Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

2DE : Summary

Code

2DE

One-letter code

X

Molecule name

(2E,6E)-7,11-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate

Systematic names

ProgramVersionName
ACDLabs 12.01 (2E,6E)-7,11-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate
OpenEye OEToolkits 1.7.0 [(2E,6E)-7,11-dimethyldodeca-2,6,10-trienyl] phosphono hydrogen phosphate

Formula

C14 H26 O7 P2

Formal charge

0

Molecular weight

368.3 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OP(=O)(OC/C=C/CC\C=C(/C)CC\C=C(/C)C)O
SMILES CACTVS 3.370 CC(C)=CCCC(C)=CCCC=CCO[P](O)(=O)O[P](O)(O)=O
SMILES OpenEye OEToolkits 1.7.0 CC(=CCCC(=CCCC=CCOP(=O)(O)OP(=O)(O)O)C)C
Canonical SMILES CACTVS 3.370 CC(C)=CCC/C(C)=C/CC/C=C/CO[P](O)(=O)O[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.0 CC(=CCC/C(=C/CC/C=C/CO[P@](=O)(O)OP(=O)(O)O)/C)C

IUPAC InChI

InChI=1S/C14H26O7P2/c1-13(2)9-8-11-14(3)10-6-4-5-7-12-20-23(18,19)21-22(15,16)17/h5,7,9-10H,4,6,8,11-12H2,1-3H3,(H,18,19)(H2,15,16,17)/b7-5+,14-10+

IUPAC InChI key

AFSHNJXUHHFZPQ-XOBXVUKQSA-N
2DE

wwPDB Information

Atom count

49 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2010-10-29

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



2DE : Atoms of Molecule

Total Number of Atoms: 49
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 -1.608 2.065 0.128
2 O1 O O1 N N N 0 -2.387 0.894 0.384
3 C2 C C2 N N N 0 -0.149 1.755 0.347
4 C3 C C3 N N N 0 0.744 2.161 -0.521
5 C5 C C5 N N N 0 2.202 1.852 -0.302
6 C6 C C6 N N N 0 2.761 1.13 -1.53
7 C7 C C7 N N N 0 4.219 0.821 -1.311
8 C8 C C8 N N N 0 4.641 -0.418 -1.36
9 C9 C C9 N N N 0 6.115 -0.717 -1.273
10 PA P PA N N N 0 -3.991 0.861 0.248
11 PB P PB N N N 0 -5.874 -1.424 0.104
12 C10 C C10 N N N 0 3.651 -1.546 -1.502
13 C11 C C11 N N N 0 6.487 -1.031 0.178
14 C12 C C12 N N N 0 7.962 -1.33 0.264
15 C13 C C13 N N N 0 8.719 -0.656 1.094
16 C14 C C14 N N N 0 8.115 0.419 1.962
17 C15 C C15 N N N 0 10.194 -0.954 1.181
18 O1A O O1A N N N 0 -4.38 1.315 -1.106
19 O1B O O1B N N N 0 -6.244 -1.119 -1.297
20 O2A O O2A N N N 0 -4.643 1.837 1.349
21 O2B O O2B N N N 0 -5.642 -3.009 0.265
22 O3A O O3A N N N 0 -4.518 -0.642 0.482
23 O3B O O3B N N N 0 -7.058 -0.951 1.087
24 H1 H H1 N N N 0 -1.761 2.384 -0.903
25 H1A H H1A N N N 0 -1.916 2.862 0.804
26 H2 H H2 N N N 0 0.16 1.2 1.22
27 H3 H H3 N N N 0 0.435 2.717 -1.395
28 H5 H H5 N N N 0 2.751 2.781 -0.146
29 H5A H H5A N N N 0 2.311 1.214 0.575
30 H6 H H6 N N N 0 2.212 0.201 -1.687
31 H6A H H6A N N N 0 2.652 1.768 -2.407
32 H7 H H7 N N N 0 4.917 1.621 -1.114
33 H9 H H9 N N N 0 6.35 -1.575 -1.902
34 H9A H H9A N N N 0 6.682 0.149 -1.613
35 H10 H H10 N N N 0 3.415 -1.691 -2.556
36 H10A H H10A N N N 0 4.082 -2.461 -1.096
37 H10B H H10B N N N 0 2.74 -1.3 -0.956
38 H11 H H11 N N N 0 6.253 -0.173 0.807
39 H11A H H11A N N N 0 5.921 -1.898 0.518
40 H12 H H12 N N N 0 8.395 -2.1 -0.357
41 H14 H H14 N N N 0 7.349 -0.019 2.601
42 H14A H H14A N N N 0 8.893 0.866 2.581
43 H14B H H14B N N N 0 7.668 1.186 1.33
44 H15 H H15 N N N 0 10.733 -0.33 0.468
45 H15A H H15A N N N 0 10.548 -0.743 2.19
46 H15B H H15B N N N 0 10.366 -2.005 0.947
47 HO2A H HO2A N N N 0 -4.43 1.599 2.262
48 HO2B H HO2B N N N 0 -6.42 -3.543 0.053
49 HO3B H HO3B N N N 0 -6.883 -1.12 2.023



2DE : Chemical Bonds

Total Number of Bonds: 48
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 O1 C O sing 1.43 N N
2 C1 C2 C C sing 1.51 N N
3 O1 PA O P sing 1.61 N N
4 C2 C3 C C doub 1.31 N N
5 C3 C5 C C sing 1.51 N N
6 C5 C6 C C sing 1.53 E N
7 C6 C7 C C sing 1.51 N N
8 C7 C8 C C doub 1.31 N N
9 C8 C9 C C sing 1.51 N N
10 C8 C10 C C sing 1.51 N N
11 C9 C11 C C sing 1.53 N N
12 PA O1A P O doub 1.48 N N
13 PA O2A P O sing 1.61 N N
14 PA O3A P O sing 1.61 N N
15 PB O1B P O doub 1.48 N N
16 PB O2B P O sing 1.61 E N
17 PB O3A P O sing 1.61 N N
18 PB O3B P O sing 1.61 N N
19 C11 C12 C C sing 1.51 N N
20 C12 C13 C C doub 1.31 N N
21 C13 C14 C C sing 1.51 N N
22 C13 C15 C C sing 1.51 N N
23 C1 H1 C H sing 1.09 N N
24 C1 H1A C H sing 1.09 N N
25 C2 H2 C H sing 1.08 N N
26 C3 H3 C H sing 1.08 N N
27 C5 H5 C H sing 1.09 N N
28 C5 H5A C H sing 1.09 N N
29 C6 H6 C H sing 1.09 N N
30 C6 H6A C H sing 1.09 N N
31 C7 H7 C H sing 1.08 N N
32 C9 H9 C H sing 1.09 N N
33 C9 H9A C H sing 1.09 N N
34 C10 H10 C H sing 1.09 N N
35 C10 H10A C H sing 1.09 N N
36 C10 H10B C H sing 1.09 N N
37 C11 H11 C H sing 1.09 N N
38 C11 H11A C H sing 1.09 N N
39 C12 H12 C H sing 1.08 N N
40 C14 H14 C H sing 1.09 N N
41 C14 H14A C H sing 1.09 N N
42 C14 H14B C H sing 1.09 N N
43 C15 H15 C H sing 1.09 N N
44 C15 H15A C H sing 1.09 N N
45 C15 H15B C H sing 1.09 N N
46 O2A HO2A O H sing 0.97 N N
47 O2B HO2B O H sing 0.97 N N
48 O3B HO3B O H sing 0.97 N N



2DE : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
2DE 3aqc Open in New Window Bound ligand 2 1