Chemical Components in the PDB

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6EF : Summary

Code

6EF

One-letter code

X

Molecule name

N-(2-{2-[(2R,5S)-5-{[(benzylcarbamoyl)oxy]methyl}morpholin-2-yl]ethyl}phenyl)-Nalpha-(methoxycarbonyl)-beta-phenyl-L-phenylalaninamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-(2-{2-[(2R,5S)-5-{[(benzylcarbamoyl)oxy]methyl}morpholin-2-yl]ethyl}phenyl)-Nalpha-(methoxycarbonyl)-beta-phenyl-L-phenylalaninamide
OpenEye OEToolkits 2.0.4 methyl ~{N}-[(2~{S})-1-oxidanylidene-3,3-diphenyl-1-[[2-[2-[(2~{R},5~{S})-5-[(phenylmethyl)carbamoyloxymethyl]morpholin-2-yl]ethyl]phenyl]amino]propan-2-yl]carbamate

Formula

C38 H42 N4 O6

Formal charge

0

Molecular weight

650.763 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C(OC)(NC(C(=O)Nc3c(CCC1CNC(CO1)COC(=O)NCc2ccccc2)cccc3)C(c4ccccc4)c5ccccc5)=O
SMILES CACTVS 3.385 COC(=O)N[CH](C(c1ccccc1)c2ccccc2)C(=O)Nc3ccccc3CC[CH]4CN[CH](CO4)COC(=O)NCc5ccccc5
SMILES OpenEye OEToolkits 2.0.4 COC(=O)NC(C(c1ccccc1)c2ccccc2)C(=O)Nc3ccccc3CCC4CNC(CO4)COC(=O)NCc5ccccc5
Canonical SMILES CACTVS 3.385 COC(=O)N[C@@H](C(c1ccccc1)c2ccccc2)C(=O)Nc3ccccc3CC[C@@H]4CN[C@@H](CO4)COC(=O)NCc5ccccc5
Canonical SMILES OpenEye OEToolkits 2.0.4 COC(=O)N[C@@H](C(c1ccccc1)c2ccccc2)C(=O)Nc3ccccc3CC[C@@H]4CN[C@@H](CO4)COC(=O)NCc5ccccc5

IUPAC InChI

InChI=1S/C38H42N4O6/c1-46-38(45)42-35(34(29-16-7-3-8-17-29)30-18-9-4-10-19-30)36(43)41-33-20-12-11-15-28(33)21-22-32-24-39-31(25-47-32)26-48-37(44)40-23-27-13-5-2-6-14-27/h2-20,31-32,34-35,39H,21-26H2,1H3,(H,40,44)(H,41,43)(H,42,45)/t31-,32+,35-/m0/s1

