Chemical Components in the PDB

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EB4 : Summary

Code

EB4

One-letter code

X

Molecule name

N,N',N''-[(3S,7S,11S)-2,6,10-trioxo-1,5,9-trioxacyclododecane-3,7,11-triyl]tris(2,3-dihydroxybenzamide)

Systematic names

ProgramVersionName
ACDLabs 10.04 N,N',N''-[(3S,7S,11S)-2,6,10-trioxo-1,5,9-trioxacyclododecane-3,7,11-triyl]tris(2,3-dihydroxybenzamide)
OpenEye OEToolkits 1.5.0 N-[(3S,7S,11S)-7,11-bis[(2,3-dihydroxyphenyl)carbonylamino]-2,6,10-trioxo-1,5,9-trioxacyclododec-3-yl]-2,3-dihydroxy-benzamide

Formula

C30 H27 N3 O15

Formal charge

0

Molecular weight

669.546 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C2OCC(C(=O)OCC(C(=O)OCC2NC(=O)c1cccc(O)c1O)NC(=O)c3cccc(O)c3O)NC(=O)c4cccc(O)c4O
SMILES CACTVS 3.341 Oc1cccc(C(=O)N[CH]2COC(=O)[CH](COC(=O)[CH](COC2=O)NC(=O)c3cccc(O)c3O)NC(=O)c4cccc(O)c4O)c1O
SMILES OpenEye OEToolkits 1.5.0 c1cc(c(c(c1)O)O)C(=O)NC2COC(=O)C(COC(=O)C(COC2=O)NC(=O)c3cccc(c3O)O)NC(=O)c4cccc(c4O)O
Canonical SMILES CACTVS 3.341 Oc1cccc(C(=O)N[C@H]2COC(=O)[C@H](COC(=O)[C@H](COC2=O)NC(=O)c3cccc(O)c3O)NC(=O)c4cccc(O)c4O)c1O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1cc(c(c(c1)O)O)C(=O)N[C@H]2COC(=O)[C@H](COC(=O)[C@H](COC2=O)NC(=O)c3cccc(c3O)O)NC(=O)c4cccc(c4O)O

IUPAC InChI

InChI=1S/C30H27N3O15/c34-19-7-1-4-13(22(19)37)25(40)31-16-10-46-29(44)18(33-27(42)15-6-3-9-21(36)24(15)39)12-48-30(45)17(11-47-28(16)43)32-26(41)14-5-2-8-20(35)23(14)38/h1-9,16-18,34-39H,10-12H2,(H,31,40)(H,32,41)(H,33,42)/t16-,17-,18-/m0/s1

