SMTL ID : 6vux.1

Crystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT388

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-hexamer

Ligands

6 x H66: 2-{[(7S)-4-amino-7-ethyl-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-2-yl]sulfanyl}-N-[2-(piperidin-1-yl)ethyl]acetamide(Non-covalent)

H66.1: 14 residues within 4Å: Chain A: W.33, F.37, F.44, D.46, A.53, W.56, R.57, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: GOL.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.33, A:F.37, A:F.44, A:A.53, A:W.56, A:R.57, A:L.83, A:F.104, A:F.104, A:F.104 Hydrogen bonds: A:S.103, A:F.422, A:F.422 Salt bridges: A:D.46 pi-Stacking: A:W.56, A:W.56 H66.10: 14 residues within 4Å: Chain B: W.33, F.37, F.44, D.46, A.53, W.56, R.57, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: GOL.12 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.33, B:F.37, B:F.44, B:A.53, B:W.56, B:R.57, B:L.83, B:F.104, B:F.104, B:F.104 Hydrogen bonds: B:S.103, B:F.422, B:F.422 Salt bridges: B:D.46 pi-Stacking: B:W.56, B:W.56 H66.19: 14 residues within 4Å: Chain C: W.33, F.37, F.44, D.46, A.53, W.56, R.57, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: GOL.21 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:W.33, C:F.37, C:F.44, C:A.53, C:W.56, C:R.57, C:L.83, C:F.104, C:F.104, C:F.104 Hydrogen bonds: C:S.103, C:F.422, C:F.422 Salt bridges: C:D.46 pi-Stacking: C:W.56, C:W.56 H66.28: 14 residues within 4Å: Chain D: W.33, F.37, F.44, D.46, A.53, W.56, R.57, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: GOL.30 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:W.33, D:F.37, D:F.44, D:A.53, D:W.56, D:R.57, D:L.83, D:F.104, D:F.104, D:F.104 Hydrogen bonds: D:S.103, D:F.422, D:F.422, D:F.422 Salt bridges: D:D.46 pi-Stacking: D:W.56, D:W.56 H66.37: 14 residues within 4Å: Chain E: W.33, F.37, F.44, D.46, A.53, W.56, R.57, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: GOL.39 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:W.33, E:F.37, E:F.44, E:A.53, E:W.56, E:R.57, E:L.83, E:F.104, E:F.104, E:F.104 Hydrogen bonds: E:S.103, E:F.422, E:F.422, E:F.422 Salt bridges: E:D.46 pi-Stacking: E:W.56, E:W.56 H66.46: 14 residues within 4Å: Chain F: W.33, F.37, F.44, D.46, A.53, W.56, R.57, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: GOL.48 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:W.33, F:F.37, F:F.44, F:A.53, F:W.56, F:R.57, F:L.83, F:F.104, F:F.104, F:F.104 Hydrogen bonds: F:S.103, F:F.422, F:F.422, F:F.422 Salt bridges: F:D.46 pi-Stacking: F:W.56, F:W.56

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: W.202, L.261, A.263, H.269, T.289, H.290, D.293, P.294, Q.417 Ligand excluded by PLIP GOL.3: 7 residues within 4Å: Chain A: S.103, F.104, V.105, H.139, S.141, Y.146 Ligands: H66.1 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: W.56, R.212, L.216, E.219, L.220, E.223, F.420 Ligand excluded by PLIP GOL.11: 9 residues within 4Å: Chain B: W.202, L.261, A.263, H.269, T.289, H.290, D.293, P.294, Q.417 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain B: S.103, F.104, V.105, H.139, S.141, Y.146 Ligands: H66.10 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain B: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.15: 7 residues within 4Å: Chain B: W.56, R.212, L.216, E.219, L.220, E.223, F.420 Ligand excluded by PLIP GOL.20: 9 residues within 4Å: Chain C: W.202, L.261, A.263, H.269, T.289, H.290, D.293, P.294, Q.417 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain C: S.103, F.104, V.105, H.139, S.141, Y.146 Ligands: H66.19 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain C: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain C: W.56, R.212, L.216, E.219, L.220, E.223, F.420 Ligand excluded by PLIP GOL.29: 9 residues within 4Å: Chain D: W.202, L.261, A.263, H.269, T.289, H.290, D.293, P.294, Q.417 Ligand excluded by PLIP GOL.30: 7 residues within 4Å: Chain D: S.103, F.104, V.105, H.139, S.141, Y.146 Ligands: H66.28 Ligand excluded by PLIP GOL.32: 6 residues within 4Å: Chain D: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.33: 7 residues within 4Å: Chain D: W.56, R.212, L.216, E.219, L.220, E.223, F.420 Ligand excluded by PLIP GOL.38: 9 residues within 4Å: Chain E: W.202, L.261, A.263, H.269, T.289, H.290, D.293, P.294, Q.417 Ligand excluded by PLIP GOL.39: 7 residues within 4Å: Chain E: S.103, F.104, V.105, H.139, S.141, Y.146 Ligands: H66.37 Ligand excluded by PLIP GOL.41: 6 residues within 4Å: Chain E: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.42: 7 residues within 4Å: Chain E: W.56, R.212, L.216, E.219, L.220, E.223, F.420 Ligand excluded by PLIP GOL.47: 9 residues within 4Å: Chain F: W.202, L.261, A.263, H.269, T.289, H.290, D.293, P.294, Q.417 Ligand excluded by PLIP GOL.48: 7 residues within 4Å: Chain F: S.103, F.104, V.105, H.139, S.141, Y.146 Ligands: H66.46 Ligand excluded by PLIP GOL.50: 6 residues within 4Å: Chain F: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.51: 7 residues within 4Å: Chain F: W.56, R.212, L.216, E.219, L.220, E.223, F.420 Ligand excluded by PLIP