IUPAC InChI key

MYPZZBCHYVILMP-UKAHRKLESA-N
6EF

wwPDB Information

Atom count

90 (48 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2016-03-22

Last modified at

2016-05-13

Status

Released

Obsoleted

Not Assigned



6EF : Atoms of Molecule

Total Number of Atoms: 90
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C2 C C1 N N N 0 -3.366 -3.158 -0.407
2 C5 C C2 N N N 0 -3.785 -4.79 -2.096
3 C7 C C3 N Y N 0 -1.099 -1.388 -0.375
4 C9 C C4 N Y N 0 -1.242 -3.588 1.76
5 C10 C C5 N Y N 0 -0.652 -4.562 2.545
6 C11 C C6 N Y N 0 0.296 -4.209 3.488
7 C12 C C7 N Y N 0 0.652 -2.883 3.646
8 C13 C C8 N Y N 0 0.063 -1.91 2.861
9 C15 C C9 N Y N 0 -0.904 -0.54 -2.606
10 C18 C C10 N Y N 0 -0.507 -2.572 -0.773
11 C20 C C11 N Y N 0 -4.188 3.137 -0.438
12 C21 C C12 N Y N 0 -4.88 3.975 -1.29
13 C22 C C13 N Y N 0 -5.891 3.47 -2.089
14 C C C14 N N N 0 -3.688 -0.376 0.176
15 N N N1 N N N 0 -3.451 -2.694 0.856
16 O O O1 N N N 0 -4.102 -0.796 -0.884
17 C1 C C15 S N N 0 -3.046 -1.319 1.16
18 O3 O O2 N N N 0 -3.798 -4.399 -0.698
19 O4 O O3 N N N 0 -2.905 -2.454 -1.283
20 C6 C C16 N N N 0 -1.523 -1.202 1.059
21 C8 C C17 N Y N 0 -0.88 -2.263 1.914
22 C14 C C18 N Y N 0 -1.298 -0.372 -1.292
23 C16 C C19 N Y N 0 -0.312 -1.724 -3.004
24 C17 C C20 N Y N 0 -0.113 -2.74 -2.087
25 C19 C C21 N Y N 0 -4.507 1.786 -0.384
26 C23 C C22 N Y N 0 -6.21 2.126 -2.037
27 C24 C C23 N Y N 0 -5.525 1.284 -1.184
28 C25 C C24 N N N 0 0.521 3.706 2.681
29 C26 C C25 S N N 0 1.862 3.621 1.947
30 N27 N N2 N N N 0 1.796 4.433 0.723
31 C28 C C26 N N N 0 0.712 3.968 -0.153
32 C29 C C27 R N N 0 -0.618 4.049 0.602
33 O30 O O4 N N N 0 -0.525 3.279 1.804
34 C31 C C28 N N N 0 -1.739 3.491 -0.277
35 N32 N N3 N N N 0 -3.803 0.933 0.473
36 C33 C C29 N N N 0 -3.083 3.686 0.427
37 C34 C C30 N N N 0 2.152 2.165 1.579
38 O35 O O5 N N N 0 3.475 2.069 0.989
39 C36 C C31 N N N 0 3.887 0.846 0.607
40 N37 N N4 N N N 0 5.105 0.688 0.052
41 O38 O O6 N N N 0 3.161 -0.116 0.762
42 C39 C C32 N N N 0 5.554 -0.644 -0.364
43 C40 C C33 N Y N 0 6.939 -0.547 -0.949
44 C41 C C34 N Y N 0 8.045 -0.684 -0.131
45 C42 C C35 N Y N 0 9.316 -0.595 -0.667
46 C43 C C36 N Y N 0 9.481 -0.371 -2.022
47 C44 C C37 N Y N 0 8.375 -0.235 -2.839
48 C45 C C38 N Y N 0 7.104 -0.328 -2.303
49 H1 H H1 N N N 0 -4.238 -5.776 -2.202
50 H2 H H2 N N N 0 -4.352 -4.066 -2.681
51 H3 H H3 N N N 0 -2.757 -4.822 -2.455
52 H4 H H4 N N N 0 -1.982 -3.864 1.023
53 H5 H H5 N N N 0 -0.931 -5.597 2.421
54 H6 H H6 N N N 0 0.756 -4.969 4.101
55 H7 H H7 N N N 0 1.392 -2.607 4.383
56 H8 H H8 N N N 0 0.342 -0.874 2.985
57 H9 H H9 N N N 0 -1.06 0.253 -3.322
58 H10 H H10 N N N 0 -0.351 -3.365 -0.057
59 H11 H H11 N N N 0 -4.633 5.025 -1.332
60 H12 H H12 N N N 0 -6.431 4.128 -2.753
61 H13 H H13 N N N 0 -3.78 -3.27 1.563
62 H14 H H14 N N N 0 -3.364 -1.061 2.17
63 H15 H H15 N N N 0 -1.211 -0.217 1.406
64 H16 H H16 N N N 0 -1.761 0.553 -0.981
65 H17 H H17 N N N 0 -0.005 -1.856 -4.031
66 H18 H H18 N N N 0 0.351 -3.664 -2.398
67 H19 H H19 N N N 0 -7.0 1.736 -2.662
68 H20 H H20 N N N 0 -5.775 0.234 -1.144
69 H21 H H21 N N N 0 0.545 3.06 3.559
70 H22 H H22 N N N 0 0.34 4.735 2.991
71 H23 H H23 N N N 0 2.655 3.999 2.593
72 H24 H H24 N N N 0 1.688 5.412 0.944
73 H26 H H26 N N N 0 0.665 4.6 -1.041
74 H27 H H27 N N N 0 0.9 2.937 -0.45
75 H28 H H28 N N N 0 -0.832 5.089 0.85
76 H29 H H29 N N N 0 -1.749 4.018 -1.231
77 H30 H H30 N N N 0 -1.57 2.429 -0.45
78 H31 H H31 N N N 0 -3.398 1.284 1.281
79 H32 H H32 N N N 0 -3.252 4.749 0.601
80 H33 H H33 N N N 0 -3.073 3.159 1.382
81 H34 H H34 N N N 0 2.109 1.548 2.476
82 H35 H H35 N N N 0 1.409 1.816 0.862
83 H36 H H36 N N N 0 5.569 -1.308 0.5
84 H37 H H37 N N N 0 7.917 -0.859 0.927
85 H38 H H38 N N N 0 10.181 -0.701 -0.029
86 H39 H H39 N N N 0 10.474 -0.301 -2.441
87 H40 H H40 N N N 0 8.503 -0.059 -3.897
88 H41 H H41 N N N 0 6.24 -0.226 -2.943
89 H25 H H25 N N N 0 5.685 1.455 -0.072
90 H42 H H42 N N N 0 4.869 -1.039 -1.114



