SMTL ID : 5mtf.1

A modular route to novel potent and selective inhibitors of rhomboid intramembrane proteases

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-hexamer

Ligands

6 x ACE- ARG- VAL- ARG- HIS- W6Q: inhibitor(Non-covalent)

ACE-ARG-VAL-ARG-HIS-W6Q.1: 27 residues within 4Å: Chain A: M.34, F.60, H.64, F.67, N.68, Q.103, S.107, W.110, F.111, G.112, G.113, L.114, S.115, V.118, W.150, F.159, M.161, S.162, M.163, A.164, N.165, H.168 Chain E: D.30, Q.31 Ligands: CL.2, ACE-ARG-VAL-ARG-HIS-W6Q.33, ACE-ARG-VAL-ARG-HIS-W6Q.33 25 PLIP interactions: 22 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:F.60, A:F.67, A:V.118, A:F.159, A:A.164, E:D.30 Hydrogen bonds: A:H.64, A:N.68, A:S.107, A:W.110, A:G.112, A:G.112, A:S.115, A:S.162, A:S.162, A:M.163, A:M.163, A:A.164, A:H.168, E:D.30, E:Q.31 Water bridges: A:S.107, A:S.162 pi-Stacking: A:F.60, A:H.64 ACE-ARG-VAL-ARG-HIS-W6Q.9: 27 residues within 4Å: Chain B: M.34, F.60, H.64, F.67, N.68, Q.103, S.107, W.110, F.111, G.112, G.113, L.114, S.115, V.118, W.150, F.159, M.161, S.162, M.163, A.164, N.165, H.168 Chain D: D.30, Q.31 Ligands: CL.10, ACE-ARG-VAL-ARG-HIS-W6Q.25, ACE-ARG-VAL-ARG-HIS-W6Q.25 25 PLIP interactions: 22 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:F.60, B:F.67, B:V.118, B:F.159, B:A.164, D:D.30 Hydrogen bonds: B:H.64, B:N.68, B:S.107, B:W.110, B:G.112, B:G.112, B:S.115, B:S.162, B:S.162, B:M.163, B:M.163, B:A.164, B:H.168, D:D.30, D:Q.31 Water bridges: B:S.107, B:S.162 pi-Stacking: B:F.60, B:H.64 ACE-ARG-VAL-ARG-HIS-W6Q.17: 27 residues within 4Å: Chain C: M.34, F.60, H.64, F.67, N.68, Q.103, S.107, W.110, F.111, G.112, G.113, L.114, S.115, V.118, W.150, F.159, M.161, S.162, M.163, A.164, N.165, H.168 Chain F: D.30, Q.31 Ligands: CL.18, ACE-ARG-VAL-ARG-HIS-W6Q.41, ACE-ARG-VAL-ARG-HIS-W6Q.41 25 PLIP interactions: 22 interactions with chain C, 3 interactions with chain F Hydrophobic interactions: C:F.60, C:F.67, C:V.118, C:F.159, C:A.164, F:D.30 Hydrogen bonds: C:H.64, C:N.68, C:S.107, C:W.110, C:G.112, C:G.112, C:S.115, C:S.162, C:S.162, C:M.163, C:M.163, C:A.164, C:H.168, F:D.30, F:Q.31 Water bridges: C:S.107, C:S.162 pi-Stacking: C:F.60, C:H.64 ACE-ARG-VAL-ARG-HIS-W6Q.25: 27 residues within 4Å: Chain B: D.30, Q.31 Chain D: M.34, F.60, H.64, F.67, N.68, Q.103, S.107, W.110, F.111, G.112, G.113, L.114, S.115, V.118, W.150, F.159, M.161, S.162, M.163, A.164, N.165, H.168 Ligands: ACE-ARG-VAL-ARG-HIS-W6Q.9, ACE-ARG-VAL-ARG-HIS-W6Q.9, CL.26 25 PLIP interactions: 21 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:F.60, D:F.67, D:V.118, D:F.159, D:A.164, B:D.30 Hydrogen bonds: D:H.64, D:N.68, D:S.107, D:W.110, D:G.112, D:G.112, D:S.115, D:S.162, D:M.163, D:M.163, D:A.164, D:H.168, B:D.30, B:D.30, B:Q.31 Water bridges: D:S.107, D:S.162 pi-Stacking: D:F.60, D:H.64 ACE-ARG-VAL-ARG-HIS-W6Q.33: 27 residues within 4Å: Chain A: D.30, Q.31 Chain E: M.34, F.60, H.64, F.67, N.68, Q.103, S.107, W.110, F.111, G.112, G.113, L.114, S.115, V.118, W.150, F.159, M.161, S.162, M.163, A.164, N.165, H.168 Ligands: ACE-ARG-VAL-ARG-HIS-W6Q.1, ACE-ARG-VAL-ARG-HIS-W6Q.1, CL.34 25 PLIP interactions: 21 interactions with chain E, 4 interactions with chain A Hydrophobic interactions: E:F.60, E:F.67, E:V.118, E:F.159, E:A.164, A:D.30 Hydrogen bonds: E:H.64, E:N.68, E:S.107, E:W.110, E:G.112, E:G.112, E:S.115, E:S.162, E:M.163, E:M.163, E:A.164, E:H.168, A:D.30, A:D.30, A:Q.31 Water bridges: E:S.107, E:S.162 pi-Stacking: E:F.60, E:H.64 ACE-ARG-VAL-ARG-HIS-W6Q.41: 27 residues within 4Å: Chain C: D.30, Q.31 Chain F: M.34, F.60, H.64, F.67, N.68, Q.103, S.107, W.110, F.111, G.112, G.113, L.114, S.115, V.118, W.150, F.159, M.161, S.162, M.163, A.164, N.165, H.168 Ligands: ACE-ARG-VAL-ARG-HIS-W6Q.17, ACE-ARG-VAL-ARG-HIS-W6Q.17, CL.42 25 PLIP interactions: 4 interactions with chain C, 21 interactions with chain F Hydrophobic interactions: C:D.30, F:F.60, F:F.67, F:V.118, F:F.159, F:A.164 Hydrogen bonds: C:D.30, C:D.30, C:Q.31, F:H.64, F:N.68, F:S.107, F:W.110, F:G.112, F:G.112, F:S.115, F:S.162, F:M.163, F:M.163, F:A.164, F:H.168 Water bridges: F:S.107, F:S.162 pi-Stacking: F:F.60, F:H.64