IUPAC InChI key

SERBHKJMVBATSJ-BZSNNMDCSA-N
EB4

wwPDB Information

Atom count

75 (48 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2008-04-08

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



EB4 : Atoms of Molecule

Total Number of Atoms: 75
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O6 O O6 N N N 0 3.664 -4.78 3.535
2 O4 O O4 N N N 0 -5.885 -0.658 3.769
3 O5 O O5 N N N 0 2.529 5.436 3.577
4 N1 N N1 N N N 0 -2.549 1.052 -1.007
5 C5 C C5 N Y N 0 2.387 4.234 2.956
6 C4 C C4 N Y N 0 -4.794 -0.158 3.129
7 C1 C C1 N Y N 0 -4.784 -0.064 1.74
8 C2 C C2 N Y N 0 2.407 4.162 1.566
9 C6 C C6 N Y N 0 2.659 -4.078 2.945
10 C8 C C8 N Y N 0 2.228 3.081 3.707
11 N2 N N2 N N N 0 2.14 1.635 -1.142
12 C9 C C9 N Y N 0 1.784 -3.337 3.72
13 C10 C C10 N Y N 0 -2.58 0.773 3.213
14 O3 O O3 N N N 0 3.374 -4.82 0.796
15 N3 N N3 N N N 0 0.316 -2.69 -1.079
16 C16 C C16 N Y N 0 -3.658 0.451 1.088
17 C7 C C7 N Y N 0 -3.695 0.263 3.858
18 C3 C C3 N Y N 0 2.515 -4.099 1.561
19 C11 C C11 N Y N 0 2.083 1.854 3.082
20 O1 O O1 N N N 0 -5.862 -0.471 1.022
21 O2 O O2 N N N 0 2.568 5.288 0.827
22 C12 C C12 N Y N 0 0.758 -2.62 3.127
23 C15 C C15 N Y N 0 0.599 -2.636 1.759
24 C14 C C14 N Y N 0 2.096 1.767 1.707
25 C13 C C13 N Y N 0 -2.554 0.867 1.839
26 O7 O O7 N N N 0 -4.597 0.193 -1.033
27 C19 C C19 N N N 0 -3.635 0.555 -0.383
28 C22 C C22 S N N 0 -2.527 1.156 -2.469
29 C25 C C25 N N N 0 -2.086 -0.159 -3.059
30 O10 O O10 N N N 0 -2.07 -0.308 -4.257
31 O15 O O15 N N N 0 -1.712 -1.165 -2.252
32 C30 C C30 N N N 0 -1.304 -2.404 -2.889
33 C24 C C24 S N N 0 0.154 -2.704 -2.535
34 C21 C C21 N N N 0 1.315 -3.389 -0.505
35 O12 O O12 N N N 0 1.11 -1.548 -4.352
36 C18 C C18 N Y N 0 1.479 -3.374 0.961
37 O9 O O9 N N N 0 2.082 -4.032 -1.196
38 C27 C C27 N N N 0 1.046 -1.657 -3.15
39 C28 C C28 N N N 0 -1.55 2.256 -2.887
40 O13 O O13 N N N 0 -0.249 1.998 -2.297
41 C26 C C26 N N N 0 0.778 1.819 -3.143
42 O11 O O11 N N N 0 0.596 1.877 -4.336
43 C23 C C23 S N N 0 2.159 1.546 -2.604
44 C29 C C29 N N N 0 2.602 0.143 -3.024
45 O14 O O14 N N N 0 1.769 -0.845 -2.363
46 C20 C C20 N N N 0 2.281 2.831 -0.538
47 O8 O O8 N N N 0 2.424 3.837 -1.206
48 C17 C C17 N Y N 0 2.261 2.921 0.935
49 HO6 H HO6 N N N 0 4.485 -4.28 3.639
50 HO4 H HO4 N N N 0 -5.858 -1.615 3.902
51 HO5 H HO5 N N N 0 1.694 5.896 3.738
52 HN1 H HN1 N N N 0 -1.782 1.341 -0.489
53 H8 H H8 N N N 0 2.217 3.14 4.785
54 HN2 H HN2 N N N 0 2.025 0.833 -0.609
55 H9 H H9 N N N 0 1.901 -3.319 4.794
56 H10 H H10 N N N 0 -1.728 1.099 3.79
57 HO3 H HO3 N N N 0 3.093 -5.732 0.641
58 HN3 H HN3 N N N 0 -0.296 -2.177 -0.528
59 H7 H H7 N N N 0 -3.707 0.193 4.936
60 H11 H H11 N N N 0 1.961 0.96 3.675
61 HO1 H HO1 N N N 0 -6.516 0.225 0.866
62 HO2 H HO2 N N N 0 3.491 5.502 0.632
63 H12 H H12 N N N 0 0.08 -2.045 3.74
64 H15 H H15 N N N 0 -0.203 -2.076 1.302
65 H14 H H14 N N N 0 1.983 0.807 1.225
66 H30A H H30A N N N 0 -1.403 -2.306 -3.97
67 H13 H H13 N N N 0 -1.682 1.265 1.341
68 H22 H H22 N N N 0 -3.526 1.4 -2.831
69 H30 H H30 N N N 0 -1.938 -3.218 -2.538
70 H24 H H24 N N N 0 0.427 -3.687 -2.921
71 H28 H H28 N N N 0 -1.461 2.269 -3.973
72 H28A H H28A N N N 0 -1.921 3.221 -2.542
73 H23 H H23 N N N 0 2.857 2.283 -3.004
74 H29 H H29 N N N 0 2.503 0.039 -4.104
75 H29A H H29A N N N 0 3.643 -0.009 -2.739



