SMTL ID : 7bmk.1

ATP-Competitive Partial Antagonists-'PAIR's-Rheostatically Modulate IRE1alpha's Kinase Helix-alphaC to Segregate its RNase-Mediated Biological Outputs

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x U4N: 2,2,2-tris(fluoranyl)-~{N}-[4-[3-[2-[[(3~{S})-piperidin-3-yl]amino]pyrimidin-4-yl]pyridin-2-yl]oxynaphthalen-1-yl]ethanesulfonamide(Non-covalent)

U4N.1: 22 residues within 4Å: Chain A: L.34, V.43, A.54, K.56, E.69, V.70, L.73, I.83, Y.85, I.97, I.99, E.100, L.101, C.102, A.103, A.104, E.108, L.152, S.167, D.168, F.169 Ligands: GOL.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.43, A:K.56, A:I.97, A:I.99, A:I.99, A:I.99, A:L.152 Hydrogen bonds: A:K.56, A:C.102, A:C.102, A:E.108, A:D.168, A:F.169 Water bridges: A:G.170 pi-Cation interactions: A:K.56 U4N.22: 21 residues within 4Å: Chain B: L.34, V.43, A.54, K.56, E.69, V.70, L.73, I.83, Y.85, I.97, I.99, E.100, L.101, C.102, A.103, A.104, E.108, L.152, S.167, D.168, F.169 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.34, B:V.43, B:K.56, B:I.97, B:I.99, B:I.99, B:I.99, B:L.152 Hydrogen bonds: B:K.56, B:C.102, B:C.102, B:E.108, B:D.168, B:F.169 Water bridges: B:G.170 pi-Cation interactions: B:K.56

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: L.284, K.285, F.289, W.290, K.294 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.285, A:K.285, A:K.294 Water bridges: A:F.289, A:F.289, A:S.291, A:S.291 GOL.3: 7 residues within 4Å: Chain A: E.264, K.268, H.286, Y.402, R.403, E.406 Ligands: PEG.21 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.406 Water bridges: A:H.282, A:H.282 GOL.4: 4 residues within 4Å: Chain A: D.32, L.34, R.45 Ligands: U4N.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.45 Water bridges: A:R.45 GOL.7: 4 residues within 4Å: Chain A: H.137, S.138, N.140, Y.210 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.140 Water bridges: A:S.279, A:A.280 GOL.9: 3 residues within 4Å: Chain A: K.234, S.235, R.238 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.235, A:R.238 Water bridges: A:E.111, A:E.111, A:G.228, A:G.233 GOL.10: 4 residues within 4Å: Chain A: I.225, S.226, C.251, D.259 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.259 Water bridges: A:D.259 GOL.16: 6 residues within 4Å: Chain A: P.231, F.232, G.233, N.241, A.246, S.248 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.232, A:N.241 GOL.17: 2 residues within 4Å: Chain A: R.184, R.185 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.184, A:R.185, A:R.185 GOL.23: 5 residues within 4Å: Chain A: R.362, H.366 Chain B: R.362, H.366, H.367 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.362, A:R.362, A:H.367, B:R.362, B:R.362, B:H.366 GOL.26: 4 residues within 4Å: Chain B: C.247, S.248, L.249, R.263 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.249, B:R.263

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

EDO.5: 5 residues within 4Å: Chain A: A.103, H.117, L.118, M.155, P.156 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: S.154, M.155, P.156, N.157 Chain B: E.78 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: S.226, E.227, G.228, S.229, C.251 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain A: Q.300, D.304, R.362, H.366 Chain B: Q.300, D.304, R.362, H.366 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: S.381, L.382, P.383, D.384, D.385 Chain B: R.412 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: H.159, G.160, K.161 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: S.138, L.139, N.140, K.174 Chain B: A.158, H.159 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: Q.297, K.365 Chain B: Q.297, D.301, Y.417 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: P.254, V.260, R.263, H.396 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: W.290, L.292, Q.295 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: P.189, E.192, I.195, L.200, Q.239 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain A: H.159 Chain B: S.138, K.281 Ligands: PEG.25, PEG.30 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain B: P.60, F.63, S.64 Ligand excluded by PLIP EDO.31: 8 residues within 4Å: Chain B: D.77, H.79, P.80, V.82, R.84, E.100, K.163, M.165 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain B: S.154, M.155, N.157, K.161, I.162, K.163 Ligand excluded by PLIP EDO.33: 7 residues within 4Å: Chain B: T.378, L.379, G.380, D.385, C.388, Y.389 Ligands: EDO.34 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain B: S.392, R.393 Ligands: EDO.33 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain B: Q.127, L.284, K.285, H.286, F.289, W.290, K.294 Ligand excluded by PLIP EDO.36: 1 residues within 4Å: Chain B: K.174 Ligand excluded by PLIP

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.21: 7 residues within 4Å: Chain A: K.268, Q.275, K.276, R.277, P.278, H.282 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.268, A:K.268 Water bridges: A:Q.275, A:R.277 PEG.25: 7 residues within 4Å: Chain A: N.157, H.159, K.161 Chain B: E.78, H.79, H.135 Ligands: EDO.24 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.135 Water bridges: B:E.78, B:H.79 PEG.27: 6 residues within 4Å: Chain A: R.412 Chain B: S.381, L.382, P.383, D.384, D.385 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.384, B:D.385, B:D.385 PEG.30: 6 residues within 4Å: Chain B: H.79, S.131, A.134, K.281, L.284 Ligands: EDO.24 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.79

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.28: 5 residues within 4Å: Chain B: E.320, R.321, G.322, G.323, R.324 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.322, B:G.323, B:R.324 Water bridges: B:G.322, B:A.325

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feldman, H.C. et al., ATP-competitive partial antagonists of the IRE1 alpha RNase segregate outputs of the UPR. Nat.Chem.Biol. (2021)

Release Date

2021-09-29

Peptides

Serine/threonine-protein kinase/endoribonuclease IRE1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine/threonine-protein kinase/endoribonuclease IRE1