Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

8SP : Summary

Code

8SP

One-letter code

S

Molecule name

O-[(R)-{[(2R)-2,3-bis(octanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine

Systematic names

ProgramVersionName
ACDLabs 12.01 O-[(R)-{[(2R)-2,3-bis(octanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
OpenEye OEToolkits 1.7.6 (2S)-2-azanyl-3-[[(2R)-2,3-di(octanoyloxy)propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid

Formula

C22 H42 N O10 P

Formal charge

0

Molecular weight

511.543 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(OC(COP(=O)(OCC(C(=O)O)N)O)COC(=O)CCCCCCC)CCCCCCC
SMILES CACTVS 3.370 CCCCCCCC(=O)OC[CH](CO[P](O)(=O)OC[CH](N)C(O)=O)OC(=O)CCCCCCC
SMILES OpenEye OEToolkits 1.7.6 CCCCCCCC(=O)OCC(COP(=O)(O)OCC(C(=O)O)N)OC(=O)CCCCCCC
Canonical SMILES CACTVS 3.370 CCCCCCCC(=O)OC[C@H](CO[P](O)(=O)OC[C@H](N)C(O)=O)OC(=O)CCCCCCC
Canonical SMILES OpenEye OEToolkits 1.7.6 CCCCCCCC(=O)OC[C@H](COP(=O)(O)OC[C@@H](C(=O)O)N)OC(=O)CCCCCCC

IUPAC InChI

InChI=1S/C22H42NO10P/c1-3-5-7-9-11-13-20(24)30-15-18(33-21(25)14-12-10-8-6-4-2)16-31-34(28,29)32-17-19(23)22(26)27/h18-19H,3-17,23H2,1-2H3,(H,26,27)(H,28,29)/t18-,19+/m1/s1

IUPAC InChI key

TWOCGGYLNFTSJO-MOPGFXCFSA-N
8SP

wwPDB Information

Atom count

76 (34 without Hydrogen)

Polymer type

Amino Acid

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

Yes

Standard parent

SER

Defined at

2013-01-22

Last modified at

2013-02-08

Status

Released

Obsoleted

Not Assigned



8SP : Atoms of Molecule

Total Number of Atoms: 76
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 1.977 3.075 2.247
2 P P P N N N 0 0.442 1.993 -1.733
3 OG O OG N N N 0 1.395 2.203 -0.453
4 C1A C C1A N N N 0 1.663 -2.359 -1.046
5 O1A O O1A N N N 0 1.853 -3.391 -1.644
6 C1B C C1B N N N 0 -3.67 -1.125 -0.964
7 O1B O O1B N N N 0 -4.25 -0.974 -2.013
8 CB C CB N N N 0 2.065 3.433 -0.174
9 C1G C C1G N N N 0 -0.439 -2.238 -2.162
10 O1G O O1G N N N 0 0.522 -1.676 -1.229
11 C2G C C2G R N N 0 -1.667 -1.328 -2.239
12 C2A C C2A N N N 0 2.708 -1.837 -0.093
13 C2B C C2B N N N 0 -4.438 -1.1 0.333
14 CA C CA S N N 0 2.883 3.289 1.11
15 O2G O O2G N N N 0 -2.341 -1.315 -0.953
16 O2P O O2P N N N 0 -0.61 3.035 -1.741
17 C3A C C3A N N N 0 3.9 -2.796 -0.069
18 C3B C C3B N N N 0 -5.923 -0.869 0.041
19 C C C N N N 0 3.686 4.544 1.338
20 O O O N N N 0 3.297 5.376 2.123
21 OXT O OXT N N Y 0 4.833 4.737 0.669
22 C3G C C3G N N N 0 -1.227 0.093 -2.597
23 O3G O O3G N N N 0 -0.245 0.539 -1.66
24 O3P O O3P N N N 0 1.318 2.105 -3.079
25 C4A C C4A N N N 0 4.961 -2.266 0.899
26 C4B C C4B N N N 0 -6.702 -0.844 1.357
27 C5A C C5A N N N 0 6.153 -3.225 0.922
28 C5B C C5B N N N 0 -8.187 -0.613 1.066
29 C6A C C6A N N N 0 7.214 -2.696 1.89
30 C6B C C6B N N N 0 -8.967 -0.588 2.382
31 C7A C C7A N N N 0 8.406 -3.654 1.913
32 C7B C C7B N N N 0 -10.451 -0.357 2.091
33 C8A C C8A N N N 0 9.467 -3.125 2.881
34 C8B C C8B N N N 0 -11.231 -0.332 3.408
35 HB3 H HB3 N N N 0 2.73 3.681 -1.002
36 HB2 H HB2 N N N 0 1.329 4.228 -0.049
37 H11G H H11G N N N 0 0.016 -2.318 -3.149
38 H21G H H21G N N N 0 -0.742 -3.227 -1.82
39 H H H N N N 0 1.341 3.851 2.353
40 H12A H H12A N N N 0 3.04 -0.852 -0.421
41 H22A H H22A N N N 0 2.282 -1.762 0.908
42 H12B H H12B N N N 0 -4.313 -2.052 0.848
43 H22B H H22B N N N 0 -4.062 -0.294 0.962
44 HA H HA N N N 0 3.558 2.438 1.018
45 H2G H H2G N N N 0 -2.348 -1.701 -3.003
46 H2 H H2 N N Y 0 1.474 2.206 2.149
47 H13A H H13A N N N 0 3.568 -3.781 0.259
48 H23A H H23A N N N 0 4.326 -2.871 -1.069
49 H13B H H13B N N N 0 -6.048 0.083 -0.474
50 H23B H H23B N N N 0 -6.299 -1.676 -0.588
51 H13G H H13G N N N 0 -0.8 0.099 -3.601
52 H23G H H23G N N N 0 -2.089 0.76 -2.565
53 H14A H H14A N N N 0 5.293 -1.281 0.57
54 H24A H H24A N N N 0 4.535 -2.192 1.899
55 H14B H H14B N N N 0 -6.577 -1.796 1.873
56 H24B H H24B N N N 0 -6.326 -0.038 1.987
57 H15A H H15A N N N 0 5.821 -4.21 1.25
58 H25B H H25B N N N 0 -8.563 -1.42 0.437
59 H25A H H25A N N N 0 6.579 -3.3 -0.078
60 H15B H H15B N N N 0 -8.312 0.339 0.551
61 H16A H H16A N N N 0 7.546 -1.711 1.561
62 H26A H H26A N N N 0 6.788 -2.621 2.89
63 H16B H H16B N N N 0 -8.841 -1.54 2.898
64 H26B H H26B N N N 0 -8.59 0.218 3.012
65 H17A H H17A N N N 0 8.074 -4.639 2.242
66 H27A H H27A N N N 0 8.832 -3.729 0.913
67 H17B H H17B N N N 0 -10.576 0.595 1.576
68 H27B H H27B N N N 0 -10.827 -1.164 1.462
69 H28A H H28A N N N 0 10.316 -3.808 2.898
70 H18A H H18A N N N 0 9.041 -3.05 3.881
71 H38A H H38A N N N 0 9.799 -2.14 2.553
72 H18B H H18B N N N 0 -10.854 0.474 4.037
73 H28B H H28B N N N 0 -12.288 -0.168 3.2
74 H38B H H38B N N N 0 -11.105 -1.284 3.923
75 HXT H HXT N N Y 0 5.313 5.557 0.849
76 H42 H H42 N N N 0 2.028 1.452 -3.142