EB4 : Chemical Bonds

Total Number of Bonds: 78
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O6 C6 O C sing 1.36 N N
2 O6 HO6 O H sing 0.97 N N
3 O4 HO4 O H sing 0.97 N N
4 O5 C5 O C sing 1.36 N N
5 O5 HO5 O H sing 0.97 N N
6 N1 C22 N C sing 1.47 N N
7 N1 HN1 N H sing 0.97 N N
8 C5 C2 C C doub 1.39 N Y
9 C5 C8 C C sing 1.39 N Y
10 C4 O4 C O sing 1.36 N N
11 C4 C1 C C sing 1.39 N Y
12 C1 O1 C O sing 1.36 N N
13 C2 C17 C C sing 1.4 N Y
14 C6 C3 C C sing 1.39 N Y
15 C8 C11 C C doub 1.38 N Y
16 C8 H8 C H sing 1.08 N N
17 N2 C23 N C sing 1.46 N N
18 N2 HN2 N H sing 0.97 N N
19 C9 C6 C C doub 1.38 N Y
20 C9 C12 C C sing 1.39 N Y
21 C9 H9 C H sing 1.08 N N
22 C10 C7 C C sing 1.39 N Y
23 C10 C13 C C doub 1.38 N Y
24 C10 H10 C H sing 1.08 N N
25 O3 HO3 O H sing 0.97 N N
26 N3 C21 N C sing 1.35 N N
27 N3 C24 N C sing 1.47 N N
28 N3 HN3 N H sing 0.97 N N
29 C16 C1 C C doub 1.4 N Y
30 C16 C19 C C sing 1.47 N N
31 C7 C4 C C doub 1.38 N Y
32 C7 H7 C H sing 1.08 N N
33 C3 O3 C O sing 1.36 N N
34 C3 C18 C C doub 1.4 N Y
35 C11 C14 C C sing 1.38 N Y
36 C11 H11 C H sing 1.08 N N
37 O1 HO1 O H sing 0.97 N N
38 O2 C2 O C sing 1.36 N N
39 O2 HO2 O H sing 0.97 N N
40 C12 C15 C C doub 1.38 N Y
41 C12 H12 C H sing 1.08 N N
42 C15 C18 C C sing 1.4 N Y
43 C15 H15 C H sing 1.08 N N
44 C14 H14 C H sing 1.08 N N
45 C13 C16 C C sing 1.4 N Y
46 C13 H13 C H sing 1.08 N N
47 O7 C19 O C doub 1.22 N N
48 C19 N1 C N sing 1.35 N N
49 C22 C25 C C sing 1.51 N N
50 C22 C28 C C sing 1.53 N N
51 C22 H22 C H sing 1.09 N N
52 C25 O15 C O sing 1.34 N N
53 O10 C25 O C doub 1.21 N N
54 O15 C30 O C sing 1.45 N N
55 C30 C24 C C sing 1.53 N N
56 C30 H30 C H sing 1.09 N N
57 C30 H30A C H sing 1.09 N N
58 C24 H24 C H sing 1.09 N N
59 C21 O9 C O doub 1.22 N N
60 C18 C21 C C sing 1.48 N N
61 C27 C24 C C sing 1.51 N N
62 C27 O14 C O sing 1.34 N N
63 O12 C27 O C doub 1.21 N N
64 C28 H28 C H sing 1.09 N N
65 C28 H28A C H sing 1.09 N N
66 O13 C28 O C sing 1.45 N N
67 O13 C26 O C sing 1.34 N N
68 C26 C23 C C sing 1.51 N N
69 O11 C26 O C doub 1.21 N N
70 C23 C29 C C sing 1.53 N N
71 C23 H23 C H sing 1.09 N N
72 C29 O14 C O sing 1.45 N N
73 C29 H29 C H sing 1.09 N N
74 C29 H29A C H sing 1.09 N N
75 C20 N2 C N sing 1.35 N N
76 O8 C20 O C doub 1.22 N N
77 C17 C14 C C doub 1.4 N Y
78 C17 C20 C C sing 1.48 N N



EB4 : Used in PDB Entries

Total Number of PDB Entries: 10
Ligand Code PDB Entry ID Type Total Distinct
EB4 2kt4 Open in New Window Bound ligand 1 1
EB4 2lbv Open in New Window Bound ligand 1 1
EB4 2xuz Open in New Window Bound ligand 1 1
EB4 3cmp Open in New Window Bound ligand 2 1
EB4 3tlk Open in New Window Bound ligand 4 1
EB4 4zfx Open in New Window Bound ligand 2 1
EB4 6gi1 Open in New Window Bound ligand 1 1
EB4 6i2j Open in New Window Bound ligand 1 1
EB4 6q5e Open in New Window Bound ligand 1 1
EB4 6r1f Open in New Window Bound ligand 1 1