Chemical Components in the PDB

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5EX : Summary

Code

5EX

One-letter code

X

Molecule name

ethyl (2Z,4S)-4-[(N-{[(cyclobutylmethyl)amino](oxo)acetyl}-L-phenylalanyl)amino]-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate

Systematic names

ProgramVersionName
ACDLabs 12.01 ethyl (2Z,4S)-4-[(N-{[(cyclobutylmethyl)amino](oxo)acetyl}-L-phenylalanyl)amino]-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate
OpenEye OEToolkits 1.9.2 ethyl (4S)-4-[[(2S)-2-[[2-(cyclobutylmethylamino)-2-oxidanylidene-ethanoyl]amino]-3-phenyl-propanoyl]amino]-5-[(3S)-2-oxidanylidenepyrrolidin-3-yl]pent-2-enoate

Formula

C27 H36 N4 O6

Formal charge

0

Molecular weight

512.598 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C1(CCC1)CNC(=O)C(NC(Cc2ccccc2)C(NC(CC3CCNC3=O)[C@H]=[C@H]C(OCC)=O)=O)=O
SMILES CACTVS 3.385 CCOC(=O)C=C[CH](C[CH]1CCNC1=O)NC(=O)[CH](Cc2ccccc2)NC(=O)C(=O)NCC3CCC3
SMILES OpenEye OEToolkits 1.9.2 CCOC(=O)C=CC(CC1CCNC1=O)NC(=O)C(Cc2ccccc2)NC(=O)C(=O)NCC3CCC3
Canonical SMILES CACTVS 3.385 CCOC(=O)\C=C/[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccccc2)NC(=O)C(=O)NCC3CCC3
Canonical SMILES OpenEye OEToolkits 1.9.2 CCOC(=O)C=C[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccccc2)NC(=O)C(=O)NCC3CCC3

IUPAC InChI

InChI=1S/C27H36N4O6/c1-2-37-23(32)12-11-21(16-20-13-14-28-24(20)33)30-25(34)22(15-18-7-4-3-5-8-18)31-27(36)26(35)29-17-19-9-6-10-19/h3-5,7-8,11-12,19-22H,2,6,9-10,13-17H2,1H3,(H,28,33)(H,29,35)(H,30,34)(H,31,36)/t20-,21+,22-/m0/s1

