SMTL ID : 8wuz.1

Development of 2-imino-2,3,5,6,7,8-hexahydropyrido[4,3-d]pyrimidin-4(1H)-one derivatives as human caseinolytic peptidase P (hClpP) activators

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-14-mer

Ligands

14 x XFU: 5-[(3-fluorophenyl)methyl]-9-[[4-(trifluoromethyl)phenyl]methyl]-1,5,9,11-tetrazatricyclo[8.4.0.0^{2,7}]tetradeca-2(7),10-dien-8-one(Non-covalent)

XFU.1: 15 residues within 4Å: Chain A: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 Chain B: I.44, L.48, F.49, S.52, T.79, Y.82 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.23, A:E.26, A:Y.62, A:W.90, A:L.114, A:L.114, B:L.48, B:L.48, B:Y.82 Hydrogen bonds: A:Y.62 Halogen bonds: A:R.22 pi-Stacking: B:Y.82 XFU.3: 15 residues within 4Å: Chain B: R.22, L.23, E.26, H.60, Y.62, W.90, V.92, L.114 Chain D: I.44, A.45, L.48, F.49, S.52, T.79, Y.82 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:L.23, B:E.26, B:Y.62, B:W.90, B:L.114, D:L.48 Hydrogen bonds: B:Y.62 pi-Stacking: D:Y.82 Halogen bonds: D:A.45 XFU.6: 12 residues within 4Å: Chain C: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92 Chain E: L.48, F.49, S.52, T.79 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: C:L.23, C:E.26, C:I.28, C:Y.62, C:V.92, E:L.48 Hydrogen bonds: C:Y.62 Halogen bonds: C:R.22, C:R.22 pi-Stacking: E:Y.82 XFU.8: 15 residues within 4Å: Chain D: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 Chain G: A.45, L.48, F.49, S.52, T.79, Y.82 12 PLIP interactions: 3 interactions with chain G, 9 interactions with chain D Hydrophobic interactions: G:L.48, D:L.23, D:E.26, D:I.28, D:Y.62, D:Y.62, D:W.90, D:V.92, D:L.114 pi-Stacking: G:Y.82 Halogen bonds: G:A.45 Hydrogen bonds: D:Y.62 XFU.10: 16 residues within 4Å: Chain A: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain E: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 10 PLIP interactions: 7 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:L.23, E:E.26, E:I.28, E:Y.62, E:L.114, A:L.48 Hydrogen bonds: E:Y.62, A:Q.51 Halogen bonds: E:R.22 pi-Stacking: A:Y.82 XFU.12: 15 residues within 4Å: Chain C: I.44, L.48, F.49, S.52, T.79, Y.82 Chain F: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 13 PLIP interactions: 3 interactions with chain C, 10 interactions with chain F Hydrophobic interactions: C:I.44, C:L.48, F:L.23, F:E.26, F:I.28, F:Y.62, F:Y.62, F:W.90, F:V.92, F:L.114 pi-Stacking: C:Y.82 Hydrogen bonds: F:Y.62 Halogen bonds: F:R.22 XFU.14: 12 residues within 4Å: Chain F: L.48, F.49, S.52, T.79, Y.82 Chain G: R.22, L.23, E.26, I.28, H.60, Y.62, W.90 9 PLIP interactions: 2 interactions with chain F, 7 interactions with chain G Hydrophobic interactions: F:L.48, G:L.23, G:E.26, G:I.28, G:Y.62, G:Y.62 pi-Stacking: F:Y.82 Hydrogen bonds: G:Y.62 Halogen bonds: G:R.22 XFU.16: 15 residues within 4Å: Chain H: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 Chain I: I.44, L.48, F.49, S.52, T.79, Y.82 12 PLIP interactions: 8 interactions with chain H, 4 interactions with chain I Hydrophobic interactions: H:L.23, H:E.26, H:Y.62, H:W.90, H:L.114, H:L.114, I:L.48, I:L.48, I:Y.82 Hydrogen bonds: H:E.26 Halogen bonds: H:R.22 pi-Stacking: I:Y.82 XFU.18: 15 residues within 4Å: Chain I: R.22, L.23, E.26, H.60, Y.62, W.90, V.92, L.114 Chain K: I.44, A.45, L.48, F.49, S.52, T.79, Y.82 9 PLIP interactions: 6 interactions with chain I, 3 interactions with chain K Hydrophobic interactions: I:L.23, I:E.26, I:Y.62, I:W.90, I:L.114, K:L.48 Hydrogen bonds: I:E.26 pi-Stacking: K:Y.82 Halogen bonds: K:A.45 XFU.21: 12 residues within 4Å: Chain J: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92 Chain L: L.48, F.49, S.52, T.79 10 PLIP interactions: 2 interactions with chain L, 8 interactions with chain J Hydrophobic interactions: L:L.48, J:L.23, J:E.26, J:I.28, J:Y.62, J:V.92 pi-Stacking: L:Y.82 Hydrogen bonds: J:E.26 Halogen bonds: J:R.22, J:R.22 XFU.23: 15 residues within 4Å: Chain K: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 Chain N: A.45, L.48, F.49, S.52, T.79, Y.82 12 PLIP interactions: 3 interactions with chain N, 9 interactions with chain K Hydrophobic interactions: N:L.48, K:L.23, K:E.26, K:I.28, K:Y.62, K:Y.62, K:W.90, K:V.92, K:L.114 pi-Stacking: N:Y.82 Halogen bonds: N:A.45 Hydrogen bonds: K:E.26 XFU.25: 16 residues within 4Å: Chain H: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain L: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 10 PLIP interactions: 7 interactions with chain L, 3 interactions with chain H Hydrophobic interactions: L:L.23, L:E.26, L:I.28, L:Y.62, L:L.114, H:L.48 Hydrogen bonds: L:E.26, H:Q.51 Halogen bonds: L:R.22 pi-Stacking: H:Y.82 XFU.27: 15 residues within 4Å: Chain J: I.44, L.48, F.49, S.52, T.79, Y.82 Chain M: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 13 PLIP interactions: 10 interactions with chain M, 3 interactions with chain J Hydrophobic interactions: M:L.23, M:E.26, M:I.28, M:Y.62, M:Y.62, M:W.90, M:V.92, M:L.114, J:I.44, J:L.48 Hydrogen bonds: M:E.26 Halogen bonds: M:R.22 pi-Stacking: J:Y.82 XFU.29: 12 residues within 4Å: Chain M: L.48, F.49, S.52, T.79, Y.82 Chain N: R.22, L.23, E.26, I.28, H.60, Y.62, W.90 9 PLIP interactions: 7 interactions with chain N, 2 interactions with chain M Hydrophobic interactions: N:L.23, N:E.26, N:I.28, N:Y.62, N:Y.62, M:L.48 Hydrogen bonds: N:E.26 Halogen bonds: N:R.22 pi-Stacking: M:Y.82

