Chemical Components in the PDB

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EB6 : Summary

Code

EB6

One-letter code

X

Molecule name

methyl (2~{S})-3-[4-[3-(4-methoxy-2-oxidanyl-phenyl)prop-2-ynoyloxy]phenyl]-2-[[2-(phenylcarbonyl)phenyl]amino]propanoate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 methyl (2~{S})-3-[4-[3-(4-methoxy-2-oxidanyl-phenyl)prop-2-ynoyloxy]phenyl]-2-[[2-(phenylcarbonyl)phenyl]amino]propanoate

Formula

C33 H27 N O7

Formal charge

0

Molecular weight

549.57 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 COC(=O)[CH](Cc1ccc(OC(=O)C#Cc2ccc(OC)cc2O)cc1)Nc3ccccc3C(=O)c4ccccc4
SMILES OpenEye OEToolkits 2.0.7 COc1ccc(c(c1)O)C#CC(=O)Oc2ccc(cc2)CC(C(=O)OC)Nc3ccccc3C(=O)c4ccccc4
Canonical SMILES CACTVS 3.385 COC(=O)[C@H](Cc1ccc(OC(=O)C#Cc2ccc(OC)cc2O)cc1)Nc3ccccc3C(=O)c4ccccc4
Canonical SMILES OpenEye OEToolkits 2.0.7 COc1ccc(c(c1)O)C#CC(=O)Oc2ccc(cc2)C[C@@H](C(=O)OC)Nc3ccccc3C(=O)c4ccccc4

IUPAC InChI

InChI=1S/C33H27NO7/c1-39-26-18-14-23(30(35)21-26)15-19-31(36)41-25-16-12-22(13-17-25)20-29(33(38)40-2)34-28-11-7-6-10-27(28)32(37)24-8-4-3-5-9-24/h3-14,16-18,21,29,34-35H,20H2,1-2H3/t29-/m0/s1

IUPAC InChI key

CEHNFAIQCQNZKE-LJAQVGFWSA-N
EB6

wwPDB Information

Atom count

68 (41 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-12-06

Last modified at

2020-02-07

Status

Released

Obsoleted

Not Assigned



EB6 : Atoms of Molecule

Total Number of Atoms: 68
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 N Y N 0 -4.298 -3.522 -1.663
2 C2 C C2 N Y N 0 -6.436 -3.158 -2.681
3 O4 O O1 N N N 0 2.92 1.018 -1.99
4 C23 C C3 N N N 0 3.278 0.764 -0.856
5 C24 C C4 N N N 0 4.656 0.479 -0.587
6 C25 C C5 N N N 0 5.785 0.245 -0.367
7 C26 C C6 N Y N 0 7.162 -0.04 -0.098
8 C31 C C7 N Y N 0 8.104 -0.022 -1.141
9 O6 O O2 N N N 0 7.712 0.261 -2.409
10 C30 C C8 N Y N 0 9.433 -0.294 -0.868
11 C29 C C9 N Y N 0 9.828 -0.582 0.431
12 O5 O O3 N N N 0 11.132 -0.848 0.697
13 C32 C C10 N N N 0 11.472 -1.136 2.055
14 C28 C C11 N Y N 0 8.893 -0.599 1.462
15 C27 C C12 N Y N 0 7.579 -0.333 1.207
16 O3 O O4 N N N 0 2.378 0.751 0.15
17 C20 C C13 N Y N 0 1.102 1.127 -0.131
18 C19 C C14 N Y N 0 0.252 0.256 -0.798
19 C18 C C15 N Y N 0 -1.044 0.641 -1.082
20 C21 C C16 N Y N 0 0.647 2.38 0.253
21 C22 C C17 N Y N 0 -0.65 2.76 -0.034
22 C16 C C18 N Y N 0 -1.494 1.892 -0.703
23 C15 C C19 N N N 0 -2.908 2.309 -1.015
24 C13 C C20 S N N 0 -3.824 1.911 0.144
25 C14 C C21 N N N 0 -5.214 2.435 -0.111
26 O2 O O5 N N N 0 -6.143 1.668 -0.193
27 O1 O O6 N N N 0 -5.419 3.755 -0.247
28 C17 C C22 N N N 0 -6.783 4.188 -0.491
29 N N N1 N N N 0 -3.866 0.45 0.253
30 C12 C C23 N Y N 0 -4.17 -0.146 1.469
31 C11 C C24 N Y N 0 -4.555 0.633 2.552
32 C10 C C25 N Y N 0 -4.856 0.038 3.76
33 C9 C C26 N Y N 0 -4.78 -1.339 3.903
34 C8 C C27 N Y N 0 -4.402 -2.13 2.84
35 C7 C C28 N Y N 0 -4.097 -1.543 1.608
36 C6 C C29 N N N 0 -3.692 -2.382 0.468
37 O O O7 N N N 0 -2.57 -2.851 0.426
38 C5 C C30 N Y N 0 -4.647 -2.654 -0.627
39 C3 C C32 N Y N 0 -5.193 -3.767 -2.684
40 C C C31 N Y N 0 -5.903 -2.043 -0.629
41 H5 H H5 N N N 0 11.212 -0.284 2.683
42 C1 C C33 N Y N 0 -6.79 -2.301 -1.654
43 H1 H H1 N N N 0 -3.329 -3.998 -1.667
44 H2 H H2 N N N 0 -7.132 -3.353 -3.483
45 H3 H H3 N N N 0 7.745 1.202 -2.63
46 H4 H H4 N N N 0 10.163 -0.282 -1.665
47 H6 H H6 N N N 0 10.92 -2.015 2.388
48 H7 H H7 N N N 0 12.542 -1.33 2.128
49 H8 H H8 N N N 0 9.21 -0.825 2.47
50 H9 H H9 N N N 0 6.86 -0.344 2.013
51 H10 H H10 N N N 0 0.603 -0.721 -1.094
52 H11 H H11 N N N 0 -1.706 -0.036 -1.601
53 H12 H H12 N N N 0 1.305 3.057 0.776
54 H13 H H13 N N N 0 -1.005 3.735 0.265
55 H14 H H14 N N N 0 -2.946 3.39 -1.153
56 H15 H H15 N N N 0 -3.24 1.815 -1.928
57 H16 H H16 N N N 0 -3.441 2.334 1.072
58 H17 H H17 N N N 0 -7.147 3.739 -1.415
59 H18 H H18 N N N 0 -7.417 3.878 0.339
60 H19 H H19 N N N 0 -6.808 5.274 -0.581
61 H20 H H20 N N N 0 -3.681 -0.1 -0.524
62 H21 H H21 N N N 0 -4.617 1.706 2.45
63 H22 H H22 N N N 0 -5.154 0.648 4.6
64 H23 H H23 N N N 0 -5.017 -1.794 4.853
65 H24 H H24 N N N 0 -4.348 -3.202 2.956
66 H25 H H25 N N N 0 -6.18 -1.37 0.169
67 H26 H H26 N N N 0 -4.923 -4.435 -3.488
68 H27 H H27 N N N 0 -7.761 -1.829 -1.657