8SP : Chemical Bonds

Total Number of Bonds: 75
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N CA N C sing 1.47 N N
2 N H N H sing 1.01 N N
3 N H2 N H sing 1.01 N N
4 P OG P O sing 1.61 N N
5 P O2P P O doub 1.48 N N
6 P O3G P O sing 1.61 N N
7 P O3P P O sing 1.61 N N
8 OG CB O C sing 1.43 N N
9 C1A O1A C O doub 1.21 N N
10 C1A O1G C O sing 1.34 N N
11 C1A C2A C C sing 1.51 N N
12 C1B O1B C O doub 1.21 N N
13 C1B C2B C C sing 1.51 N N
14 C1B O2G C O sing 1.34 N N
15 CB CA C C sing 1.53 N N
16 CB HB3 C H sing 1.09 N N
17 CB HB2 C H sing 1.09 N N
18 C1G O1G C O sing 1.45 N N
19 C1G C2G C C sing 1.53 N N
20 C1G H11G C H sing 1.09 N N
21 C1G H21G C H sing 1.09 N N
22 C2A C3A C C sing 1.53 N N
23 C2A H12A C H sing 1.09 N N
24 C2A H22A C H sing 1.09 N N
25 C2B C3B C C sing 1.53 N N
26 C2B H12B C H sing 1.09 N N
27 C2B H22B C H sing 1.09 N N
28 CA C C C sing 1.51 N N
29 CA HA C H sing 1.09 N N
30 C2G O2G C O sing 1.45 N N
31 C2G C3G C C sing 1.53 N N
32 C2G H2G C H sing 1.09 N N
33 C3A C4A C C sing 1.53 N N
34 C3A H13A C H sing 1.09 N N
35 C3A H23A C H sing 1.09 N N
36 C3B C4B C C sing 1.53 N N
37 C3B H13B C H sing 1.09 N N
38 C3B H23B C H sing 1.09 N N
39 C O C O doub 1.21 N N
40 C OXT C O sing 1.34 N N
41 C3G O3G C O sing 1.43 N N
42 C3G H13G C H sing 1.09 N N
43 C3G H23G C H sing 1.09 N N
44 C4A C5A C C sing 1.53 N N
45 C4A H14A C H sing 1.09 N N
46 C4A H24A C H sing 1.09 N N
47 C4B C5B C C sing 1.53 N N
48 C4B H14B C H sing 1.09 N N
49 C4B H24B C H sing 1.09 N N
50 C5A C6A C C sing 1.53 N N
51 C5A H15A C H sing 1.09 N N
52 C5A H25A C H sing 1.09 N N
53 C5B C6B C C sing 1.53 N N
54 C5B H15B C H sing 1.09 N N
55 C5B H25B C H sing 1.09 N N
56 C6A C7A C C sing 1.53 N N
57 C6A H16A C H sing 1.09 N N
58 C6A H26A C H sing 1.09 N N
59 C6B C7B C C sing 1.53 N N
60 C6B H16B C H sing 1.09 N N
61 C6B H26B C H sing 1.09 N N
62 C7A C8A C C sing 1.53 N N
63 C7A H17A C H sing 1.09 N N
64 C7A H27A C H sing 1.09 N N
65 C7B C8B C C sing 1.53 N N
66 C7B H17B C H sing 1.09 N N
67 C7B H27B C H sing 1.09 N N
68 C8A H18A C H sing 1.09 N N
69 C8A H28A C H sing 1.09 N N
70 C8A H38A C H sing 1.09 N N
71 C8B H18B C H sing 1.09 N N
72 C8B H28B C H sing 1.09 N N
73 C8B H38B C H sing 1.09 N N
74 OXT HXT O H sing 0.97 N N
75 O3P H42 O H sing 0.97 N N



8SP : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
8SP 2lyb Open in New Window Bound ligand 1 1
8SP 6nhh Open in New Window Bound ligand 2 1
8SP 6uxn Open in New Window Bound ligand 18 1