Chemical Components in the PDB

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DEB : Summary

Code

DEB

One-letter code

X

Molecule name

6-DEOXYERYTHRONOLIDE B

Systematic names

ProgramVersionName
ACDLabs 10.04 (3R,4S,5R,6S,7S,9R,11R,12S,13R,14R)-14-ethyl-4,6,12-trihydroxy-3,5,7,9,11,13-hexamethyloxacyclotetradecane-2,10-dione
OpenEye OEToolkits 1.5.0 (3R,4S,5R,6S,7S,9R,11R,12S,13R,14R)-14-ethyl-4,6,12-trihydroxy-3,5,7,9,11,13-hexamethyl-1-oxacyclotetradecane-2,10-dione

Formula

C21 H38 O6

Formal charge

0

Molecular weight

386.523 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1OC(C(C(O)C(C(=O)C(CC(C)C(O)C(C)C(O)C1C)C)C)C)CC
SMILES CACTVS 3.341 CC[CH]1OC(=O)[CH](C)[CH](O)[CH](C)[CH](O)[CH](C)C[CH](C)C(=O)[CH](C)[CH](O)[CH]1C
SMILES OpenEye OEToolkits 1.5.0 CCC1C(C(C(C(=O)C(CC(C(C(C(C(C(=O)O1)C)O)C)O)C)C)C)O)C
Canonical SMILES CACTVS 3.341 CC[C@H]1OC(=O)[C@H](C)[C@@H](O)[C@H](C)[C@@H](O)[C@@H](C)C[C@@H](C)C(=O)[C@H](C)[C@@H](O)[C@H]1C
Canonical SMILES OpenEye OEToolkits 1.5.0 CC[C@@H]1[C@@H]([C@@H]([C@H](C(=O)[C@@H](C[C@@H]([C@@H]([C@H]([C@@H]([C@H](C(=O)O1)C)O)C)O)C)C)C)O)C

IUPAC InChI

InChI=1S/C21H38O6/c1-8-16-12(4)19(24)13(5)17(22)10(2)9-11(3)18(23)14(6)20(25)15(7)21(26)27-16/h10-16,18-20,23-25H,8-9H2,1-7H3/t10-,11+,12+,13+,14-,15-,16-,18+,19+,20+/m1/s1

IUPAC InChI key

HQZOLNNEQAKEHT-IBBGRPSASA-N
DEB

wwPDB Information

Atom count

65 (27 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



DEB : Atoms of Molecule

Total Number of Atoms: 65
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 2.111 0.242 0.167
2 C10 C C10 R N N 0 -2.249 -0.111 2.39
3 C11 C C11 S N N 0 -0.798 0.304 2.107
4 C12 C C12 R N N 0 0.196 -0.394 3.02
5 C13 C C13 R N N 0 1.64 0.0090 2.557
6 C14 C C14 N N N 0 2.611 -0.47 3.676
7 C15 C C15 N N N 0 4.031 -0.0010 3.356
8 C18 C C18 N N N 0 3.769 -0.476 -1.446
9 C2 C C2 R N N 0 2.299 -0.434 -1.165
10 C20 C C20 N N N 0 0.919 -0.974 -4.183
11 C22 C C22 N N N 0 -2.537 -1.053 -3.045
12 C23 C C23 N N N 0 -2.751 -2.026 0.151
13 C25 C C25 N N N 0 -2.706 0.73 3.527
14 C27 C C27 N N N 0 0.075 -1.86 2.76
15 C3 C C3 S N N 0 1.662 0.463 -2.203
16 C4 C C4 R N N 0 0.435 -0.288 -2.82
17 C5 C C5 S N N 0 -0.652 0.636 -3.141
18 C6 C C6 S N N 0 -1.977 0.233 -2.432
19 C7 C C7 N N N 0 -1.647 0.062 -0.914
20 C8 C C8 R N N 0 -2.907 -0.495 -0.141
21 C9 C C9 N N N 0 -3.088 0.251 1.147
22 H10 H H10 N N N 0 -2.373 -1.141 2.629
23 H11 H H11 N N N 0 -0.567 0.116 0.972
24 H12 H H12 N N N 0 -0.052 -0.145 4.002
25 H13 H H13 N N N 0 1.715 1.138 2.562
26 H141 H 1H14 N N N 0 2.592 -1.559 3.731
27 H142 H 2H14 N N N 0 2.297 -0.053 4.633
28 H151 H 1H15 N N N 0 4.71 -0.337 4.139
29 H152 H 2H15 N N N 0 4.345 -0.418 2.399
30 H153 H 3H15 N N N 0 4.05 1.087 3.301
31 H181 H 1H18 N N N 0 4.273 -1.037 -0.659
32 H182 H 2H18 N N N 0 3.941 -0.962 -2.407
33 H183 H 3H18 N N N 0 4.162 0.539 -1.477
34 H2 H H2 N N N 0 1.811 -1.425 -1.097
35 H201 H 1H20 N N N 0 1.725 -1.677 -3.971
36 H202 H 2H20 N N N 0 0.083 -1.507 -4.638
37 H203 H 3H20 N N N 0 1.277 -0.207 -4.87
38 H221 H 1H22 N N N 0 -3.464 -1.322 -2.539
39 H222 H 2H22 N N N 0 -2.735 -0.894 -4.105
40 H223 H 3H22 N N N 0 -1.812 -1.858 -2.927
41 H231 H 1H23 N N N 0 -3.631 -2.386 0.683
42 H232 H 2H23 N N N 0 -2.649 -2.567 -0.789
43 H233 H 3H23 N N N 0 -1.863 -2.19 0.762
44 H251 H 1H25 N N N 0 -3.761 0.538 3.721
45 H252 H 2H25 N N N 0 -2.123 0.487 4.416
46 H253 H 3H25 N N N 0 -2.567 1.782 3.279
47 H271 H 1H27 N N N 0 0.774 -2.401 3.397
48 H272 H 2H27 N N N 0 -0.942 -2.185 2.979
49 H273 H 3H27 N N N 0 0.304 -2.064 1.714
50 H3 H H3 N N N 0 1.254 1.406 -1.823
51 H4 H H4 N N N 0 0.076 -1.076 -2.143
52 H5 H H5 N N N 0 -0.436 1.616 -2.798
53 H6 H H6 N N N 0 -2.681 1.038 -2.486
54 H71 H 1H7 N N N 0 -0.797 -0.652 -0.737
55 H72 H 2H7 N N N 0 -1.468 0.993 -0.411
56 H8 H H8 N N N 0 -3.822 -0.398 -0.78
57 HO1 H HO1 N N N 0 -1.661 1.294 -4.649
58 HO6 H HO6 N N N 0 -1.251 2.159 1.584
59 HO9 H HO9 N N N 0 3.329 1.256 -2.804
60 O16 O O16 N N N 0 1.94 -0.548 1.328
61 O17 O O17 N N N 0 2.048 1.432 0.274
62 O19 O O19 N N N 0 2.592 0.798 -3.232
63 O21 O O21 N N N 0 -0.938 0.664 -4.526
64 O24 O O24 N N N 0 -3.945 1.079 1.217
65 O26 O O26 N N N 0 -0.653 1.762 2.233



