SMTL ID : 7b12.1

HUMAN IMMUNOPROTEASOME 20S PARTICLE IN COMPLEX WITH [2-(3-ethylphenyl)-1-[(2S)-3-phenyl-2-[(pyrazin-2-yl)formamido]propanamido]ethyl]boronic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

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

Ligands

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: Y.97, S.98, F.101 Chain X: Y.54, W.55, Y.90 1 PLIP interactions: 1 interactions with chain X Hydrogen bonds: X:Y.90 SO4.2: 1 residues within 4Å: Chain A: D.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.169 SO4.5: 4 residues within 4Å: Chain F: V.88, L.95 Chain L: K.62, N.63 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:N.63 SO4.8: 5 residues within 4Å: Chain M: Y.54, W.55, Y.90 Chain N: Y.97, R.100 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain N Hydrogen bonds: M:Y.90, N:Y.97 SO4.11: 4 residues within 4Å: Chain W: Y.59, N.63 Chain Z: S.92, L.95 1 PLIP interactions: 1 interactions with chain W Hydrogen bonds: W:N.63

6 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain C: T.11, Y.122, N.125, A.126, M.128 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.122 NA.7: 6 residues within 4Å: Chain M: R.19, T.164, D.167, S.168, S.170 Chain V: D.204 3 PLIP interactions: 3 interactions with chain M Hydrogen bonds: M:R.19, M:S.168, M:S.170 NA.9: 5 residues within 4Å: Chain P: T.11, Y.122, N.125, A.126, M.128 2 PLIP interactions: 2 interactions with chain P Hydrogen bonds: P:T.11, P:A.126 NA.13: 6 residues within 4Å: Chain K: D.204 Chain X: R.19, T.164, D.167, S.168, S.170 4 PLIP interactions: 3 interactions with chain X, 1 interactions with chain K Hydrogen bonds: X:R.19, X:S.170, X:S.170, K:D.204 NA.15: 4 residues within 4Å: Chain A: D.213 Chain Y: I.163, D.166, S.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.213 NA.17: 5 residues within 4Å: Chain 1: I.163, L.164, D.166, S.169 Chain N: D.213 3 PLIP interactions: 2 interactions with chain 1, 1 interactions with chain N Hydrogen bonds: 1:L.164, 1:D.166, N:D.213

6 x SKN: ((R)-2-(3-ethylphenyl)-1-((S)-3-phenyl-2-(pyrazine-2-carboxamido)propanamido)ethyl)boronic acid(Covalent)

