Chemical Components in the PDB

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PSF : Summary

Code

PSF

One-letter code

X

Molecule name

1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE

Systematic names

ProgramVersionName
ACDLabs 10.04 O-[(S)-{[(2R)-2,3-bis(hexanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
OpenEye OEToolkits 1.5.0 (2S)-2-amino-3-[2,3-di(hexanoyloxy)propoxy-hydroxy-phosphoryl]oxy-propanoic acid

Formula

C18 H34 N O10 P

Formal charge

0

Molecular weight

455.437 Da

SMILES

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

IUPAC InChI

InChI=1S/C18H34NO10P/c1-3-5-7-9-16(20)26-11-14(29-17(21)10-8-6-4-2)12-27-30(24,25)28-13-15(19)18(22)23/h14-15H,3-13,19H2,1-2H3,(H,22,23)(H,24,25)/t14-,15+/m1/s1

IUPAC InChI key

MIQYPPGTNIFAPO-CABCVRRESA-N
PSF

wwPDB Information

Atom count

64 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2000-01-12

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



PSF : Atoms of Molecule

Total Number of Atoms: 64
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O2 O O2 N N N 0 3.938 -8.474 5.875
2 O1 O O1 N N N 0 4.81 -7.227 3.847
3 P P P R N N 0 5.297 -8.205 5.042
4 O4 O O4 N N N 0 6.454 -7.693 5.852
5 O3 O O3 N N N 0 5.577 -9.625 4.316
6 C2 C C2 N N N 0 2.801 -8.96 5.17
7 C3 C C3 N N N 0 1.635 -9.144 6.134
8 O11 O O11 N N N 0 1.348 -7.888 6.752
9 O12 O O12 N N N 0 0.917 -6.964 4.683
10 C1 C C1 N N N 0 1.0 -6.877 5.901
11 C4 C C4 N N N 0 1.973 -10.143 7.233
12 C5 C C5 N N N 0 1.016 -11.12 9.164
13 O51 O O51 N N N 0 2.014 -11.791 9.391
14 O52 O O52 N N N 0 0.855 -10.253 8.121
15 C6 C C6 N N N 0 -0.231 -11.095 10.02
16 C7 C C7 N N N 0 -0.12 -11.966 11.272
17 C13 C C13 N N N 0 0.697 -5.634 6.709
18 C14 C C14 N N N 0 1.91 -5.101 7.471
19 C15 C C15 N N N 0 3.065 -4.717 6.54
20 N N N N N N 0 5.881 -5.519 0.771
21 CA C CA S N N 0 4.999 -5.951 1.828
22 CB C CB N N N 0 5.709 -6.87 2.811
23 C C C N N N 0 4.496 -4.707 2.531
24 OT1 O OT1 N N N 0 5.152 -3.692 2.723
25 OT2 O OT2 N N N 0 3.223 -4.859 2.982
26 C8 C C8 N N N 0 -1.394 -11.935 12.121
27 C9 C C9 N N N 0 -1.24 -12.787 13.381
28 C10 C C10 N N N 0 -2.485 -12.726 14.251
29 C16 C C16 N N N 0 4.274 -4.221 7.333
30 C17 C C17 N N N 0 5.439 -3.88 6.418
31 HO3 H HO3 N N N 0 5.995 -10.346 4.833
32 H21 H 1H2 N N N 0 2.561 -8.243 4.379
33 H22 H 2H2 N N N 0 3.086 -9.912 4.71
34 H31 H 1H3 N N N 0 0.726 -9.449 5.603
35 H41 H 1H4 N N N 0 2.836 -9.81 7.82
36 H42 H 2H4 N N N 0 2.174 -11.135 6.817
37 H61 H 1H6 N N N 0 -1.086 -11.422 9.418
38 H62 H 2H6 N N N 0 -0.396 -10.054 10.32
39 H71 H 1H7 N N N 0 0.717 -11.596 11.876
40 H72 H 2H7 N N N 0 0.118 -13.0 10.994
41 H131 H 1H13 N N N 0 -0.114 -5.852 7.412
42 H132 H 2H13 N N N 0 0.351 -4.868 6.005
43 H141 H 1H14 N N N 0 2.256 -5.882 8.16
44 H142 H 2H14 N N N 0 1.624 -4.238 8.084
45 H151 H 1H15 N N N 0 2.742 -3.936 5.842
46 H152 H 2H15 N N N 0 3.354 -5.587 5.937
47 H1 H 1H N N N 0 6.868 -5.462 0.953
48 H2 H 2H N N N 0 5.485 -5.095 -0.05
49 HA H HA N N N 0 4.169 -6.458 1.325
50 HB1 H 1HB N N N 0 6.567 -6.368 3.27
51 HB2 H 2HB N N N 0 6.064 -7.785 2.323
52 HXT H HXT N N N 0 2.86 -4.093 3.476
53 H81 H 1H8 N N N 0 -2.246 -12.303 11.536
54 H82 H 2H8 N N N 0 -1.621 -10.9 12.404
55 H91 H 1H9 N N N 0 -1.046 -13.83 13.104
56 H92 H 2H9 N N N 0 -0.378 -12.44 13.962
57 H101 H 1H10 N N N 0 -2.689 -11.7 14.573
58 H102 H 2H10 N N N 0 -3.361 -13.097 13.709
59 H103 H 3H10 N N N 0 -2.353 -13.343 15.146
60 H161 H 1H16 N N N 0 3.999 -3.331 7.911
61 H162 H 2H16 N N N 0 4.591 -4.988 8.048
62 H171 H 1H17 N N N 0 5.76 -4.758 5.848
63 H172 H 2H17 N N N 0 5.165 -3.092 5.71
64 H173 H 3H17 N N N 0 6.292 -3.527 7.006



