Chemical Components in the PDB

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S1P : Summary

Code

S1P

One-letter code

X

Molecule name

(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate

Synonyms

sphingosine 1-phosphate

Systematic names

ProgramVersionName
ACDLabs 11.02 (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
OpenEye OEToolkits 1.6.1 [(E,2S,3R)-2-azanyl-3-hydroxy-octadec-4-enyl] dihydrogen phosphate

Formula

C18 H38 N O5 P

Formal charge

0

Molecular weight

379.472 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 11.02 O=P(OCC(N)C(O)/C=C/CCCCCCCCCCCCC)(O)O
SMILES CACTVS 3.352 CCCCCCCCCCCCCC=C[CH](O)[CH](N)CO[P](O)(O)=O
SMILES OpenEye OEToolkits 1.7.0 CCCCCCCCCCCCCC=CC(C(COP(=O)(O)O)N)O
Canonical SMILES CACTVS 3.352 CCCCCCCCCCCCC\C=C\[C@@H](O)[C@@H](N)CO[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.0 CCCCCCCCCCCCC/C=C/[C@H]([C@H](COP(=O)(O)O)N)O

IUPAC InChI

InChI=1S/C18H38NO5P/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-18(20)17(19)16-24-25(21,22)23/h14-15,17-18,20H,2-13,16,19H2,1H3,(H2,21,22,23)/b15-14+/t17-,18+/m0/s1

IUPAC InChI key

DUYSYHSSBDVJSM-KRWOKUGFSA-N
S1P

wwPDB Information

Atom count

63 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2009-07-14

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



S1P : Atoms of Molecule

Total Number of Atoms: 63
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 -6.232 0.235 -0.103
2 O1 O O1 N N N 0 -6.676 -1.041 0.364
3 C2 C C2 S N N 0 -4.845 0.533 0.47
4 N2 N N2 N N N 0 -4.935 0.664 1.93
5 C3 C C3 R N N 0 -4.317 1.839 -0.127
6 O3 O O3 N N N 0 -4.228 1.712 -1.548
7 C4 C C4 N N N 0 -2.95 2.133 0.437
8 C5 C C5 N N N 0 -1.937 2.329 -0.37
9 C6 C C6 N N N 0 -0.571 2.622 0.194
10 C7 C C7 N N N 0 0.438 1.615 -0.362
11 C8 C C8 N N N 0 1.825 1.913 0.21
12 C9 C C9 N N N 0 2.833 0.905 -0.345
13 C10 C C10 N N N 0 4.221 1.204 0.227
14 C11 C C11 N N N 0 5.229 0.196 -0.329
15 C12 C C12 N N N 0 6.616 0.494 0.244
16 C13 C C13 N N N 0 7.625 -0.513 -0.312
17 C14 C C14 N N N 0 9.012 -0.215 0.26
18 C15 C C15 N N N 0 10.02 -1.223 -0.295
19 C16 C C16 N N N 0 11.407 -0.924 0.277
20 C17 C C17 N N N 0 12.416 -1.932 -0.279
21 C18 C C18 N N N 0 13.803 -1.634 0.294
22 P22 P P22 N N N 0 -8.098 -1.677 -0.041
23 O23 O O23 N N N 0 -8.123 -1.972 -1.624
24 O24 O O24 N N N 0 -8.32 -3.052 0.765
25 O25 O O25 N N N 0 -9.179 -0.725 0.3
26 H1 H H1 N N N 0 -6.181 0.226 -1.191
27 H1A H H1A N N N 0 -6.932 1.004 0.222
28 H2 H H2 N N N 0 -4.165 -0.282 0.219
29 HN2 H HN2 N N N 0 -4.022 0.797 2.339
30 HN2A H HN2A N N N 0 -5.56 1.413 2.188
31 H3 H H3 N N N 0 -4.996 2.654 0.123
32 HO3 H HO3 N N N 0 -3.639 1.004 -1.844
33 H4 H H4 N N N 0 -2.806 2.182 1.506
34 H5 H H5 N N N 0 -2.081 2.28 -1.439
35 H6 H H6 N N N 0 -0.27 3.631 -0.089
36 H6A H H6A N N N 0 -0.601 2.544 1.28
37 H7 H H7 N N N 0 0.137 0.606 -0.079
38 H7A H H7A N N N 0 0.469 1.693 -1.449
39 H8 H H8 N N N 0 2.126 2.922 -0.073
40 H8A H H8A N N N 0 1.794 1.834 1.297
41 H9 H H9 N N N 0 2.533 -0.103 -0.062
42 H9A H H9A N N N 0 2.864 0.984 -1.432
43 H10 H H10 N N N 0 4.521 2.212 -0.056
44 H10A H H10A N N N 0 4.19 1.125 1.314
45 H11 H H11 N N N 0 4.928 -0.813 -0.046
46 H11A H H11A N N N 0 5.26 0.275 -1.416
47 H12 H H12 N N N 0 6.917 1.503 -0.039
48 H12A H H12A N N N 0 6.585 0.416 1.33
49 H13 H H13 N N N 0 7.324 -1.522 -0.029
50 H13A H H13A N N N 0 7.655 -0.435 -1.399
51 H14 H H14 N N N 0 9.312 0.794 -0.023
52 H14A H H14A N N N 0 8.981 -0.294 1.347
53 H15 H H15 N N N 0 9.72 -2.231 -0.012
54 H15A H H15A N N N 0 10.051 -1.144 -1.382
55 H16 H H16 N N N 0 11.708 0.084 -0.0060
56 H16A H H16A N N N 0 11.377 -1.003 1.364
57 H17 H H17 N N N 0 12.115 -2.941 0.0040
58 H17A H H17A N N N 0 12.447 -1.854 -1.365
59 H18 H H18 N N N 0 14.104 -0.625 0.011
60 H18A H H18A N N N 0 13.772 -1.712 1.38
61 H18B H H18B N N N 0 14.521 -2.352 -0.102
62 HO23 H HO23 N N N 0 -7.44 -2.589 -1.919
63 HO24 H HO24 N N N 0 -9.159 -3.492 0.569