6EF : Chemical Bonds

Total Number of Bonds: 94
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C22 C23 C C doub 1.38 N Y
2 C22 C21 C C sing 1.38 N Y
3 C23 C24 C C sing 1.38 N Y
4 C21 C20 C C doub 1.38 N Y
5 C24 C19 C C doub 1.39 N Y
6 C20 C19 C C sing 1.39 N Y
7 C20 C33 C C sing 1.51 N N
8 C19 N32 C N sing 1.4 N N
9 C33 C31 C C sing 1.53 N N
10 C25 O30 C O sing 1.43 N N
11 C25 C26 C C sing 1.53 N N
12 O30 C29 O C sing 1.43 N N
13 N32 C N C sing 1.35 N N
14 N37 C36 N C sing 1.35 N N
15 N37 C39 N C sing 1.47 N N
16 C29 C31 C C sing 1.53 N N
17 C29 C28 C C sing 1.53 N N
18 C26 N27 C N sing 1.47 N N
19 C26 C34 C C sing 1.53 N N
20 C36 O35 C O sing 1.35 N N
21 C36 O38 C O doub 1.22 N N
22 C39 C40 C C sing 1.51 N N
23 O35 C34 O C sing 1.45 N N
24 C O C O doub 1.21 N N
25 C C1 C C sing 1.51 N N
26 N27 C28 N C sing 1.47 N N
27 O4 C2 O C doub 1.21 N N
28 C5 O3 C O sing 1.45 N N
29 C2 O3 C O sing 1.35 N N
30 C2 N C N sing 1.35 N N
31 C1 N C N sing 1.47 N N
32 C1 C6 C C sing 1.53 N N
33 C40 C41 C C doub 1.38 N Y
34 C40 C45 C C sing 1.38 N Y
35 C41 C42 C C sing 1.38 N Y
36 C13 C12 C C doub 1.38 N Y
37 C13 C8 C C sing 1.38 N Y
38 C45 C44 C C doub 1.38 N Y
39 C12 C11 C C sing 1.38 N Y
40 C6 C8 C C sing 1.51 N N
41 C6 C7 C C sing 1.51 N N
42 C8 C9 C C doub 1.38 N Y
43 C11 C10 C C doub 1.38 N Y
44 C9 C10 C C sing 1.38 N Y
45 C42 C43 C C doub 1.38 N Y
46 C44 C43 C C sing 1.38 N Y
47 C7 C14 C C doub 1.38 N Y
48 C7 C18 C C sing 1.38 N Y
49 C14 C15 C C sing 1.38 N Y
50 C18 C17 C C doub 1.38 N Y
51 C15 C16 C C doub 1.38 N Y
52 C17 C16 C C sing 1.38 N Y
53 C5 H1 C H sing 1.09 N N
54 C5 H2 C H sing 1.09 N N
55 C5 H3 C H sing 1.09 N N
56 C9 H4 C H sing 1.08 N N
57 C10 H5 C H sing 1.08 N N
58 C11 H6 C H sing 1.08 N N
59 C12 H7 C H sing 1.08 N N
60 C13 H8 C H sing 1.08 N N
61 C15 H9 C H sing 1.08 N N
62 C18 H10 C H sing 1.08 N N
63 C21 H11 C H sing 1.08 N N
64 C22 H12 C H sing 1.08 N N
65 N H13 N H sing 0.97 N N
66 C1 H14 C H sing 1.09 N N
67 C6 H15 C H sing 1.09 N N
68 C14 H16 C H sing 1.08 N N
69 C16 H17 C H sing 1.08 N N
70 C17 H18 C H sing 1.08 N N
71 C23 H19 C H sing 1.08 N N
72 C24 H20 C H sing 1.08 N N
73 C25 H21 C H sing 1.09 N N
74 C25 H22 C H sing 1.09 N N
75 C26 H23 C H sing 1.09 N N
76 N27 H24 N H sing 1.01 N N
77 C28 H26 C H sing 1.09 N N
78 C28 H27 C H sing 1.09 N N
79 C29 H28 C H sing 1.09 N N
80 C31 H29 C H sing 1.09 N N
81 C31 H30 C H sing 1.09 N N
82 N32 H31 N H sing 0.97 N N
83 C33 H32 C H sing 1.09 N N
84 C33 H33 C H sing 1.09 N N
85 C34 H34 C H sing 1.09 N N
86 C34 H35 C H sing 1.09 N N
87 C39 H36 C H sing 1.09 N N
88 C41 H37 C H sing 1.08 N N
89 C42 H38 C H sing 1.08 N N
90 C43 H39 C H sing 1.08 N N
91 C44 H40 C H sing 1.08 N N
92 C45 H41 C H sing 1.08 N N
93 N37 H25 N H sing 0.97 N N
94 C39 H42 C H sing 1.09 N N



6EF : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
6EF 5ivs Open in New Window Bound ligand 1 1