SMTL ID : 5wmt.5 (4 other biounits)

Structure of GRP94 N-terminal Domain bound to resorcinylic inhibitor BnIm.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-tetramer

Ligands

15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 3 residues within 4Å: Chain A: R.92, T.155, H.157 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.155, A:H.157 EDO.2: 3 residues within 4Å: Chain A: K.150, N.152, D.154 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.150, A:D.154 EDO.3: 2 residues within 4Å: Chain A: K.71, W.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.71, A:K.71 EDO.4: 3 residues within 4Å: Chain A: K.71, Y.216, W.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.71, A:Y.216 EDO.6: 7 residues within 4Å: Chain B: S.105, K.144, E.160, D.162, E.165, F.166, S.167 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.144, B:K.144, B:F.166 EDO.7: 2 residues within 4Å: Chain B: R.92, H.157 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.157 EDO.8: 3 residues within 4Å: Chain B: H.82, T.148, R.173 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.148, B:T.148, B:R.173, B:R.173 EDO.11: 7 residues within 4Å: Chain C: S.105, K.144, E.160, D.162, E.165, F.166, S.167 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.144, C:K.144, C:F.166 EDO.12: 3 residues within 4Å: Chain C: T.148, R.173 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.148, C:R.173, C:R.173 EDO.13: 4 residues within 4Å: Chain C: K.73, H.82, T.84 Ligands: EDO.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.84 EDO.14: 3 residues within 4Å: Chain C: R.92, T.155, H.157 No protein-ligand interaction detected (PLIP) EDO.17: 2 residues within 4Å: Chain D: R.92, H.157 No protein-ligand interaction detected (PLIP) EDO.18: 2 residues within 4Å: Chain D: K.71, W.232 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.71 EDO.19: 3 residues within 4Å: Chain D: K.150, N.152, D.154 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.150 EDO.20: 5 residues within 4Å: Chain D: T.155, Q.156, A.170, D.171, G.174 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.156, D:G.174

4 x 9QY: methyl 2-[2-(1-benzyl-1H-imidazol-2-yl)ethyl]-3-chloro-4,6-dihydroxybenzoate(Non-covalent)

9QY.5: 11 residues within 4Å: Chain A: N.43, A.44, A.47, D.85, M.90, E.94, N.98, F.131, W.159, T.181, I.183 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:N.98, A:F.131, A:I.183 Hydrogen bonds: A:N.43, A:D.85 Water bridges: A:L.40, A:G.87 pi-Stacking: A:F.131, A:W.159 9QY.10: 10 residues within 4Å: Chain B: N.43, A.44, A.47, D.85, M.90, N.98, F.131, W.159, T.181, I.183 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:N.98, B:F.131, B:I.183 Hydrogen bonds: B:D.85 Water bridges: B:L.40, B:A.44, B:G.87 pi-Stacking: B:F.131, B:W.159 9QY.16: 11 residues within 4Å: Chain C: N.43, A.44, A.47, D.85, M.90, N.98, L.99, F.131, W.159, T.181, I.183 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:N.98, C:L.99, C:F.131, C:I.183, C:I.183 Hydrogen bonds: C:N.43, C:D.85, C:T.181 Water bridges: C:L.40, C:A.44 pi-Stacking: C:F.131, C:W.159 9QY.21: 13 residues within 4Å: Chain D: L.40, N.43, A.44, A.47, D.85, M.90, L.95, N.98, L.99, F.131, W.159, T.181, I.183 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:N.43, D:L.95, D:N.98, D:L.99, D:F.131, D:I.183 Hydrogen bonds: D:N.43, D:D.85, D:T.181 Water bridges: D:G.87 pi-Stacking: D:F.131, D:W.159

2 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 2 residues within 4Å: Chain B: W.218, W.230 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain C: W.218, W.230 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Que, N.L.S. et al., Structure Based Design of a Grp94-Selective Inhibitor: Exploiting a Key Residue in Grp94 To Optimize Paralog-Selective Binding. J. Med. Chem. (2018)

Release Date

2018-04-18

Peptides

Endoplasmin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Endoplasmin

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