SMTL ID : 6c91.1

Structure of GRP94 with a resorcinylic inhibitor.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

homo-dimer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: K.71, W.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.232 Salt bridges: A:K.71 SO4.2: 2 residues within 4Å: Chain A: K.150, N.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.153, A:D.154 Water bridges: A:N.152 Salt bridges: A:K.150 SO4.7: 4 residues within 4Å: Chain B: K.150, N.152, N.153, D.154 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.153, B:D.154, B:N.175 Salt bridges: B:K.150 SO4.8: 2 residues within 4Å: Chain B: K.71, W.232 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.232 Salt bridges: B:K.71 SO4.9: 3 residues within 4Å: Chain B: T.155, H.157, A.170 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.155 Salt bridges: B:H.157 SO4.10: 3 residues within 4Å: Chain B: H.151, N.152, N.153 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.153 Salt bridges: B:H.151

2 x EQD: 5-[2-(1-benzyl-1H-imidazol-2-yl)ethyl]-4,6-dichlorobenzene-1,3-diol(Non-covalent)

EQD.3: 12 residues within 4Å: Chain A: N.43, A.44, A.47, D.85, M.90, E.94, L.95, N.98, F.131, W.159, T.181, I.183 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.95, A:N.98, A:F.131 Hydrogen bonds: A:T.181 Water bridges: A:N.43, A:G.87 pi-Stacking: A:F.131, A:W.159 EQD.11: 11 residues within 4Å: Chain B: L.40, N.43, A.44, A.47, D.85, M.90, N.98, F.131, W.159, T.181, I.183 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:N.98, B:F.131 Hydrogen bonds: B:T.181, B:T.181 Water bridges: B:E.39, B:N.43, B:A.44, B:G.87 pi-Stacking: B:F.131, B:W.159

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

EDO.4: 5 residues within 4Å: Chain A: T.155, Q.156, A.170, D.171, G.174 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.155, A:Q.156, A:D.171 EDO.5: 3 residues within 4Å: Chain A: Y.30 Ligands: EDO.6, EDO.14 No protein-ligand interaction detected (PLIP) EDO.6: 6 residues within 4Å: Chain A: Y.30, N.32, I.35, R.38, Y.207 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.38 EDO.12: 3 residues within 4Å: Chain B: T.84, W.232 Ligands: EDO.13 No protein-ligand interaction detected (PLIP) EDO.13: 4 residues within 4Å: Chain B: H.82, T.148, R.173 Ligands: EDO.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.148, B:R.173, B:R.173 EDO.14: 3 residues within 4Å: Chain A: L.29 Chain B: F.14 Ligands: EDO.5 No protein-ligand interaction detected (PLIP) EDO.15: 1 residues within 4Å: Chain B: K.144 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.144 EDO.16: 6 residues within 4Å: Chain B: S.105, E.160, D.162, E.165, F.166, S.167 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.167 EDO.17: 2 residues within 4Å: Chain B: W.218, W.230 1 PLIP interactions: 1 interactions with chain B Water bridges: B:C.74

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

Endoplasmin

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