SMTL ID : 7awe.1

HUMAN IMMUNOPROTEASOME 20S PARTICLE IN COMPLEX WITH [(1R)-2-(1-benzofuran-3-yl)-1-{[(1S,2R,4R)-7-oxabicyclo[2.2.1]heptan-2-yl]formamido}ethyl]boronic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

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

Ligands

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

NA.1: 5 residues within 4Å: Chain A: T.11, Y.122, N.125, A.126, M.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.11, A:M.128 NA.4: 4 residues within 4Å: Chain H: R.19, M.163, D.166, S.169 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:R.19, H:D.166 NA.5: 5 residues within 4Å: Chain 0: D.213 Chain I: R.19, I.163, D.166, S.169 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:R.19, I:D.166 NA.6: 3 residues within 4Å: Chain J: V.174, D.177, S.180 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:D.204 Water bridges: J:M.182 NA.7: 2 residues within 4Å: Chain J: V.137, S.138 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:S.138 Water bridges: J:G.139, I:N.22 NA.11: 6 residues within 4Å: Chain L: R.19, T.164, D.167, S.168, S.170 Chain X: D.204 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:R.19, L:S.168 NA.12: 5 residues within 4Å: Chain M: R.28, A.183, D.186, T.189, D.213 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:R.28, M:D.213 NA.16: 5 residues within 4Å: Chain O: T.11, Y.122, N.125, A.126, M.128 3 PLIP interactions: 3 interactions with chain O Hydrogen bonds: O:T.11, O:A.126 Water bridges: O:T.11 NA.20: 4 residues within 4Å: Chain V: R.19, M.163, D.166, S.169 2 PLIP interactions: 2 interactions with chain V Hydrogen bonds: V:R.19, V:D.166 NA.21: 6 residues within 4Å: Chain M: D.213 Chain W: R.19, I.163, D.166, L.167, S.169 3 PLIP interactions: 2 interactions with chain W, 1 interactions with chain M Hydrogen bonds: W:R.19, W:I.163, M:D.213 NA.22: 3 residues within 4Å: Chain X: V.174, D.177, S.180 3 PLIP interactions: 3 interactions with chain X Hydrogen bonds: X:S.180 Water bridges: X:D.175, X:M.182 NA.24: 6 residues within 4Å: Chain J: D.204 Chain Z: R.19, T.164, D.167, S.168, S.170 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain Z Hydrogen bonds: J:D.204, Z:R.19 NA.26: 5 residues within 4Å: Chain 0: R.28, A.183, D.186, T.189, D.213 2 PLIP interactions: 2 interactions with chain 0 Hydrogen bonds: 0:R.28, 0:T.189

11 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.2: 2 residues within 4Å: Chain F: Q.87, D.91 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.87, F:D.91 SCN.8: 1 residues within 4Å: Chain K: N.63 No protein-ligand interaction detected (PLIP) SCN.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SCN.13: 2 residues within 4Å: Chain L: Y.54, Y.90 No protein-ligand interaction detected (PLIP) SCN.14: 2 residues within 4Å: Chain M: S.123, S.129 1 PLIP interactions: 1 interactions with chain M Water bridges: M:S.129 SCN.15: 1 residues within 4Å: Chain M: Y.5 No protein-ligand interaction detected (PLIP) SCN.17: 3 residues within 4Å: Chain 0: M.74 Chain T: Q.87, D.91 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:Q.87 SCN.18: 2 residues within 4Å: Chain U: K.61, L.63 No protein-ligand interaction detected (PLIP) SCN.25: 2 residues within 4Å: Chain S: D.63 Chain Z: L.68 No protein-ligand interaction detected (PLIP) SCN.27: 1 residues within 4Å: Chain Z: Y.90 No protein-ligand interaction detected (PLIP) SCN.28: 2 residues within 4Å: Chain 0: S.123, S.129 1 PLIP interactions: 1 interactions with chain 0 Water bridges: 0:K.136

4 x S5K: [(1R)-2-(1-benzofuran-3-yl)-1-{[(1S,2R,4R)-7-oxabicyclo[2.2.1]heptan-2-yl]formamido}ethyl]boronic acid(Covalent)

S5K.3: 13 residues within 4Å: Chain H: T.1, V.20, S.21, F.31, K.33, L.45, S.46, G.47, S.48, A.49, A.52, Q.53, S.168 13 PLIP interactions: 13 interactions with chain H Hydrophobic interactions: H:F.31, H:L.45, H:L.45, H:A.49, H:A.52, H:Q.53 Hydrogen bonds: H:T.1, H:S.21, H:G.47, H:G.47, H:A.49, H:S.129 Water bridges: H:A.50 S5K.10: 15 residues within 4Å: Chain L: T.1, R.19, A.20, S.21, V.31, N.32, K.33, M.45, S.46, G.47, C.48, A.49, C.52, Q.53, Y.169 11 PLIP interactions: 11 interactions with chain L Hydrophobic interactions: L:M.45, L:A.49, L:Q.53 Hydrogen bonds: L:T.1, L:S.21, L:G.47, L:G.47, L:G.47, L:A.49 Water bridges: L:A.50, L:S.130 S5K.19: 11 residues within 4Å: Chain V: T.1, V.20, S.21, F.31, L.45, S.46, G.47, S.48, A.49, A.52, Q.53 13 PLIP interactions: 13 interactions with chain V Hydrophobic interactions: V:F.31, V:L.45, V:L.45, V:A.49, V:A.52, V:Q.53 Hydrogen bonds: V:T.1, V:S.21, V:G.47, V:G.47, V:G.47, V:A.49 Water bridges: V:A.50 S5K.23: 15 residues within 4Å: Chain Z: T.1, R.19, A.20, S.21, V.31, N.32, K.33, M.45, S.46, G.47, C.48, A.49, C.52, Q.53, Y.169 10 PLIP interactions: 10 interactions with chain Z Hydrophobic interactions: Z:M.45, Z:A.49, Z:Q.53 Hydrogen bonds: Z:T.1, Z:S.21, Z:G.47, Z:G.47, Z:G.47, Z:A.49 Water bridges: Z:A.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sanderson, M.P. et al., M3258 is a selective inhibitor of the immunoproteasome subunit LMP7 ( beta 5i) delivering efficacy in multiple myeloma models. Mol.Cancer Ther. (2021)

Release Date

2021-06-09

Peptides

Proteasome subunit alpha type-6: AO
Proteasome subunit alpha type-2: BP
Proteasome subunit alpha type-4: CQ
Proteasome subunit alpha type-7: DR
Proteasome subunit alpha type-5: ES
Proteasome subunit alpha type-1: FT
Proteasome subunit alpha type-3: GU
Proteasome subunit beta type-9: HV
Proteasome subunit beta type-10: IW
Proteasome subunit beta type-3: JX
Proteasome subunit beta type-2: KY
Proteasome subunit beta type-8: LZ
Proteasome subunit beta type-1: M0
Proteasome subunit beta type-4: N1

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

O
O

B
B

P
P

C
C

Q
Q

D
D

R
R

E
E

S
S

F
F

T
T

G
G

U
U

H
H

V
V

I
I

W
W

J
J

X
X

K
K

Y
Y

L
L

Z
Z

M
M

0
a

N
N

1
b

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-10

Proteasome subunit beta type-3

Proteasome subunit beta type-2

Proteasome subunit beta type-8

Proteasome subunit beta type-1

Proteasome subunit beta type-4

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