EB6 : Chemical Bonds

Total Number of Bonds: 71
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O5 C29 O C sing 1.36 N N
2 O5 C32 O C sing 1.43 N N
3 C30 C29 C C doub 1.39 N Y
4 C30 C31 C C sing 1.38 N Y
5 O6 C31 O C sing 1.36 N N
6 C29 C28 C C sing 1.39 N Y
7 C31 C26 C C doub 1.41 N Y
8 C28 C27 C C doub 1.36 N Y
9 C26 C27 C C sing 1.4 N Y
10 C26 C25 C C sing 1.43 N N
11 C1 C2 C C doub 1.38 N Y
12 C1 C C C sing 1.38 N Y
13 C2 C3 C C sing 1.38 N Y
14 C25 C24 C C trip 1.17 N N
15 O4 C23 O C doub 1.22 N N
16 C24 C23 C C sing 1.43 N N
17 C23 O3 C O sing 1.35 N N
18 C C5 C C doub 1.4 N Y
19 C3 C4 C C doub 1.38 N Y
20 O3 C20 O C sing 1.36 N N
21 C5 C4 C C sing 1.4 N Y
22 C5 C6 C C sing 1.48 N N
23 C19 C20 C C doub 1.39 N Y
24 C19 C18 C C sing 1.38 N Y
25 C20 C21 C C sing 1.39 N Y
26 C6 O C O doub 1.22 N N
27 C6 C7 C C sing 1.47 N N
28 C8 C7 C C doub 1.4 N Y
29 C8 C9 C C sing 1.38 N Y
30 C18 C16 C C doub 1.38 N Y
31 C7 C12 C C sing 1.41 N Y
32 C21 C22 C C doub 1.38 N Y
33 C9 C10 C C doub 1.39 N Y
34 C16 C22 C C sing 1.38 N Y
35 C16 C15 C C sing 1.51 N N
36 C12 N C N sing 1.39 N N
37 C12 C11 C C doub 1.39 N Y
38 N C13 N C sing 1.47 N N
39 C10 C11 C C sing 1.38 N Y
40 C15 C13 C C sing 1.53 N N
41 C13 C14 C C sing 1.51 N N
42 C14 O1 C O sing 1.34 N N
43 C14 O2 C O doub 1.21 N N
44 O1 C17 O C sing 1.45 N N
45 C4 H1 C H sing 1.08 N N
46 C2 H2 C H sing 1.08 N N
47 O6 H3 O H sing 0.97 N N
48 C30 H4 C H sing 1.08 N N
49 C32 H5 C H sing 1.09 N N
50 C32 H6 C H sing 1.09 N N
51 C32 H7 C H sing 1.09 N N
52 C28 H8 C H sing 1.08 N N
53 C27 H9 C H sing 1.08 N N
54 C19 H10 C H sing 1.08 N N
55 C18 H11 C H sing 1.08 N N
56 C21 H12 C H sing 1.08 N N
57 C22 H13 C H sing 1.08 N N
58 C15 H14 C H sing 1.09 N N
59 C15 H15 C H sing 1.09 N N
60 C13 H16 C H sing 1.09 N N
61 C17 H17 C H sing 1.09 N N
62 C17 H18 C H sing 1.09 N N
63 C17 H19 C H sing 1.09 N N
64 N H20 N H sing 0.97 N N
65 C11 H21 C H sing 1.08 N N
66 C10 H22 C H sing 1.08 N N
67 C9 H23 C H sing 1.08 N N
68 C8 H24 C H sing 1.08 N N
69 C H25 C H sing 1.08 N N
70 C3 H26 C H sing 1.08 N N
71 C1 H27 C H sing 1.08 N N



EB6 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
EB6 6jf0 Open in New Window Bound ligand 1 1