SKN.4: 16 residues within 4Å: Chain J: T.1, R.19, V.20, S.21, V.27, F.31, K.33, L.45, S.46, G.47, A.49, A.52, Q.53, S.168 Chain Y: H.114, Y.119 16 PLIP interactions: 16 interactions with chain J Hydrophobic interactions: J:V.20, J:F.31, J:F.31, J:L.45, J:L.45, J:A.49, J:A.52, J:Q.53 Hydrogen bonds: J:T.1, J:S.21, J:S.21, J:G.47, J:G.47, J:G.47, J:A.49 Water bridges: J:A.50 SKN.6: 16 residues within 4Å: Chain M: T.1, R.19, A.20, S.21, S.27, V.31, N.32, K.33, M.45, G.47, C.48, A.49, Q.53, Y.169 Chain N: D.125, S.129 15 PLIP interactions: 14 interactions with chain M, 1 interactions with chain N Hydrophobic interactions: M:A.20, M:V.31, M:M.45, M:A.49, M:Q.53 Hydrogen bonds: M:T.1, M:S.21, M:S.21, M:S.27, M:G.47, M:G.47, M:G.47, M:A.49, N:S.129 Water bridges: M:A.50 SKN.10: 15 residues within 4Å: Chain 1: H.114, Y.119 Chain U: T.1, V.20, S.21, V.27, F.31, K.33, L.45, S.46, G.47, A.49, A.52, Q.53, S.168 15 PLIP interactions: 14 interactions with chain U, 1 interactions with chain 1 Hydrophobic interactions: U:V.20, U:F.31, U:F.31, U:L.45, U:A.49, U:A.52 Hydrogen bonds: U:T.1, U:S.21, U:G.47, U:G.47, U:G.47, U:A.49 Water bridges: U:A.50, U:S.129 pi-Stacking: 1:H.114 SKN.12: 17 residues within 4Å: Chain A: D.125 Chain X: T.1, R.19, A.20, S.21, S.27, V.31, N.32, K.33, M.45, S.46, G.47, C.48, A.49, Q.53, S.130, Y.169 16 PLIP interactions: 15 interactions with chain X, 1 interactions with chain A Hydrophobic interactions: X:A.20, X:V.31, X:V.31, X:A.49, X:Q.53, X:Y.169 Hydrogen bonds: X:T.1, X:S.21, X:S.21, X:G.47, X:G.47, X:G.47, X:A.49 Water bridges: X:A.50, X:S.130, A:S.129 SKN.14: 15 residues within 4Å: Chain K: D.124, C.128 Chain Y: T.1, R.19, A.20, T.21, A.27, C.31, E.32, K.33, H.35, G.47, A.49, A.52, G.168 14 PLIP interactions: 13 interactions with chain Y, 1 interactions with chain K Hydrophobic interactions: Y:A.20, Y:A.49, Y:A.52 Hydrogen bonds: Y:T.1, Y:T.21, Y:T.21, Y:T.21, Y:T.21, Y:K.33, Y:G.47, Y:G.47, Y:G.47, Y:A.49, K:D.124 SKN.16: 16 residues within 4Å: Chain 1: T.1, R.19, A.20, T.21, A.27, C.31, E.32, K.33, H.35, G.45, G.47, A.49, E.53, G.168 Chain V: D.124, C.128 13 PLIP interactions: 13 interactions with chain 1 Hydrophobic interactions: 1:A.20, 1:K.33, 1:A.49, 1:E.53 Hydrogen bonds: 1:T.1, 1:T.21, 1:T.21, 1:T.21, 1:K.33, 1:G.47, 1:G.47, 1:A.49 Water bridges: 1:A.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klein, M. et al., Structure-Based Optimization and Discovery of M3258, a Specific Inhibitor of the Immunoproteasome Subunit LMP7 ( beta 5i). J.Med.Chem. (2021)

Release Date

2021-12-01

Peptides

Proteasome subunit beta type-1: AN
Proteasome subunit beta type-4: BO
Proteasome subunit alpha type-6: CP
Proteasome subunit alpha type-2: DQ
Proteasome subunit alpha type-4: ER
Proteasome subunit alpha type-7: FZ
Proteasome subunit alpha type-5: G0
Proteasome subunit alpha type-1: HS
Proteasome subunit alpha type-3: IT
Proteasome subunit beta type-9: JU
Proteasome subunit beta type-3: KV
Proteasome subunit beta type-2: LW
Proteasome subunit beta type-8: MX
Proteasome subunit beta type-10: Y1

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

N
M

B
2

O
N

C
A

P
O

D
B

Q
P

E
C

R
Q

F
D

Z
r

G
E

0
s

H
F

S
T

I
G

T
U

J
H

U
V

K
J

V
X

L
K

W
Y

M
L

X
Z

Y
i

1
w

Proteasome subunit beta type-1

Proteasome subunit beta type-4

Proteasome subunit alpha type-6

Proteasome subunit alpha type-2

Proteasome subunit alpha type-4

Proteasome subunit alpha type-7

Proteasome subunit alpha type-5

Proteasome subunit alpha type-1

Proteasome subunit alpha type-3

Proteasome subunit beta type-9

Proteasome subunit beta type-3

Proteasome subunit beta type-2

Proteasome subunit beta type-8

Proteasome subunit beta type-10

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