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 6 residues within 4Å: Chain A: Q.103, S.107, M.163, N.165, G.166 Ligands: ACE-ARG-VAL-ARG-HIS-W6Q.1 Ligand excluded by PLIP CL.3: 6 residues within 4Å: Chain A: R.6, A.7, W.73 Chain C: Q.140, R.141, G.142 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain B: Q.103, S.107, M.163, N.165, G.166 Ligands: ACE-ARG-VAL-ARG-HIS-W6Q.9 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain A: Q.140, R.141, G.142 Chain B: R.6, A.7, W.73 Ligand excluded by PLIP CL.18: 6 residues within 4Å: Chain C: Q.103, S.107, M.163, N.165, G.166 Ligands: ACE-ARG-VAL-ARG-HIS-W6Q.17 Ligand excluded by PLIP CL.19: 6 residues within 4Å: Chain B: Q.140, R.141, G.142 Chain C: R.6, A.7, W.73 Ligand excluded by PLIP CL.26: 6 residues within 4Å: Chain D: Q.103, S.107, M.163, N.165, G.166 Ligands: ACE-ARG-VAL-ARG-HIS-W6Q.25 Ligand excluded by PLIP CL.27: 6 residues within 4Å: Chain D: R.6, A.7, W.73 Chain F: Q.140, R.141, G.142 Ligand excluded by PLIP CL.34: 6 residues within 4Å: Chain E: Q.103, S.107, M.163, N.165, G.166 Ligands: ACE-ARG-VAL-ARG-HIS-W6Q.33 Ligand excluded by PLIP CL.35: 6 residues within 4Å: Chain D: Q.140, R.141, G.142 Chain E: R.6, A.7, W.73 Ligand excluded by PLIP CL.42: 6 residues within 4Å: Chain F: Q.103, S.107, M.163, N.165, G.166 Ligands: ACE-ARG-VAL-ARG-HIS-W6Q.41 Ligand excluded by PLIP CL.43: 6 residues within 4Å: Chain E: Q.140, R.141, G.142 Chain F: R.6, A.7, W.73 Ligand excluded by PLIP

30 x BNG: nonyl beta-D-glucopyranoside(Non-covalent)

