SMTL ID : 6hvy.1

Yeast 20S proteasome in complex with 5 (7- and 6-membered ring)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

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

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain G: T.17, Y.128, R.131, A.132, M.134 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:T.17, G:Y.128, G:R.131, G:M.134 MG.6: 4 residues within 4Å: Chain I: A.175, D.178, S.181, D.205 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.178, I:S.181 MG.7: 6 residues within 4Å: Chain I: D.205 Chain Y: R.19, A.165, D.168, A.169, S.171 5 PLIP interactions: 1 interactions with chain I, 3 interactions with chain Y, 1 Ligand-Water interactions Metal complexes: I:D.205, Y:A.165, Y:D.168, Y:S.171, H2O.18 MG.8: 6 residues within 4Å: Chain K: A.165, H.166, D.168, A.169, S.171 Chain W: D.205 3 PLIP interactions: 1 interactions with chain W, 2 interactions with chain K Metal complexes: W:D.205, K:A.165, K:D.168 MG.9: 7 residues within 4Å: Chain L: D.222 Chain V: G.162, I.163, W.164, D.166, L.167, S.169 3 PLIP interactions: 2 interactions with chain V, 1 interactions with chain L Metal complexes: V:I.163, V:D.166, L:D.222 MG.10: 5 residues within 4Å: Chain 0: L.47 Chain N: R.19, I.163, D.166, S.169 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:I.163, N:S.169 MG.15: 4 residues within 4Å: Chain W: A.175, D.178, S.181, D.205 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:A.175, W:D.178, W:S.181 MG.16: 6 residues within 4Å: Chain Z: R.28, T.192, H.195, I.196, V.198, D.222 2 PLIP interactions: 2 interactions with chain Z Metal complexes: Z:T.192, Z:V.198

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain G: R.120, N.123 Chain H: Y.69 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain U: R.120, N.123 Chain V: Y.69 Ligand excluded by PLIP

2 x GVZ: (2~{S})-~{N}-[(2~{S},3~{R})-1-[(1~{S},4~{a}~{S},8~{a}~{R})-1,2,3,4,4~{a},5,6,7,8,8~{a}-decahydronaphthalen-1-yl]-4-methyl-3,4-bis(oxidanyl)pentan-2-yl]-3-(4-methoxyphenyl)-2-[[(2~{S})-2-(2-morpholin-4-ylethanoylamino)propanoyl]amino]propanamide(Covalent)

GVZ.3: 22 residues within 4Å: Chain H: T.1, R.19, S.20, T.21, Q.22, C.31, A.32, K.33, H.35, G.45, A.46, G.47, T.48, A.49, T.52, E.53, S.129, G.168 Chain I: D.125, L.126 Ligands: GW2.4, MES.5 13 PLIP interactions: 10 interactions with chain H, 3 interactions with chain I Hydrophobic interactions: H:T.1, H:T.21, H:T.52, H:E.53 Hydrogen bonds: H:T.1, H:T.21, H:T.21, H:G.47, H:G.47, H:A.49, I:D.125, I:D.125 Salt bridges: I:D.125 GVZ.12: 22 residues within 4Å: Chain V: T.1, R.19, S.20, T.21, Q.22, C.31, A.32, K.33, H.35, G.45, A.46, G.47, T.48, A.49, T.52, E.53, S.129, G.168 Chain W: D.125, L.126 Ligands: GW2.13, MES.14 13 PLIP interactions: 10 interactions with chain V, 3 interactions with chain W Hydrophobic interactions: V:T.21, V:T.52, V:E.53 Hydrogen bonds: V:T.1, V:T.21, V:T.21, V:G.47, V:G.47, V:A.49, W:D.125, W:D.125 Water bridges: V:A.50 Salt bridges: W:D.125

2 x GW2: (2~{S})-~{N}-[(2~{S},3~{S},4~{R})-1-[(1~{S},4~{a}~{S},8~{a}~{R})-1,2,3,4,4~{a},5,6,7,8,8~{a}-decahydronaphthalen-1-yl]-4-methyl-3,5-bis(oxidanyl)pentan-2-yl]-3-(4-methoxyphenyl)-2-[[(2~{S})-2-(2-morpholin-4-ylethanoylamino)propanoyl]amino]propanamide(Covalent)

GW2.4: 22 residues within 4Å: Chain H: T.1, R.19, S.20, T.21, Q.22, C.31, A.32, K.33, H.35, G.45, A.46, G.47, T.48, A.49, T.52, S.129, G.168 Chain I: D.125, L.126, I.127 Ligands: GVZ.3, MES.5 15 PLIP interactions: 12 interactions with chain H, 3 interactions with chain I Hydrophobic interactions: H:T.1, H:K.33, H:T.52 Hydrogen bonds: H:T.1, H:T.21, H:T.21, H:T.21, H:G.47, H:G.47, H:G.47, H:A.49, H:S.129, I:D.125, I:D.125 Salt bridges: I:D.125 GW2.13: 23 residues within 4Å: Chain V: T.1, R.19, S.20, T.21, Q.22, C.31, A.32, K.33, H.35, G.45, A.46, G.47, T.48, A.49, T.52, E.53, S.129, G.168 Chain W: D.125, L.126, I.127 Ligands: GVZ.12, MES.14 15 PLIP interactions: 12 interactions with chain V, 3 interactions with chain W Hydrophobic interactions: V:T.52, V:E.53 Hydrogen bonds: V:T.1, V:T.21, V:T.21, V:T.21, V:G.47, V:G.47, V:G.47, V:A.49, V:S.129, W:D.125, W:D.125 Water bridges: V:A.50 Salt bridges: W:D.125

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.5: 7 residues within 4Å: Chain H: A.46, G.47, G.128, S.129 Chain Z: Y.33 Ligands: GVZ.3, GW2.4 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:G.47, H:S.129 MES.14: 8 residues within 4Å: Chain L: Y.33 Chain V: T.1, A.46, G.47, G.128, S.129 Ligands: GVZ.12, GW2.13 3 PLIP interactions: 3 interactions with chain V Hydrogen bonds: V:T.1, V:G.47, V:S.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xin, B.T. et al., Structure-Based Design of Inhibitors Selective for Human Proteasome beta 2c or beta 2i Subunits. J.Med.Chem. (2019)

Release Date

2019-01-30

Peptides

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

Proteasome subunit alpha type-3

Proteasome subunit alpha type-4

Proteasome subunit alpha type-5

Proteasome subunit alpha type-6

Probable proteasome subunit alpha type-7

Proteasome subunit alpha type-1

Proteasome subunit beta type-2

Proteasome subunit beta type-3

Proteasome subunit beta type-4

Proteasome subunit beta type-5

Proteasome subunit beta type-6

Proteasome subunit beta type-7

Proteasome subunit beta type-1

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