRIPXDCMGANCAE-PKTZIBPZSA-M
PS1

wwPDB Information

Atom count

87 (38 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2004-08-02

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



PS1 : Atoms of Molecule

Total Number of Atoms: 87
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O1 O O1 N N N -1 -0.87 -3.544 0.888
2 O2 O O2 N N N 0 1.194 -3.333 2.323
3 P1 P P1 N N N 0 0.429 -2.741 1.118
4 O3 O O3 N N N 0 1.353 -2.826 -0.198
5 C1 C C1 N N N 0 1.545 -4.214 -0.479
6 C2 C C2 S N N 0 2.419 -4.366 -1.725
7 C3 C C3 N N N 0 2.723 -5.825 -1.95
8 O4 O O4 N N N 0 2.096 -6.453 -2.771
9 O5 O O5 N N N 0 3.69 -6.427 -1.24
10 N1 N N1 N N N 0 1.707 -3.828 -2.891
11 O6 O O6 N N N 0 0.063 -1.202 1.418
12 C4 C C4 N N N 0 -0.848 -1.202 2.519
13 C5 C C5 R N N 0 -1.238 0.238 2.857
14 C6 C C6 N N N 0 0.025 1.063 3.111
15 O7 O O7 N N N 0 0.911 0.957 1.965
16 C7 C C7 N N N 0 2.087 1.602 1.964
17 O8 O O8 N N N 0 2.41 2.272 2.916
18 C8 C C8 N N N 0 3.006 1.492 0.774
19 C9 C C9 N N N 0 4.27 2.317 1.028
20 C10 C C10 N N N 0 5.202 2.205 -0.18
21 C11 C C11 N N N 0 6.466 3.03 0.073
22 C12 C C12 N N N 0 7.399 2.918 -1.134
23 C13 C C13 N N N 0 8.662 3.742 -0.881
24 C14 C C14 N N N 0 9.595 3.631 -2.089
25 C15 C C15 N N N 0 10.859 4.455 -1.835
26 C16 C C16 N N N 0 11.791 4.343 -3.043
27 O9 O O9 N N N 0 -1.977 0.813 1.747
28 C17 C C17 N N N 0 -3.313 0.7 1.7
29 O10 O O10 N N N 0 -3.902 0.12 2.581
30 C18 C C18 N N N 0 -4.08 1.296 0.548
31 C19 C C19 N N N 0 -5.574 1.028 0.736
32 C20 C C20 N N N 0 -6.352 1.634 -0.434
33 C21 C C21 N N N 0 -7.847 1.365 -0.246
34 C22 C C22 N N N 0 -8.625 1.971 -1.416
35 C23 C C23 N N N 0 -10.119 1.702 -1.228
36 C24 C C24 N N N 0 -10.898 2.308 -2.398
37 C25 C C25 N N N 0 -12.392 2.04 -2.21
38 C26 C C26 N N N 0 -13.17 2.645 -3.379
39 H1 H H1 N N N 0 2.035 -4.692 0.37
40 H2 H H2 N N N 0 0.578 -4.687 -0.653
41 H3 H H3 N N N 0 3.351 -3.819 -1.584
42 H4 H H4 N N N 0 3.885 -7.363 -1.384
43 H5 H H5 N N N 0 2.271 -4.042 -3.7
44 H6 H H6 N N N 0 0.855 -4.362 -2.983
45 H7 H H7 N N N 0 -0.372 -1.662 3.385
46 H8 H H8 N N N 0 -1.741 -1.767 2.252
47 H9 H H9 N N N 0 -1.862 0.246 3.751
48 H10 H H10 N N N 0 0.533 0.686 3.998
49 H11 H H11 N N N 0 -0.247 2.107 3.264
50 H12 H H12 N N N 0 2.498 1.869 -0.113
51 H13 H H13 N N N 0 3.278 0.448 0.621
52 H14 H H14 N N N 0 4.778 1.94 1.915
53 H15 H H15 N N N 0 3.997 3.361 1.181
54 H16 H H16 N N N 0 4.694 2.582 -1.068
55 H17 H H17 N N N 0 5.475 1.161 -0.333
56 H18 H H18 N N N 0 6.974 2.653 0.961
57 H19 H H19 N N N 0 6.194 4.074 0.227
58 H20 H H20 N N N 0 6.891 3.295 -2.022
59 H21 H H21 N N N 0 7.671 1.874 -1.288
60 H22 H H22 N N N 0 9.17 3.365 0.007
61 H23 H H23 N N N 0 8.39 4.787 -0.728
62 H24 H H24 N N N 0 9.087 4.008 -2.976
63 H25 H H25 N N N 0 9.867 2.586 -2.242
64 H26 H H26 N N N 0 11.367 4.078 -0.948
65 H27 H H27 N N N 0 10.586 5.499 -1.682
66 H28 H H28 N N N 0 12.692 4.931 -2.862
67 H29 H H29 N N N 0 12.064 3.299 -3.196
68 H30 H H30 N N N 0 11.283 4.721 -3.93
69 H31 H H31 N N N 0 -3.905 2.372 0.513
70 H32 H H32 N N N 0 -3.744 0.844 -0.385
71 H33 H H33 N N N 0 -5.749 -0.047 0.77
72 H34 H H34 N N N 0 -5.91 1.481 1.669
73 H35 H H35 N N N 0 -6.178 2.709 -0.469
74 H36 H H36 N N N 0 -6.017 1.181 -1.367
75 H37 H H37 N N N 0 -8.021 0.29 -0.212
76 H38 H H38 N N N 0 -8.183 1.818 0.687
77 H39 H H39 N N N 0 -8.451 3.046 -1.45
78 H40 H H40 N N N 0 -8.289 1.518 -2.349
79 H41 H H41 N N N 0 -10.294 0.627 -1.193
80 H42 H H42 N N N 0 -10.455 2.155 -0.295
81 H43 H H43 N N N 0 -10.723 3.384 -2.432
82 H44 H H44 N N N 0 -10.562 1.855 -3.331
83 H45 H H45 N N N 0 -12.567 0.964 -2.175
84 H46 H H46 N N N 0 -12.728 2.492 -1.277
85 H47 H H47 N N N 0 -14.235 2.454 -3.245
86 H48 H H48 N N N 0 -12.996 3.721 -3.414
87 H49 H H49 N N N 0 -12.834 2.193 -4.312