16 x BR: BROMIDE ION(Non-covalent)

BR.2: 3 residues within 4Å: Chain A: S.97, H.122, P.124 Ligand excluded by PLIP BR.4: 3 residues within 4Å: Chain B: S.97, M.98, H.122 Ligand excluded by PLIP BR.5: 4 residues within 4Å: Chain B: M.80, Q.81, I.83, N.85 Ligand excluded by PLIP BR.7: 2 residues within 4Å: Chain C: S.97, H.122 Ligand excluded by PLIP BR.9: 4 residues within 4Å: Chain D: V.70, S.97, M.98, H.122 Ligand excluded by PLIP BR.11: 2 residues within 4Å: Chain E: S.97, H.122 Ligand excluded by PLIP BR.13: 4 residues within 4Å: Chain F: V.70, S.97, M.98, H.122 Ligand excluded by PLIP BR.15: 2 residues within 4Å: Chain G: S.97, H.122 Ligand excluded by PLIP BR.17: 3 residues within 4Å: Chain H: S.97, H.122, P.124 Ligand excluded by PLIP BR.19: 3 residues within 4Å: Chain I: S.97, M.98, H.122 Ligand excluded by PLIP BR.20: 4 residues within 4Å: Chain I: M.80, Q.81, I.83, N.85 Ligand excluded by PLIP BR.22: 2 residues within 4Å: Chain J: S.97, H.122 Ligand excluded by PLIP BR.24: 4 residues within 4Å: Chain K: V.70, S.97, M.98, H.122 Ligand excluded by PLIP BR.26: 2 residues within 4Å: Chain L: S.97, H.122 Ligand excluded by PLIP BR.28: 4 residues within 4Å: Chain M: V.70, S.97, M.98, H.122 Ligand excluded by PLIP BR.30: 2 residues within 4Å: Chain N: S.97, H.122 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, J.-X. et al., Development of 2-imino-2,3,5,6,7,8-hexahydropyrido[4,3-d]pyrimidin-4(1H)-one derivatives as human caseinolytic peptidase P (hClpP) activators. To Be Published

Release Date

2024-10-23

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
A

I
B

J
C

K
D

L
E

M
F

N
G

ATP-dependent Clp protease proteolytic subunit, mitochondrial

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