12 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 4 residues within 4Å: Chain A: V.60, P.61, T.62, A.65 No protein-ligand interaction detected (PLIP) DMS.7: 5 residues within 4Å: Chain A: A.367, E.368, E.370, R.396, T.397 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.398 Salt bridges: A:E.370 DMS.13: 4 residues within 4Å: Chain B: V.60, P.61, T.62, A.65 No protein-ligand interaction detected (PLIP) DMS.16: 5 residues within 4Å: Chain B: A.367, E.368, E.370, R.396, T.397 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.398 Salt bridges: B:E.370 DMS.22: 4 residues within 4Å: Chain C: V.60, P.61, T.62, A.65 No protein-ligand interaction detected (PLIP) DMS.25: 5 residues within 4Å: Chain C: A.367, E.368, E.370, R.396, T.397 2 PLIP interactions: 2 interactions with chain C Water bridges: C:K.398 Salt bridges: C:E.370 DMS.31: 4 residues within 4Å: Chain D: V.60, P.61, T.62, A.65 No protein-ligand interaction detected (PLIP) DMS.34: 5 residues within 4Å: Chain D: A.367, E.368, E.370, R.396, T.397 2 PLIP interactions: 2 interactions with chain D Water bridges: D:T.397 Salt bridges: D:E.370 DMS.40: 4 residues within 4Å: Chain E: V.60, P.61, T.62, A.65 No protein-ligand interaction detected (PLIP) DMS.43: 5 residues within 4Å: Chain E: A.367, E.368, E.370, R.396, T.397 2 PLIP interactions: 2 interactions with chain E Water bridges: E:T.397 Salt bridges: E:E.370 DMS.49: 4 residues within 4Å: Chain F: V.60, P.61, T.62, A.65 No protein-ligand interaction detected (PLIP) DMS.52: 5 residues within 4Å: Chain F: A.367, E.368, E.370, R.396, T.397 2 PLIP interactions: 2 interactions with chain F Water bridges: F:T.397 Salt bridges: F:E.370

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

SO4.8: 3 residues within 4Å: Chain A: E.159, R.257, W.309 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.257 SO4.17: 3 residues within 4Å: Chain B: E.159, R.257, W.309 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.257 SO4.26: 3 residues within 4Å: Chain C: E.159, R.257, W.309 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.257 SO4.35: 3 residues within 4Å: Chain D: E.159, R.257, W.309 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.257 SO4.44: 3 residues within 4Å: Chain E: E.159, R.257, W.309 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.257 SO4.53: 3 residues within 4Å: Chain F: E.159, R.257, W.309 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.257

6 x NA: SODIUM ION(Non-functional Binders)

NA.9: 3 residues within 4Å: Chain A: E.94, Q.205, V.414 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.94, A:Q.205 NA.18: 3 residues within 4Å: Chain B: E.94, Q.205, V.414 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.94, B:Q.205 NA.27: 3 residues within 4Å: Chain C: E.94, Q.205, V.414 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.94, C:Q.205 NA.36: 3 residues within 4Å: Chain D: E.94, Q.205, V.414 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.94 NA.45: 3 residues within 4Å: Chain E: E.94, Q.205, V.414 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.205 NA.54: 3 residues within 4Å: Chain F: E.94, Q.205, V.414 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Punetha, A. et al., Structure-Guided Optimization of Inhibitors of Acetyltransferase Eis fromMycobacterium tuberculosis. Acs Chem.Biol. (2020)

Release Date

2020-06-03

Peptides

N-acetyltransferase Eis: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

N-acetyltransferase Eis

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