SMTL ID : 9kuf.1

Cryo-EM structure of HsClpP bound to CLPP-2068

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-14-mer

Ligands

14 x 01: 3-[[(7~{R})-2-[(4-bromophenyl)methylamino]-7-methyl-4-oxidanylidene-3,5,7,8-tetrahydropyrido[4,3-d]pyrimidin-6-yl]methyl]benzenecarbonitrile

01.1: 15 residues within 4Å: Chain A: R.20, E.24, I.26, H.58, Y.60, W.88, V.90, L.112 Chain B: I.42, A.43, L.46, Q.49, S.50, T.77, Y.80 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:E.24, A:I.26, A:Y.60, A:W.88, A:V.90, A:L.112, B:L.46, B:Y.80, B:Y.80 Hydrogen bonds: A:E.24, A:E.24, A:Y.60, B:Q.49 01.2: 16 residues within 4Å: Chain B: R.20, E.24, I.26, H.58, Y.60, W.88, V.90, L.112 Chain C: I.42, A.43, L.46, F.47, Q.49, S.50, T.77, Y.80 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:E.24, B:Y.60, B:W.88, B:V.90, B:L.112, C:L.46, C:L.46, C:Y.80, C:Y.80 Hydrogen bonds: B:E.24, B:E.24, B:Y.60, C:Q.49 01.3: 14 residues within 4Å: Chain C: I.17, R.20, E.24, I.26, H.58, Y.60, W.88, V.90, L.112 Chain D: I.42, A.43, L.46, Q.49, Y.80 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:E.24, C:Y.60, C:W.88, C:W.88, C:V.90, C:L.112, C:L.112, D:L.46, D:L.46 Hydrogen bonds: C:E.24, C:E.24, D:Q.49 pi-Stacking: D:Y.80 01.4: 17 residues within 4Å: Chain D: I.17, R.20, E.24, I.26, H.58, Y.60, W.88, V.90, L.112 Chain L: I.42, A.43, L.46, F.47, Q.49, S.50, T.77, Y.80 14 PLIP interactions: 9 interactions with chain D, 5 interactions with chain L Hydrophobic interactions: D:E.24, D:I.26, D:Y.60, D:W.88, D:V.90, D:L.112, L:L.46, L:L.46, L:Y.80, L:Y.80 Hydrogen bonds: D:E.24, D:E.24, D:Y.60, L:Q.49 01.5: 16 residues within 4Å: Chain E: I.17, R.20, E.24, I.26, H.58, Y.60, W.88, V.90, L.112 Chain F: I.42, A.43, L.46, Q.49, S.50, T.77, Y.80 13 PLIP interactions: 9 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: E:E.24, E:I.26, E:Y.60, E:W.88, E:V.90, E:L.112, E:L.112, F:L.46, F:L.46 Hydrogen bonds: E:E.24, E:Y.60, F:Q.49 pi-Stacking: F:Y.80 01.6: 14 residues within 4Å: Chain F: R.20, E.24, I.26, H.58, Y.60, W.88, V.90, L.112 Chain G: I.42, A.43, L.46, Q.49, S.50, Y.80 13 PLIP interactions: 9 interactions with chain F, 4 interactions with chain G Hydrophobic interactions: F:E.24, F:I.26, F:Y.60, F:W.88, F:W.88, F:V.90, F:L.112, G:L.46, G:L.46 Hydrogen bonds: F:E.24, F:Y.60, G:Q.49 pi-Stacking: G:Y.80 01.7: 15 residues within 4Å: Chain G: I.17, R.20, E.24, I.26, H.58, Y.60, W.88, V.90, L.112 Chain H: I.42, A.43, L.46, Q.49, T.77, Y.80 13 PLIP interactions: 9 interactions with chain G, 4 interactions with chain H Hydrophobic interactions: G:E.24, G:Y.60, G:W.88, G:W.88, G:V.90, G:L.112, G:L.112, H:L.46, H:L.46 Hydrogen bonds: G:E.24, G:Y.60, H:Q.49 pi-Stacking: H:Y.80 01.8: 15 residues within 4Å: Chain H: R.20, E.24, I.26, H.58, Y.60, W.88, V.90, L.112 Chain I: I.42, A.43, L.46, Q.49, S.50, T.77, Y.80 