DEB : Chemical Bonds

Total Number of Bonds: 65
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.51 N N
2 C1 O16 C O sing 1.41 N N
3 C1 O17 C O doub 1.2 N N
4 C2 C3 C C sing 1.51 N N
5 C2 C18 C C sing 1.5 N N
6 C2 H2 C H sing 1.11 N N
7 C3 C4 C C sing 1.57 N N
8 C3 O19 C O sing 1.43 N N
9 C3 H3 C H sing 1.1 N N
10 C4 C5 C C sing 1.46 N N
11 C4 C20 C C sing 1.6 N N
12 C4 H4 C H sing 1.1 N N
13 C5 C6 C C sing 1.56 N N
14 C5 O21 C O sing 1.41 N N
15 C5 H5 C H sing 1.06 N N
16 C6 C7 C C sing 1.56 N N
17 C6 C22 C C sing 1.53 N N
18 C6 H6 C H sing 1.07 N N
19 C7 C8 C C sing 1.58 N N
20 C7 H71 C H sing 1.12 N N
21 C7 H72 C H sing 1.07 N N
22 C8 C9 C C sing 1.5 N N
23 C8 C23 C C sing 1.57 N N
24 C8 H8 C H sing 1.12 N N
25 C9 C10 C C sing 1.54 N N
26 C9 O24 C O doub 1.19 N N
27 C10 C11 C C sing 1.54 N N
28 C10 C25 C C sing 1.49 N N
29 C10 H10 C H sing 1.06 N N
30 C11 C12 C C sing 1.52 N N
31 C11 O26 C O sing 1.47 N N
32 C11 H11 C H sing 1.17 N N
33 C12 C13 C C sing 1.57 N N
34 C12 C27 C C sing 1.49 N N
35 C12 H12 C H sing 1.04 N N
36 C13 C14 C C sing 1.56 N N
37 C13 O16 C O sing 1.38 N N
38 C13 H13 C H sing 1.13 N N
39 C14 C15 C C sing 1.53 N N
40 C14 H141 C H sing 1.09 N N
41 C14 H142 C H sing 1.09 N N
42 C15 H151 C H sing 1.09 N N
43 C15 H152 C H sing 1.09 N N
44 C15 H153 C H sing 1.09 N N
45 C18 H181 C H sing 1.09 N N
46 C18 H182 C H sing 1.09 N N
47 C18 H183 C H sing 1.09 N N
48 O19 HO9 O H sing 0.97 N N
49 C20 H201 C H sing 1.09 N N
50 C20 H202 C H sing 1.09 N N
51 C20 H203 C H sing 1.09 N N
52 O21 HO1 O H sing 0.97 N N
53 C22 H221 C H sing 1.09 N N
54 C22 H222 C H sing 1.09 N N
55 C22 H223 C H sing 1.09 N N
56 C23 H231 C H sing 1.09 N N
57 C23 H232 C H sing 1.09 N N
58 C23 H233 C H sing 1.09 N N
59 C25 H251 C H sing 1.09 N N
60 C25 H252 C H sing 1.09 N N
61 C25 H253 C H sing 1.09 N N
62 O26 HO6 O H sing 0.97 N N
63 C27 H271 C H sing 1.09 N N
64 C27 H272 C H sing 1.09 N N
65 C27 H273 C H sing 1.09 N N



DEB : Used in PDB Entries

Total Number of PDB Entries: 8
Ligand Code PDB Entry ID Type Total Distinct
DEB 1jio Open in New Window Bound ligand 1 1
DEB 1oxa Open in New Window Bound ligand 1 1
DEB 1z8o Open in New Window Bound ligand 1 1
DEB 1z8p Open in New Window Bound ligand 1 1
DEB 1z8q Open in New Window Bound ligand 1 1
DEB 5mns Open in New Window Bound ligand 6 1
DEB 5mnv Open in New Window Bound ligand 9 1
DEB 6zi3 Open in New Window Bound ligand 6 1