Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

SKN : Summary

Code

SKN

One-letter code

X

Molecule name

((R)-2-(3-ethylphenyl)-1-((S)-3-phenyl-2-(pyrazine-2-carboxamido)propanamido)ethyl)boronic acid

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 [(1~{R})-2-(3-ethylphenyl)-1-[[(2~{S})-3-phenyl-2-(pyrazin-2-ylcarbonylamino)propanoyl]amino]ethyl]boronic acid

Formula

C24 H27 B N4 O4

Formal charge

0

Molecular weight

446.307 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CCc1cccc(C[CH](NC(=O)[CH](Cc2ccccc2)NC(=O)c3cnccn3)B(O)O)c1
SMILES OpenEye OEToolkits 2.0.7 B(C(Cc1cccc(c1)CC)NC(=O)C(Cc2ccccc2)NC(=O)c3cnccn3)(O)O
Canonical SMILES CACTVS 3.385 CCc1cccc(C[C@H](NC(=O)[C@H](Cc2ccccc2)NC(=O)c3cnccn3)B(O)O)c1
Canonical SMILES OpenEye OEToolkits 2.0.7 B([C@H](Cc1cccc(c1)CC)NC(=O)[C@H](Cc2ccccc2)NC(=O)c3cnccn3)(O)O

IUPAC InChI

InChI=1S/C24H27BN4O4/c1-2-17-9-6-10-19(13-17)15-22(25(32)33)29-23(30)20(14-18-7-4-3-5-8-18)28-24(31)21-16-26-11-12-27-21/h3-13,16,20,22,32-33H,2,14-15H2,1H3,(H,28,31)(H,29,30)/t20-,22-/m0/s1

IUPAC InChI key

RQXXOBNVVACHIB-UNMCSNQZSA-N
SKN

wwPDB Information

Atom count

60 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-11-23

Last modified at

2024-09-27

Status

Released

Obsoleted

Not Assigned



SKN : Atoms of Molecule

Total Number of Atoms: 60
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 R N N 0 2.481 0.472 0.237
2 O4 O O1 N N N 0 2.985 2.73 1.403
3 N6 N N1 N N N 0 1.118 0.854 -0.14
4 C7 C C2 N Y N 0 4.831 0.349 -0.545
5 C8 C C3 N Y N 0 5.278 -0.938 -0.781
6 C9 C C4 N Y N 0 6.564 -1.298 -0.425
7 C10 C C5 N Y N 0 7.403 -0.372 0.168
8 C11 C C6 N Y N 0 6.956 0.914 0.403
9 C12 C C7 N Y N 0 5.671 1.276 0.042
10 C13 C C8 N N N 0 0.085 0.036 0.146
11 C14 C C9 S N N 0 -1.317 0.43 -0.242
12 C19 C C10 N Y N 0 -4.374 -1.825 -0.04
13 C20 C C11 N Y N 0 -3.039 2.202 -0.037
14 C21 C C12 N Y N 0 -3.137 3.026 -1.143
15 C22 C C13 N Y N 0 -4.377 3.45 -1.582
16 C24 C C14 N Y N 0 -5.423 2.223 0.189
17 C27 C C15 N Y N 0 -5.593 -1.979 -0.7
18 C30 C C16 N Y N 0 -4.905 -3.575 1.342
19 C32 C C17 N N N 0 7.051 -2.701 -0.681
20 C33 C C18 N N N 0 7.69 -2.773 -2.069
21 B2 B B1 N N N 0 2.934 1.313 1.483
22 O3 O O2 N N N 0 3.294 0.657 2.69
23 C5 C C19 N N N 0 3.428 0.742 -0.933
24 O15 O O3 N N N 0 0.284 -1.016 0.715
25 N16 N N2 N N N 0 -2.251 -0.618 0.176
26 C17 C C20 N N N 0 -1.686 1.746 0.445
27 C18 C C21 N N N 0 -3.429 -0.765 -0.463
28 C23 C C22 N Y N 0 -5.52 3.048 -0.916
29 C25 C C23 N Y N 0 -4.182 1.801 0.629
30 O26 O O4 N N N 0 -3.716 -0.028 -1.385
31 N28 N N3 N Y N 0 -6.432 -2.925 -0.319
32 C29 C C24 N Y N 0 -6.117 -3.725 0.684
33 N31 N N4 N Y N 0 -4.064 -2.629 0.973
34 H1 H H1 N N N 0 2.505 -0.589 0.487
35 H2 H H2 N N N 0 3.276 3.16 2.219
36 H3 H H3 N N N 0 0.958 1.696 -0.595
37 H4 H H4 N N N 0 4.623 -1.661 -1.243
38 H5 H H5 N N N 0 8.406 -0.655 0.449
39 H6 H H6 N N N 0 7.611 1.638 0.865
40 H7 H H7 N N N 0 5.322 2.282 0.226
41 H8 H H8 N N N 0 -1.373 0.556 -1.323
42 H9 H H9 N N N 0 -2.244 3.34 -1.663
43 H10 H H10 N N N 0 -4.454 4.094 -2.445
44 H11 H H11 N N N 0 -6.316 1.91 0.71
45 H12 H H12 N N N 0 -5.851 -1.324 -1.52
46 H13 H H13 N N N 0 -4.652 -4.231 2.162
47 H14 H H14 N N N 0 7.79 -2.973 0.073
48 H15 H H15 N N N 0 6.21 -3.393 -0.632
49 H16 H H16 N N N 0 8.042 -3.788 -2.255
50 H17 H H17 N N N 0 6.951 -2.502 -2.824
51 H18 H H18 N N N 0 8.531 -2.082 -2.119
52 H19 H H19 N N N 0 3.559 1.257 3.4
53 H20 H H20 N N N 0 3.114 0.158 -1.798
54 H21 H H21 N N N 0 3.404 1.803 -1.182
55 H22 H H22 N N N 0 -2.023 -1.207 0.912
56 H23 H H23 N N N 0 -1.717 1.596 1.525
57 H24 H H24 N N N 0 -0.94 2.503 0.205
58 H25 H H25 N N N 0 -6.489 3.379 -1.258
59 H26 H H26 N N N 0 -4.106 1.157 1.493
60 H27 H H27 N N N 0 -6.803 -4.501 0.99