IUPAC InChI key

JXIYUFBHNQDFQS-BDTNDASRSA-N
5EX

wwPDB Information

Atom count

73 (37 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-09-18

Last modified at

2024-09-27

Status

Released

Obsoleted

Not Assigned



5EX : Atoms of Molecule

Total Number of Atoms: 73
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C23 C C1 N N N 0 -7.408 -1.685 0.651
2 C22 C C2 N N N 0 -3.795 -0.819 0.796
3 C21 C C3 N N N 0 -6.01 -1.718 1.27
4 C20 C C4 N N N 0 -2.858 -0.018 -0.048
5 C24 C C5 N N N 0 -8.479 -2.381 1.509
6 C26 C C6 N N N 0 5.021 -2.324 -2.811
7 C27 C C7 N N N 0 -9.055 -2.939 0.197
8 C18 C C8 N N N 0 6.31 0.607 2.984
9 C10 C C9 S N N 0 3.138 0.412 -0.87
10 C7 C C10 N Y N 0 -4.627 3.851 -1.031
11 C5 C C11 N Y N 0 -3.112 2.807 0.501
12 C6 C C12 N Y N 0 -4.373 3.291 0.207
13 C2 C C13 S N N 0 -0.643 0.882 -0.522
14 C3 C C14 N N N 0 -0.73 2.356 -0.122
15 C4 C C15 N Y N 0 -2.105 2.883 -0.443
16 C11 C C16 N N N 0 3.285 -0.77 -1.831
17 C12 C C17 S N N 0 4.629 -1.459 -1.59
18 C13 C C18 N N N 0 4.519 -2.451 -0.453
19 C14 C C19 N N N 0 4.146 1.474 -1.224
20 C15 C C20 N N N 0 5.052 1.856 -0.327
21 C16 C C21 N N N 0 5.32 1.018 0.85
22 C17 C C22 N N N 0 0.765 0.387 -0.316
23 O1 O O1 N N N 0 3.967 -2.237 0.605
24 C8 C C23 N Y N 0 -3.622 3.922 -1.977
25 O2 O O2 N N N 0 6.088 1.489 1.853
26 C9 C C24 N Y N 0 -2.361 3.438 -1.683
27 N1 N N1 N N N 0 5.121 -3.606 -0.787
28 C19 C C25 N N N 0 7.198 1.309 4.013
29 O3 O O3 N N N 0 4.848 -0.1 0.92
30 N2 N N2 N N N 0 -1.562 0.096 0.305
31 C25 C C26 N N N 0 5.699 -3.536 -2.134
32 N N N3 N N N 0 1.786 0.965 -0.98
33 O4 O O4 N N N 0 0.98 -0.531 0.447
34 O21 O O5 N N N 0 -3.263 0.53 -1.052
35 O5 O O6 N N N 0 -3.39 -1.367 1.8
36 N6 N N4 N N N 0 -5.091 -0.932 0.442
37 C28 C C27 N N N 0 -7.644 -2.787 -0.396
38 H1 H H1 N N N 0 -7.699 -0.691 0.311
39 H2 H H2 N N N 0 -6.047 -1.294 2.274
40 H3 H H3 N N N 0 -5.66 -2.749 1.324
41 H4 H H4 N N N 0 -8.077 -3.148 2.171
42 H5 H H5 N N N 0 -9.147 -1.687 2.019
43 H6 H H6 N N N 0 4.137 -2.633 -3.369
44 H7 H H7 N N N 0 5.722 -1.794 -3.456
45 H8 H H8 N N N 0 -9.388 -3.974 0.272
46 H13 H H13 N N N 0 -5.612 4.229 -1.26
47 H9 H H9 N N N 0 -9.796 -2.288 -0.266
48 H10 H H10 N N N 0 5.353 0.355 3.442
49 H11 H H11 N N N 0 6.8 -0.305 2.643
50 H12 H H12 N N N 0 3.31 0.073 0.151
51 H14 H H14 N N N 0 -2.913 2.37 1.469
52 H15 H H15 N N N 0 -5.16 3.231 0.945
53 H16 H H16 N N N 0 -0.917 0.773 -1.572
54 H17 H H17 N N N 0 -0.543 2.454 0.947
55 H18 H H18 N N N 0 0.016 2.927 -0.675
56 H19 H H19 N N N 0 2.476 -1.48 -1.66
57 H20 H H20 N N N 0 3.24 -0.41 -2.859
58 H21 H H21 N N N 0 5.404 -0.721 -1.381
59 H22 H H22 N N N 0 4.134 1.926 -2.204
60 H24 H H24 N N N 0 5.591 2.782 -0.464
61 H26 H H26 N N N 0 -3.821 4.356 -2.946
62 H27 H H27 N N N 0 -1.574 3.497 -2.421
63 H28 H H28 N N N 0 5.168 -4.385 -0.211
64 H29 H H29 N N N 0 7.364 0.647 4.862
65 H30 H H30 N N N 0 8.155 1.561 3.555
66 H31 H H31 N N N 0 6.707 2.221 4.354
67 H32 H H32 N N N 0 -1.238 -0.342 1.108
68 H33 H H33 N N N 0 5.478 -4.449 -2.687
69 H34 H H34 N N N 0 6.776 -3.381 -2.075
70 H35 H H35 N N N 0 1.626 1.748 -1.531
71 H36 H H36 N N N 0 -5.415 -0.494 -0.36
72 H37 H H37 N N N 0 -7.639 -2.422 -1.423
73 H38 H H38 N N N 0 -7.015 -3.666 -0.255