S1P : Chemical Bonds

Total Number of Bonds: 62
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C2 C1 C C sing 1.53 N N
2 O1 C1 O C sing 1.43 N N
3 C1 H1 C H sing 1.09 N N
4 C1 H1A C H sing 1.09 N N
5 O1 P22 O P sing 1.61 N N
6 C3 C2 C C sing 1.53 N N
7 N2 C2 N C sing 1.47 N N
8 C2 H2 C H sing 1.09 N N
9 N2 HN2 N H sing 1.01 N N
10 N2 HN2A N H sing 1.01 N N
11 C4 C3 C C sing 1.51 N N
12 C3 O3 C O sing 1.43 N N
13 C3 H3 C H sing 1.09 N N
14 O3 HO3 O H sing 0.97 N N
15 C5 C4 C C doub 1.31 N N
16 C4 H4 C H sing 1.08 E N
17 C6 C5 C C sing 1.51 N N
18 C5 H5 C H sing 1.08 N N
19 C7 C6 C C sing 1.53 N N
20 C6 H6 C H sing 1.09 N N
21 C6 H6A C H sing 1.09 N N
22 C8 C7 C C sing 1.53 N N
23 C7 H7 C H sing 1.09 N N
24 C7 H7A C H sing 1.09 N N
25 C8 C9 C C sing 1.53 N N
26 C8 H8 C H sing 1.09 N N
27 C8 H8A C H sing 1.09 N N
28 C10 C9 C C sing 1.53 N N
29 C9 H9 C H sing 1.09 N N
30 C9 H9A C H sing 1.09 N N
31 C11 C10 C C sing 1.53 N N
32 C10 H10 C H sing 1.09 N N
33 C10 H10A C H sing 1.09 N N
34 C12 C11 C C sing 1.53 N N
35 C11 H11 C H sing 1.09 N N
36 C11 H11A C H sing 1.09 N N
37 C12 C13 C C sing 1.53 N N
38 C12 H12 C H sing 1.09 N N
39 C12 H12A C H sing 1.09 N N
40 C14 C13 C C sing 1.53 N N
41 C13 H13 C H sing 1.09 N N
42 C13 H13A C H sing 1.09 N N
43 C14 C15 C C sing 1.53 N N
44 C14 H14 C H sing 1.09 N N
45 C14 H14A C H sing 1.09 N N
46 C15 C16 C C sing 1.53 N N
47 C15 H15 C H sing 1.09 N N
48 C15 H15A C H sing 1.09 N N
49 C16 C17 C C sing 1.53 N N
50 C16 H16 C H sing 1.09 N N
51 C16 H16A C H sing 1.09 N N
52 C17 C18 C C sing 1.53 N N
53 C17 H17 C H sing 1.09 N N
54 C17 H17A C H sing 1.09 N N
55 C18 H18 C H sing 1.09 N N
56 C18 H18A C H sing 1.09 N N
57 C18 H18B C H sing 1.09 N N
58 O25 P22 O P doub 1.48 N N
59 O24 P22 O P sing 1.61 N N
60 P22 O23 P O sing 1.61 N N
61 O23 HO23 O H sing 0.97 N N
62 O24 HO24 O H sing 0.97 N N



S1P : Used in PDB Entries

Total Number of PDB Entries: 7
Ligand Code PDB Entry ID Type Total Distinct
S1P 2yg2 Open in New Window Bound ligand 2 1
S1P 3i9g Open in New Window Bound ligand 1 1
S1P 5ksi Open in New Window Bound ligand 5 1
S1P 5ksj Open in New Window Bound ligand 2 1
S1P 7c4s Open in New Window Bound ligand 2 1
S1P 7ew3 Open in New Window Bound ligand 1 1
S1P 7lhv Open in New Window Bound ligand 4 1