SMTL ID : 8uvp.1

Human p97/VCP R155H mutant structure with a triazole inhibitor (NSC819701/up)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

12 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 15 residues within 4Å: Chain A: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, D.304, I.380, H.384, G.408, A.409 Chain B: R.359 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.207, A:T.249, A:T.249, A:G.250, A:K.251, A:T.252, A:T.252, A:D.304 Salt bridges: A:K.251, A:K.251, B:R.359 ADP.2: 14 residues within 4Å: Chain A: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, D.577, E.578, I.656, A.685, T.688 Chain B: R.635 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.480, A:G.480, A:G.521, A:C.522, A:G.523, A:K.524, A:T.525, A:T.525, A:D.577, A:D.577, A:E.578, A:E.578, A:A.685 Salt bridges: A:K.524, A:K.524, B:R.635 ADP.4: 15 residues within 4Å: Chain B: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, D.304, I.380, H.384, G.408, A.409 Chain C: R.359 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.207, B:T.249, B:T.249, B:G.250, B:K.251, B:T.252, B:T.252, B:D.304 Salt bridges: B:K.251, B:K.251, C:R.359 ADP.5: 14 residues within 4Å: Chain B: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, D.577, E.578, I.656, A.685, T.688 Chain C: R.635 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.480, B:G.480, B:G.521, B:C.522, B:G.523, B:K.524, B:T.525, B:T.525, B:D.577, B:D.577, B:E.578, B:E.578, B:A.685 Salt bridges: B:K.524, B:K.524, C:R.635 ADP.7: 15 residues within 4Å: Chain C: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, D.304, I.380, H.384, G.408, A.409 Chain D: R.359 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.207, C:T.249, C:T.249, C:G.250, C:K.251, C:T.252, C:T.252, C:D.304 Salt bridges: C:K.251, C:K.251, D:R.359 ADP.8: 14 residues within 4Å: Chain C: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, D.577, E.578, I.656, A.685, T.688 Chain D: R.635 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.480, C:G.480, C:G.521, C:C.522, C:G.523, C:K.524, C:T.525, C:T.525, C:D.577, C:D.577, C:E.578, C:E.578, C:A.685 Salt bridges: C:K.524, C:K.524, D:R.635 ADP.10: 15 residues within 4Å: Chain D: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, D.304, I.380, H.384, G.408, A.409 Chain E: R.359 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:G.207, D:T.249, D:T.249, D:G.250, D:K.251, D:T.252, D:T.252, D:D.304 Salt bridges: D:K.251, D:K.251, E:R.359 ADP.11: 14 residues within 4Å: Chain D: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, D.577, E.578, I.656, A.685, T.688 Chain E: R.635 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:G.480, D:G.480, D:G.521, D:C.522, D:G.523, D:K.524, D:T.525, D:T.525, D:D.577, D:D.577, D:E.578, D:E.578, D:A.685 Salt bridges: D:K.524, D:K.524, E:R.635 ADP.13: 15 residues within 4Å: Chain E: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, D.304, I.380, H.384, G.408, A.409 Chain F: R.359 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.207, E:T.249, E:T.249, E:G.250, E:K.251, E:T.252, E:T.252, E:D.304 Salt bridges: E:K.251, E:K.251, F:R.359 ADP.14: 14 residues within 4Å: Chain E: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, D.577, E.578, I.656, A.685, T.688 Chain F: R.635 16 PLIP interactions: 15 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.480, E:G.480, E:G.521, E:C.522, E:G.523, E:K.524, E:T.525, E:T.525, E:D.577, E:D.577, E:E.578, E:E.578, E:A.685 Salt bridges: E:K.524, E:K.524, F:R.635 ADP.16: 15 residues within 4Å: Chain A: R.359 Chain F: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, D.304, I.380, H.384, G.408, A.409 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:G.207, F:T.249, F:T.249, F:G.250, F:K.251, F:T.252, F:T.252, F:D.304 Salt bridges: F:K.251, F:K.251, A:R.359 ADP.17: 14 residues within 4Å: Chain A: R.635 Chain F: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, D.577, E.578, I.656, A.685, T.688 16 PLIP interactions: 15 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:G.480, F:G.480, F:G.521, F:C.522, F:G.523, F:K.524, F:T.525, F:T.525, F:D.577, F:D.577, F:E.578, F:E.578, F:A.685 Salt bridges: F:K.524, F:K.524, A:R.635

6 x XO8: 2-[(4P)-4-(4-{[(4P)-5-(cyclohexylsulfanyl)-4-(pyridin-3-yl)-4H-1,2,4-triazol-3-yl]methoxy}-2,5-difluorophenyl)-2H-1,2,3-triazol-2-yl]-1-[(2R,6S)-2,6-dimethylmorpholin-4-yl]ethan-1-one(Non-covalent)

XO8.3: 15 residues within 4Å: Chain A: L.492, V.493, P.496, V.497, P.500, L.504, P.510, K.512, A.537, P.571, C.572, V.573, K.615, N.616 Chain F: N.401 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.493, A:P.496, A:P.510, A:A.537, A:P.571, A:V.573, A:K.615 Halogen bonds: A:P.500 XO8.6: 15 residues within 4Å: Chain A: N.401 Chain B: L.492, V.493, P.496, V.497, P.500, L.504, P.510, K.512, A.537, P.571, C.572, V.573, K.615, N.616 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.493, B:P.496, B:P.510, B:A.537, B:P.571, B:V.573, B:K.615 Halogen bonds: B:P.500 XO8.9: 15 residues within 4Å: Chain B: N.401 Chain C: L.492, V.493, P.496, V.497, P.500, L.504, P.510, K.512, A.537, P.571, C.572, V.573, K.615, N.616 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.493, C:P.496, C:P.510, C:A.537, C:P.571, C:V.573, C:K.615 Halogen bonds: C:P.500 XO8.12: 15 residues within 4Å: Chain C: N.401 Chain D: L.492, V.493, P.496, V.497, P.500, L.504, P.510, K.512, A.537, P.571, C.572, V.573, K.615, N.616 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:V.493, D:P.496, D:P.510, D:A.537, D:P.571, D:V.573, D:K.615 Halogen bonds: D:P.500 XO8.15: 15 residues within 4Å: Chain D: N.401 Chain E: L.492, V.493, P.496, V.497, P.500, L.504, P.510, K.512, A.537, P.571, C.572, V.573, K.615, N.616 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:V.493, E:P.496, E:P.510, E:A.537, E:P.571, E:V.573, E:K.615 Halogen bonds: E:P.500 XO8.18: 15 residues within 4Å: Chain E: N.401 Chain F: L.492, V.493, P.496, V.497, P.500, L.504, P.510, K.512, A.537, P.571, C.572, V.573, K.615, N.616 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:V.493, F:P.496, F:P.510, F:A.537, F:P.571, F:V.573, F:K.615 Halogen bonds: F:P.500

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nandi, P. et al., Mechanism of allosteric inhibition of human p97/VCP ATPase and its disease mutant by triazole inhibitors. Commun Chem (2024)

Release Date

2024-08-21

Peptides

Transitional endoplasmic reticulum ATPase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Transitional endoplasmic reticulum ATPase

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