5EX : Chemical Bonds

Total Number of Bonds: 75
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O3 C16 O C doub 1.22 N N
2 C16 C15 C C sing 1.47 N N
3 C16 O2 C O sing 1.35 N N
4 C19 C18 C C sing 1.53 N N
5 C18 O2 C O sing 1.45 N N
6 C15 C14 C C doub 1.33 Z N
7 C14 C10 C C sing 1.51 N N
8 C11 C10 C C sing 1.53 N N
9 C11 C12 C C sing 1.53 N N
10 C10 N C N sing 1.46 N N
11 O1 C13 O C doub 1.21 N N
12 C13 C12 C C sing 1.51 N N
13 C13 N1 C N sing 1.34 N N
14 N C17 N C sing 1.35 N N
15 C12 C26 C C sing 1.55 N N
16 C26 C25 C C sing 1.54 N N
17 N1 C25 N C sing 1.47 N N
18 O4 C17 O C doub 1.21 N N
19 C17 C2 C C sing 1.51 N N
20 C3 C2 C C sing 1.53 N N
21 C3 C4 C C sing 1.51 N N
22 C2 N2 C N sing 1.47 N N
23 C4 C5 C C doub 1.38 N Y
24 C4 C9 C C sing 1.38 N Y
25 C5 C6 C C sing 1.38 N Y
26 O21 C20 O C doub 1.21 N N
27 C9 C8 C C doub 1.38 N Y
28 N2 C20 N C sing 1.35 N N
29 C20 C22 C C sing 1.49 N N
30 C6 C7 C C doub 1.38 N Y
31 C8 C7 C C sing 1.38 N Y
32 C22 O5 C O doub 1.21 N N
33 C22 N6 C N sing 1.35 N N
34 C21 N6 C N sing 1.47 N N
35 C21 C23 C C sing 1.53 N N
36 C23 C24 C C sing 1.54 N N
37 C23 C28 C C sing 1.54 N N
38 C24 C27 C C sing 1.54 N N
39 C27 C28 C C sing 1.54 N N
40 C23 H1 C H sing 1.09 N N
41 C21 H2 C H sing 1.09 N N
42 C21 H3 C H sing 1.09 N N
43 C24 H4 C H sing 1.09 N N
44 C24 H5 C H sing 1.09 N N
45 C26 H6 C H sing 1.09 N N
46 C26 H7 C H sing 1.09 N N
47 C27 H8 C H sing 1.09 N N
48 C27 H9 C H sing 1.09 N N
49 C18 H10 C H sing 1.09 N N
50 C18 H11 C H sing 1.09 N N
51 C10 H12 C H sing 1.09 N N
52 C7 H13 C H sing 1.08 N N
53 C5 H14 C H sing 1.08 N N
54 C6 H15 C H sing 1.08 N N
55 C2 H16 C H sing 1.09 N N
56 C3 H17 C H sing 1.09 N N
57 C3 H18 C H sing 1.09 N N
58 C11 H19 C H sing 1.09 N N
59 C11 H20 C H sing 1.09 N N
60 C12 H21 C H sing 1.09 N N
61 C14 H22 C H sing 1.08 N N
62 C15 H24 C H sing 1.08 N N
63 C8 H26 C H sing 1.08 N N
64 C9 H27 C H sing 1.08 N N
65 N1 H28 N H sing 0.97 N N
66 C19 H29 C H sing 1.09 N N
67 C19 H30 C H sing 1.09 N N
68 C19 H31 C H sing 1.09 N N
69 N2 H32 N H sing 0.97 N N
70 C25 H33 C H sing 1.09 N N
71 C25 H34 C H sing 1.09 N N
72 N H35 N H sing 0.97 N N
73 N6 H36 N H sing 0.97 N N
74 C28 H37 C H sing 1.09 N N
75 C28 H38 C H sing 1.09 N N



5EX : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
5EX 5dp9 Open in New Window Bound ligand 1 1