PSF : Chemical Bonds

Total Number of Bonds: 63
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O2 P O P sing 1.62 N N
2 O2 C2 O C sing 1.42 N N
3 O1 P O P sing 1.62 N N
4 O1 CB O C sing 1.42 N N
5 P O4 P O doub 1.5 N N
6 P O3 P O sing 1.62 N N
7 O3 HO3 O H sing 0.98 N N
8 C2 C3 C C sing 1.52 N N
9 C2 H21 C H sing 1.09 N N
10 C2 H22 C H sing 1.1 N N
11 C3 O11 C O sing 1.43 N N
12 C3 C4 C C sing 1.52 N N
13 C3 H31 C H sing 1.1 N N
14 O11 C1 O C sing 1.37 N N
15 O12 C1 O C doub 1.22 N N
16 C1 C13 C C sing 1.51 N N
17 C4 O52 C O sing 1.43 N N
18 C4 H41 C H sing 1.1 N N
19 C4 H42 C H sing 1.09 N N
20 C5 O51 C O doub 1.22 N N
21 C5 O52 C O sing 1.37 N N
22 C5 C6 C C sing 1.51 N N
23 C6 C7 C C sing 1.53 N N
24 C6 H61 C H sing 1.1 N N
25 C6 H62 C H sing 1.1 N N
26 C7 C8 C C sing 1.53 N N
27 C7 H71 C H sing 1.1 N N
28 C7 H72 C H sing 1.1 N N
29 C13 C14 C C sing 1.53 N N
30 C13 H131 C H sing 1.1 N N
31 C13 H132 C H sing 1.1 N N
32 C14 C15 C C sing 1.53 N N
33 C14 H141 C H sing 1.1 N N
34 C14 H142 C H sing 1.1 N N
35 C15 C16 C C sing 1.53 N N
36 C15 H151 C H sing 1.1 N N
37 C15 H152 C H sing 1.1 N N
38 N CA N C sing 1.44 N N
39 N H1 N H sing 1.01 N N
40 N H2 N H sing 1.01 N N
41 CA CB C C sing 1.52 N N
42 CA C C C sing 1.51 N N
43 CA HA C H sing 1.09 N N
44 CB HB1 C H sing 1.09 N N
45 CB HB2 C H sing 1.1 N N
46 C OT1 C O doub 1.22 N N
47 C OT2 C O sing 1.36 N N
48 OT2 HXT O H sing 0.98 N N
49 C8 C9 C C sing 1.53 N N
50 C8 H81 C H sing 1.1 N N
51 C8 H82 C H sing 1.1 N N
52 C9 C10 C C sing 1.52 N N
53 C9 H91 C H sing 1.1 N N
54 C9 H92 C H sing 1.1 N N
55 C10 H101 C H sing 1.09 N N
56 C10 H102 C H sing 1.09 N N
57 C10 H103 C H sing 1.1 N N
58 C16 C17 C C sing 1.52 N N
59 C16 H161 C H sing 1.1 N N
60 C16 H162 C H sing 1.1 N N
61 C17 H171 C H sing 1.09 N N
62 C17 H172 C H sing 1.09 N N
63 C17 H173 C H sing 1.09 N N



PSF : Used in PDB Entries

Total Number of PDB Entries: 12
Ligand Code PDB Entry ID Type Total Distinct
PSF 1dsy Open in New Window Bound ligand 1 1
PSF 3bib Open in New Window Bound ligand 1 1
PSF 3kaa Open in New Window Bound ligand 1 1
PSF 6b8o Open in New Window Bound ligand 3 1
PSF 6roh Open in New Window Bound ligand 1 1
PSF 6snd Open in New Window Bound ligand 1 1
PSF 6wlw Open in New Window Bound ligand 1 1
PSF 6wm2 Open in New Window Bound ligand 1 1
PSF 7aqq Open in New Window Bound ligand 1 1
PSF 7ar7 Open in New Window Bound ligand 1 1
PSF 7ar8 Open in New Window Bound ligand 1 1
PSF 7arb Open in New Window Bound ligand 1 1