SMTL ID : 8yvp.1

canine immunoproteasome 20S subunit in complex with compound 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.50 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-2-mer

Ligands

6 x 01: [(~{R})-cyclohexyl-[(1-cyclohexyl-1,2,3-triazol-4-yl)carbonylamino]methyl]boronic acid

01.1: 12 residues within 4Å: Chain B: T.1, R.19, A.20, T.21, A.22, V.31, K.33, M.45, A.46, G.47, A.49 Chain L: D.152 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.22, B:V.31, B:M.45, B:A.49 Hydrogen bonds: B:T.21, B:G.47, B:G.47, B:G.47, B:A.49 01.2: 11 residues within 4Å: Chain B: W.55, L.58, R.61, Y.90 Chain L: Y.124, R.127, F.128 Chain N: N.98, F.101, T.102 Ligands: THR.3 8 PLIP interactions: 3 interactions with chain B, 4 interactions with chain L, 1 interactions with chain N Hydrophobic interactions: B:L.58, B:Y.90, L:Y.124, L:Y.124, L:R.127, L:F.128, N:F.101 pi-Stacking: B:F.54 01.4: 12 residues within 4Å: Chain F: T.1, T.20, T.21, T.22, K.33, R.45, S.46, G.47, A.49, T.52 Chain K: Y.114, S.118 11 PLIP interactions: 1 interactions with chain K, 10 interactions with chain F Hydrophobic interactions: K:Y.114, F:T.1, F:T.22, F:K.33, F:R.45, F:A.49 Hydrogen bonds: F:T.1, F:T.21, F:G.47, F:G.47, F:A.49 01.5: 11 residues within 4Å: Chain G: Y.124, R.127, F.128 Chain H: W.55, L.58, R.61, Y.90 Chain W: N.98, F.101, T.102 Ligands: THR.6 8 PLIP interactions: 3 interactions with chain H, 4 interactions with chain G, 1 interactions with chain W Hydrophobic interactions: H:L.58, H:Y.90, G:Y.124, G:Y.124, G:R.127, G:F.128, W:F.101 pi-Stacking: H:F.54 01.7: 12 residues within 4Å: Chain G: D.152 Chain H: T.1, R.19, A.20, T.21, A.22, V.31, K.33, M.45, A.46, G.47, A.49 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:A.22, H:V.31, H:M.45, H:A.49 Hydrogen bonds: H:T.21, H:G.47, H:G.47, H:G.47, H:A.49 01.8: 12 residues within 4Å: Chain A: Y.114, S.118 Chain Y: T.1, T.20, T.21, T.22, K.33, R.45, S.46, G.47, A.49, T.52 11 PLIP interactions: 10 interactions with chain Y, 1 interactions with chain A Hydrophobic interactions: Y:T.1, Y:T.22, Y:K.33, Y:R.45, Y:A.49, A:Y.114 Hydrogen bonds: Y:T.1, Y:T.21, Y:G.47, Y:G.47, Y:A.49

2 x THR: THREONINE(Non-functional Binders)

THR.3: 1 residues within 4Å: Ligands: 01.2 No protein-ligand interaction detected (PLIP) THR.6: 1 residues within 4Å: Ligands: 01.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arai, Y. et al., Optimization of alpha-amido boronic acids via cryo-electron microscopy analysis: Discovery of a novel highly selective immunoproteasome subunit LMP7 ( beta 5i)/LMP2 ( beta 1i) dual inhibitor. Bioorg.Med.Chem. (2024)

Release Date

2024-07-31

Peptides

Proteasome subunit beta type-7: AK
Proteasome subunit beta type-5: BH
Proteasome subunit alpha type-2: CP
Proteasome subunit alpha type-3: DI
Proteasome subunit alpha type-6: EO
Proteasome subunit beta type-6: FY
Proteasome subunit beta type-1: GL
Proteasome subunit beta type-3: J0
Proteasome subunit beta type-4: M1
Proteasome subunit alpha type-5: NW
Proteasome subunit beta type-2: QR
Proteasome subunit alpha type-7: SZ
Proteasome subunit alpha type-1: TV
Proteasome subunit alpha type-4: UX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

K
E

B
C

H
D

C
P

P
b

D
Q

I
J

E
R

O
K

F
F

Y
A

G
S

L
X

J
Y

0
U

M
a

1
W

N
H

W
M

Q
V

R
T

S
I

Z
N

T
L

V
G

U
O

X
Z

Proteasome subunit beta type-7

Proteasome subunit beta type-5

Proteasome subunit alpha type-2

Proteasome subunit alpha type-3

Proteasome subunit alpha type-6

Proteasome subunit beta type-6

Proteasome subunit beta type-1

Proteasome subunit beta type-3

Proteasome subunit beta type-4

Proteasome subunit alpha type-5

Proteasome subunit beta type-2

Proteasome subunit alpha type-7

Proteasome subunit alpha type-1

Proteasome subunit alpha type-4

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