SMTL ID : 8ylb.1

Cocrystal structures of agonists compound 1 with HsClpP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-14-mer

Ligands

14 x 01: 5-[(2-methylphenyl)methyl]-11-(phenylmethyl)-2,5,7,11-tetrazatricyclo[7.4.0.0^{2,6}]trideca-1(9),6-dien-8-one

01.1: 15 residues within 4Å: Chain A: R.21, L.22, E.25, I.27, H.59, Y.61, W.89, V.91 Chain G: I.43, L.47, F.48, Q.50, S.51, T.78, Y.81 10 PLIP interactions: 5 interactions with chain G, 5 interactions with chain A Hydrophobic interactions: G:L.47, G:L.47, G:F.48, A:E.25, A:Y.61, A:V.91 Hydrogen bonds: G:Q.50 pi-Stacking: G:Y.81, A:H.59, A:W.89 01.2: 16 residues within 4Å: Chain A: I.43, L.47, F.48, Q.50, S.51, T.78, Y.81 Chain B: R.21, L.22, E.25, I.27, H.59, Y.61, W.89, V.91, L.113 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:E.25, B:I.27, B:Y.61, B:Y.61, A:L.47, A:F.48 pi-Stacking: B:H.59, A:Y.81 Hydrogen bonds: A:Q.50 01.3: 15 residues within 4Å: Chain B: I.43, L.47, F.48, Q.50, S.51, T.78, Y.81 Chain C: R.21, L.22, E.25, I.27, H.59, Y.61, W.89, V.91 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:E.25, C:I.27, C:Y.61, C:W.89, C:V.91, B:L.47, B:F.48 pi-Stacking: C:H.59, C:W.89, B:Y.81 Hydrogen bonds: B:Q.50 01.4: 16 residues within 4Å: Chain C: I.43, L.47, F.48, Q.50, S.51, T.78, Y.81 Chain D: R.21, L.22, E.25, I.27, H.59, Y.61, W.89, V.91, L.113 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:L.47, C:L.47, C:T.78, D:E.25, D:I.27, D:Y.61, D:Y.61 Hydrogen bonds: C:Q.50, C:Y.81 pi-Stacking: C:Y.81, D:H.59 01.5: 15 residues within 4Å: Chain D: I.43, L.47, F.48, Q.50, S.51, T.78, Y.81 Chain E: R.21, L.22, E.25, I.27, H.59, Y.61, W.89, V.91 12 PLIP interactions: 7 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: E:E.25, E:I.27, E:Y.61, E:Y.61, E:V.91, D:L.47, D:F.48 pi-Stacking: E:H.59, E:W.89, D:Y.81 Hydrogen bonds: D:Q.50, D:Y.81 01.6: 16 residues within 4Å: Chain E: I.43, L.47, F.48, Q.50, S.51, T.78, Y.81 Chain F: R.21, L.22, E.25, I.27, H.59, Y.61, W.89, V.91, L.113 14 PLIP interactions: 8 interactions with chain F, 6 interactions with chain E Hydrophobic interactions: F:L.22, F:E.25, F:I.27, F:Y.61, F:V.91, E:L.47, E:L.47, E:F.48 pi-Stacking: F:H.59, F:W.89, F:W.89, E:Y.81 Hydrogen bonds: E:Q.50, E:Y.81 01.7: 16 residues within 4Å: Chain F: I.43, L.47, F.48, Q.50, S.51, T.78, Y.81 Chain G: R.21, L.22, E.25, I.27, H.59, Y.61, W.89, V.91, L.113 13 PLIP interactions: 8 interactions with chain G, 5 interactions with chain F Hydrophobic interactions: G:E.25, G:I.27, G:Y.61, G:W.89, G:V.91, F:L.47, F:L.47 pi-Stacking: G:H.59, G:W.89, G:W.89, F:Y.81 Hydrogen bonds: F:Q.50, F:Y.81 01.8: 16 residues within 4Å: Chain H: R.21, L.22, E.25, I.27, H.59, Y.61, W.89, V.91, L.113 Chain N: I.43, L.47, F.48, Q.50, S.51, T.78, Y.81 11 PLIP interactions: 7 interactions with chain H, 4 interactions with chain N Hydrophobic interactions: H:E.25, H:I.27, H:Y.61, H:Y.61, H:V.91, H:L.113, N:L.47, N:L.47 pi-Stacking: H:H.59, N:Y.81 Hydrogen bonds: N:Q.50 01.9: 14 residues within 4Å: Chain H: I.43, L.47, F.48, Q.50, S.51, T.78, Y.81 Chain I: R.21, L.22, E.25, I.27, H.59, Y.61, W.89 9 PLIP interactions: 6 interactions with chain I, 3 interactions with chain H Hydrophobic interactions: I:L.22, I:E.25, I:Y.61, I:W.89, H:L.47 pi-Stacking: I:H.59, I:W.89, H:Y.81 Hydrogen bonds: H:Q.50 01.10: 14 residues within 4Å: Chain I: I.43, L.47, F.48, Q.50, S.51, T.78, Y.81 Chain J: R.21, L.22, E.25, I.27, H.59, Y.61, W.89 8 PLIP interactions: 3 interactions with chain I, 5 interactions with chain J Hydrophobic interactions: I:L.47, J:E.25, J:I.27, J:Y.61 Hydrogen bonds: I:Q.50 pi-Stacking: I:Y.81, J:H.59, J:W.89 01.11: 14 residues within 4Å: Chain J: I.43, L.47, F.48, Q.50, S.51, T.78, Y.81 Chain K: R.21, L.22, E.25, I.27, H.59, Y.61, W.89 8 PLIP interactions: 4 interactions with chain J, 4 interactions with chain K Hydrophobic interactions: J:L.47, J:F.48, K:E.25, K:I.27, K:Y.61 Hydrogen bonds: J:Q.50 pi-Stacking: J:Y.81, K:H.59 01.12: 15 residues within 4Å: Chain K: I.43, L.47, F.48, Q.50, S.51, T.78, Y.81 Chain L: R.21, L.22, E.25, I.27, H.59, Y.61, W.89, V.91 14 PLIP interactions: 7 interactions with chain K, 7 interactions with chain L Hydrophobic interactions: K:L.47, K:L.47, K:L.47, K:F.48, L:E.25, L:I.27, L:Y.61, L:Y.61, L:V.91 Hydrogen bonds: K:Q.50, K:Y.81 pi-Stacking: K:Y.81, L:H.59, L:W.89 01.13: 15 residues within 4Å: Chain L: I.43, L.47, F.48, Q.50, S.51, T.78, Y.81 Chain M: R.21, L.22, E.25, I.27, H.59, Y.61, W.89, V.91 11 PLIP interactions: 7 interactions with chain M, 4 interactions with chain L Hydrophobic interactions: M:E.25, M:I.27, M:Y.61, M:Y.61, M:V.91, L:L.47 pi-Stacking: M:H.59, M:W.89, L:Y.81 Hydrogen bonds: L:Q.50, L:Y.81 01.14: 16 residues within 4Å: Chain M: I.43, L.47, F.48, Q.50, S.51, T.78, Y.81 Chain N: R.21, L.22, E.25, I.27, H.59, Y.61, W.89, V.91, L.188 9 PLIP interactions: 4 interactions with chain M, 5 interactions with chain N Hydrophobic interactions: M:L.47, M:F.48, N:E.25, N:I.27, N:V.91 Hydrogen bonds: M:Q.50 pi-Stacking: M:Y.81, N:H.59, N:W.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiang, X. et al., Rational Design of a Novel Class of Human ClpP Agonists through a Ring-Opening Strategy with Enhanced Antileukemia Activity. J.Med.Chem. (2024)

Release Date

2024-05-15

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