PS1 : Chemical Bonds

Total Number of Bonds: 86
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O1 P1 O P sing 1.54 N N
2 O2 P1 O P doub 1.55 N N
3 P1 O3 P O sing 1.61 N N
4 P1 O6 P O sing 1.61 N N
5 O3 C1 O C sing 1.43 N N
6 C1 C2 C C sing 1.53 N N
7 C1 H1 C H sing 1.09 N N
8 C1 H2 C H sing 1.09 N N
9 C2 C3 C C sing 1.51 N N
10 C2 N1 C N sing 1.47 N N
11 C2 H3 C H sing 1.09 N N
12 C3 O4 C O doub 1.21 N N
13 C3 O5 C O sing 1.34 N N
14 O5 H4 O H sing 0.97 N N
15 N1 H5 N H sing 1.01 N N
16 N1 H6 N H sing 1.01 N N
17 O6 C4 O C sing 1.43 N N
18 C4 C5 C C sing 1.53 N N
19 C4 H7 C H sing 1.09 N N
20 C4 H8 C H sing 1.09 N N
21 C5 C6 C C sing 1.53 N N
22 C5 O9 C O sing 1.45 N N
23 C5 H9 C H sing 1.09 N N
24 C6 O7 C O sing 1.45 N N
25 C6 H10 C H sing 1.09 N N
26 C6 H11 C H sing 1.09 N N
27 O7 C7 O C sing 1.34 N N
28 C7 O8 C O doub 1.21 N N
29 C7 C8 C C sing 1.51 N N
30 C8 C9 C C sing 1.53 N N
31 C8 H12 C H sing 1.09 N N
32 C8 H13 C H sing 1.09 N N
33 C9 C10 C C sing 1.53 N N
34 C9 H14 C H sing 1.09 N N
35 C9 H15 C H sing 1.09 N N
36 C10 C11 C C sing 1.53 N N
37 C10 H16 C H sing 1.09 N N
38 C10 H17 C H sing 1.09 N N
39 C11 C12 C C sing 1.53 N N
40 C11 H18 C H sing 1.09 N N
41 C11 H19 C H sing 1.09 N N
42 C12 C13 C C sing 1.53 N N
43 C12 H20 C H sing 1.09 N N
44 C12 H21 C H sing 1.09 N N
45 C13 C14 C C sing 1.53 N N
46 C13 H22 C H sing 1.09 N N
47 C13 H23 C H sing 1.09 N N
48 C14 C15 C C sing 1.53 N N
49 C14 H24 C H sing 1.09 N N
50 C14 H25 C H sing 1.09 N N
51 C15 C16 C C sing 1.53 N N
52 C15 H26 C H sing 1.09 N N
53 C15 H27 C H sing 1.09 N N
54 C16 H28 C H sing 1.09 N N
55 C16 H29 C H sing 1.09 N N
56 C16 H30 C H sing 1.09 N N
57 O9 C17 O C sing 1.34 N N
58 C17 O10 C O doub 1.21 N N
59 C17 C18 C C sing 1.51 N N
60 C18 C19 C C sing 1.53 N N
61 C18 H31 C H sing 1.09 N N
62 C18 H32 C H sing 1.09 N N
63 C19 C20 C C sing 1.53 N N
64 C19 H33 C H sing 1.09 N N
65 C19 H34 C H sing 1.09 N N
66 C20 C21 C C sing 1.53 N N
67 C20 H35 C H sing 1.09 N N
68 C20 H36 C H sing 1.09 N N
69 C21 C22 C C sing 1.53 N N
70 C21 H37 C H sing 1.09 N N
71 C21 H38 C H sing 1.09 N N
72 C22 C23 C C sing 1.53 N N
73 C22 H39 C H sing 1.09 N N
74 C22 H40 C H sing 1.09 N N
75 C23 C24 C C sing 1.53 N N
76 C23 H41 C H sing 1.09 N N
77 C23 H42 C H sing 1.09 N N
78 C24 C25 C C sing 1.53 N N
79 C24 H43 C H sing 1.09 N N
80 C24 H44 C H sing 1.09 N N
81 C25 C26 C C sing 1.53 N N
82 C25 H45 C H sing 1.09 N N
83 C25 H46 C H sing 1.09 N N
84 C26 H47 C H sing 1.09 N N
85 C26 H48 C H sing 1.09 N N
86 C26 H49 C H sing 1.09 N N



PS1 : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
PS1 8uo8 Open in New Window Bound ligand 1 1
PS1 8uo9 Open in New Window Bound ligand 1 1
PS1 8x90 Open in New Window Bound ligand 1 1