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SMTL ID : 2gpl.1

TMC-95 based biphenyl-ether macrocycles: specific proteasome inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

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

Ligands

2 x BIQ: BENZYL [12-(2-AMINO-2-OXOETHYL)-4-NITRO-10,13-DIOXO-15-[(PROPYLAMINO)CARBONYL]-2-OXA-11,14-DIAZATRICYCLO[15 .2.2.1~3,7~]DOCOSA-1(19),3(22),4,6,17,20-HEXAEN-9-YL]CARBAMATE(Non-covalent)

BIQ.1:

18 residues within 4Å:

Chain H: T.1, S.20, T.21, Q.22, A.27, K.33, G.45, A.46, G.47, T.48, A.49
Chain I: S.4, R.98, F.103, D.124, L.125, I.126, C.128

18 PLIP interactions:

10 interactions with chain H, 8 interactions with chain I

Hydrophobic interactions: H:K.33, I:F.103, I:D.124, I:L.125, I:L.125, I:L.125, I:I.126
Hydrogen bonds: H:S.20, H:T.21, H:T.21, H:T.21, H:Q.22, H:Q.22, H:G.47, H:A.49, I:D.124, I:D.124
Water bridges: H:A.50

BIQ.2:

18 residues within 4Å:

Chain V: T.1, S.20, T.21, Q.22, A.27, K.33, G.45, A.46, G.47, T.48, A.49
Chain W: S.4, R.98, F.103, D.124, L.125, I.126, C.128

17 PLIP interactions:

8 interactions with chain W, 9 interactions with chain V

Hydrophobic interactions: W:F.103, W:D.124, W:L.125, W:L.125, W:L.125, W:I.126, V:K.33
Hydrogen bonds: W:D.124, W:D.124, V:S.20, V:T.21, V:T.21, V:T.21, V:Q.22, V:Q.22, V:G.47, V:A.49

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Groll, M. et al., TMC-95-Based Inhibitor Design Provides Evidence for the Catalytic Versatility of the Proteasome. Chem.Biol. (2006)

Release Date

2006-07-11

Peptides

Proteasome component Y7: AO
Proteasome component Y13: BP
Proteasome component PRE6: CQ
Proteasome component PUP2: DR
Proteasome component PRE5: ES
Proteasome component C1: FT
Proteasome component C7-alpha: GU
Proteasome component PUP1: HV
Proteasome component PUP3: IW
Proteasome component C11: JX
Proteasome component PRE2: KY
Proteasome component C5: LZ
Proteasome component PRE4: M0
Proteasome component PRE3: 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
1

N
N

1
2

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Proteasome component Y7

Toggle Identical (AO)

Proteasome component Y13

Toggle Identical (BP)

Proteasome component PRE6

Toggle Identical (CQ)

Proteasome component PUP2

Toggle Identical (DR)

Proteasome component PRE5

Toggle Identical (ES)

Proteasome component C1

Toggle Identical (FT)

Proteasome component C7-alpha

Toggle Identical (GU)

Proteasome component PUP1

Toggle Identical (HV)

Proteasome component PUP3

Toggle Identical (IW)

Proteasome component C11

Toggle Identical (JX)

Proteasome component PRE2

Toggle Identical (KY)

Proteasome component C5

Toggle Identical (LZ)

Proteasome component PRE4

Toggle Identical (M0)

Proteasome component PRE3

Toggle Identical (N1)

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