12 PLIP interactions: 9 interactions with chain H, 3 interactions with chain I Hydrophobic interactions: H:E.24, H:Y.60, H:W.88, H:W.88, H:V.90, H:L.112, H:L.112, I:L.46 Hydrogen bonds: H:E.24, H:Y.60, I:Q.49 pi-Stacking: I:Y.80 01.9: 13 residues within 4Å: Chain I: R.20, E.24, I.26, H.58, Y.60, W.88, V.90, L.112 Chain J: I.42, A.43, L.46, Q.49, Y.80 13 PLIP interactions: 3 interactions with chain J, 10 interactions with chain I Hydrophobic interactions: J:L.46, I:E.24, I:I.26, I:Y.60, I:W.88, I:W.88, I:V.90, I:L.112, I:L.112 Hydrogen bonds: J:Q.49, I:E.24, I:Y.60 pi-Stacking: J:Y.80 01.10: 15 residues within 4Å: Chain J: I.17, R.20, E.24, I.26, H.58, Y.60, W.88, V.90, L.112 Chain K: I.42, A.43, L.46, Q.49, S.50, Y.80 12 PLIP interactions: 9 interactions with chain J, 3 interactions with chain K Hydrophobic interactions: J:E.24, J:Y.60, J:W.88, J:W.88, J:V.90, J:L.112, J:L.112, K:L.46 Hydrogen bonds: J:E.24, J:Y.60, K:Q.49 pi-Stacking: K:Y.80 01.11: 16 residues within 4Å: Chain E: I.42, A.43, L.46, Q.49, S.50, T.77, Y.80 Chain K: I.17, R.20, E.24, I.26, H.58, Y.60, W.88, V.90, L.112 11 PLIP interactions: 4 interactions with chain E, 7 interactions with chain K Hydrophobic interactions: E:L.46, E:Y.80, E:Y.80, K:E.24, K:Y.60, K:W.88, K:V.90, K:L.112 Hydrogen bonds: E:Q.49, K:E.24, K:Y.60 01.12: 15 residues within 4Å: Chain L: I.17, R.20, E.24, I.26, H.58, Y.60, W.88, V.90, L.112 Chain M: I.42, A.43, L.46, Q.49, T.77, Y.80 11 PLIP interactions: 4 interactions with chain M, 7 interactions with chain L Hydrophobic interactions: M:L.46, M:L.46, L:E.24, L:Y.60, L:W.88, L:V.90, L:L.112 Hydrogen bonds: M:Q.49, L:E.24, L:E.24 pi-Stacking: M:Y.80 01.13: 15 residues within 4Å: Chain M: I.17, R.20, E.24, I.26, H.58, Y.60, W.88, V.90, L.112 Chain N: I.42, A.43, L.46, Q.49, S.50, Y.80 13 PLIP interactions: 10 interactions with chain M, 3 interactions with chain N Hydrophobic interactions: M:E.24, M:Y.60, M:W.88, M:W.88, M:V.90, M:L.112, M:L.112, N:L.46 Hydrogen bonds: M:E.24, M:E.24, N:Q.49 Halogen bonds: M:I.17 pi-Stacking: N:Y.80 01.14: 14 residues within 4Å: Chain A: I.42, A.43, L.46, Q.49, Y.80 Chain N: I.17, R.20, E.24, I.26, H.58, Y.60, W.88, V.90, L.112 13 PLIP interactions: 9 interactions with chain N, 4 interactions with chain A Hydrophobic interactions: N:E.24, N:Y.60, N:W.88, N:W.88, N:V.90, N:L.112, N:L.112, A:L.46, A:L.46 Hydrogen bonds: N:E.24, N:E.24, A:Q.49 pi-Stacking: A:Y.80

Links

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Citation

Zhao, H. et al., Cryo-EM structure of HsClpP bound to CLPP-2068. Journal of Medicinal Chemistry (2025)

Release Date

2025-07-16

Peptides

ATP-dependent Clp protease proteolytic subunit, mitochondrial: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

ATP-dependent Clp protease proteolytic subunit, mitochondrial