BNG.4: 5 residues within 4Å: Chain A: A.17, V.21, W.36, L.37, W.50 Ligand excluded by PLIP BNG.5: 5 residues within 4Å: Chain A: M.122, W.126, I.144, L.148, I.151 Ligand excluded by PLIP BNG.6: 5 residues within 4Å: Chain A: I.151, W.155, H.168, I.169, L.172 Ligand excluded by PLIP BNG.7: 8 residues within 4Å: Chain A: E.5, R.6, A.7, W.73, Y.74, G.77, A.78 Chain C: Q.140 Ligand excluded by PLIP BNG.8: 1 residues within 4Å: Chain A: F.47 Ligand excluded by PLIP BNG.12: 5 residues within 4Å: Chain B: A.17, V.21, W.36, L.37, W.50 Ligand excluded by PLIP BNG.13: 5 residues within 4Å: Chain B: M.122, W.126, I.144, L.148, I.151 Ligand excluded by PLIP BNG.14: 5 residues within 4Å: Chain B: I.151, W.155, H.168, I.169, L.172 Ligand excluded by PLIP BNG.15: 8 residues within 4Å: Chain A: Q.140 Chain B: E.5, R.6, A.7, W.73, Y.74, G.77, A.78 Ligand excluded by PLIP BNG.16: 1 residues within 4Å: Chain B: F.47 Ligand excluded by PLIP BNG.20: 5 residues within 4Å: Chain C: A.17, V.21, W.36, L.37, W.50 Ligand excluded by PLIP BNG.21: 5 residues within 4Å: Chain C: M.122, W.126, I.144, L.148, I.151 Ligand excluded by PLIP BNG.22: 5 residues within 4Å: Chain C: I.151, W.155, H.168, I.169, L.172 Ligand excluded by PLIP BNG.23: 8 residues within 4Å: Chain B: Q.140 Chain C: E.5, R.6, A.7, W.73, Y.74, G.77, A.78 Ligand excluded by PLIP BNG.24: 1 residues within 4Å: Chain C: F.47 Ligand excluded by PLIP BNG.28: 5 residues within 4Å: Chain D: A.17, V.21, W.36, L.37, W.50 Ligand excluded by PLIP BNG.29: 5 residues within 4Å: Chain D: M.122, W.126, I.144, L.148, I.151 Ligand excluded by PLIP BNG.30: 5 residues within 4Å: Chain D: I.151, W.155, H.168, I.169, L.172 Ligand excluded by PLIP BNG.31: 8 residues within 4Å: Chain D: E.5, R.6, A.7, W.73, Y.74, G.77, A.78 Chain F: Q.140 Ligand excluded by PLIP BNG.32: 1 residues within 4Å: Chain D: F.47 Ligand excluded by PLIP BNG.36: 5 residues within 4Å: Chain E: A.17, V.21, W.36, L.37, W.50 Ligand excluded by PLIP BNG.37: 5 residues within 4Å: Chain E: M.122, W.126, I.144, L.148, I.151 Ligand excluded by PLIP BNG.38: 5 residues within 4Å: Chain E: I.151, W.155, H.168, I.169, L.172 Ligand excluded by PLIP BNG.39: 8 residues within 4Å: Chain D: Q.140 Chain E: E.5, R.6, A.7, W.73, Y.74, G.77, A.78 Ligand excluded by PLIP BNG.40: 1 residues within 4Å: Chain E: F.47 Ligand excluded by PLIP BNG.44: 5 residues within 4Å: Chain F: A.17, V.21, W.36, L.37, W.50 Ligand excluded by PLIP BNG.45: 5 residues within 4Å: Chain F: M.122, W.126, I.144, L.148, I.151 Ligand excluded by PLIP BNG.46: 5 residues within 4Å: Chain F: I.151, W.155, H.168, I.169, L.172 Ligand excluded by PLIP BNG.47: 8 residues within 4Å: Chain E: Q.140 Chain F: E.5, R.6, A.7, W.73, Y.74, G.77, A.78 Ligand excluded by PLIP BNG.48: 1 residues within 4Å: Chain F: F.47 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ticha, A. et al., General and Modular Strategy for Designing Potent, Selective, and Pharmacologically Compliant Inhibitors of Rhomboid Proteases. Cell Chem Biol (2017)

Release Date

2017-11-15

Peptides

Rhomboid protease GlpG: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Membrane

We predict this structure to be a membrane protein.
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Rhomboid protease GlpG