SKN : Chemical Bonds

Total Number of Bonds: 62
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C33 C32 C C sing 1.53 N N
2 C10 C11 C C doub 1.38 N Y
3 C10 C9 C C sing 1.38 N Y
4 C11 C12 C C sing 1.38 N Y
5 C32 C9 C C sing 1.51 N N
6 C9 C8 C C doub 1.38 N Y
7 C12 C7 C C doub 1.38 N Y
8 C8 C7 C C sing 1.38 N Y
9 C7 C5 C C sing 1.51 N N
10 C30 C29 C C doub 1.39 N Y
11 C30 N31 C N sing 1.32 N Y
12 C29 N28 C N sing 1.32 N Y
13 N31 C19 N C doub 1.33 N Y
14 N28 C27 N C doub 1.32 N Y
15 C5 C1 C C sing 1.53 N N
16 C19 C27 C C sing 1.39 N Y
17 C19 C18 C C sing 1.48 N N
18 C18 O26 C O doub 1.21 N N
19 C18 N16 C N sing 1.35 N N
20 C1 N6 C N sing 1.46 N N
21 C1 B2 C B sing 1.57 N N
22 N6 C13 N C sing 1.35 N N
23 N16 C14 N C sing 1.46 N N
24 C13 C14 C C sing 1.51 N N
25 C13 O15 C O doub 1.21 N N
26 C14 C17 C C sing 1.53 N N
27 B2 O3 B O sing 1.42 N N
28 B2 O4 B O sing 1.42 N N
29 C17 C20 C C sing 1.51 N N
30 C21 C20 C C doub 1.38 N Y
31 C21 C22 C C sing 1.38 N Y
32 C20 C25 C C sing 1.38 N Y
33 C22 C23 C C doub 1.38 N Y
34 C25 C24 C C doub 1.38 N Y
35 C23 C24 C C sing 1.38 N Y
36 C1 H1 C H sing 1.09 N N
37 O4 H2 O H sing 0.97 N N
38 N6 H3 N H sing 0.97 N N
39 C8 H4 C H sing 1.08 N N
40 C10 H5 C H sing 1.08 N N
41 C11 H6 C H sing 1.08 N N
42 C12 H7 C H sing 1.08 N N
43 C14 H8 C H sing 1.09 N N
44 C21 H9 C H sing 1.08 N N
45 C22 H10 C H sing 1.08 N N
46 C24 H11 C H sing 1.08 N N
47 C27 H12 C H sing 1.08 N N
48 C30 H13 C H sing 1.08 N N
49 C32 H14 C H sing 1.09 N N
50 C32 H15 C H sing 1.09 N N
51 C33 H16 C H sing 1.09 N N
52 C33 H17 C H sing 1.09 N N
53 C33 H18 C H sing 1.09 N N
54 O3 H19 O H sing 0.97 N N
55 C5 H20 C H sing 1.09 N N
56 C5 H21 C H sing 1.09 N N
57 N16 H22 N H sing 0.97 N N
58 C17 H23 C H sing 1.09 N N
59 C17 H24 C H sing 1.09 N N
60 C23 H25 C H sing 1.08 N N
61 C25 H26 C H sing 1.08 N N
62 C29 H27 C H sing 1.08 N N



SKN : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
SKN 7b12 Open in New Window Bound ligand 6 1