SMTL ID : 6vuy.1

Crystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT358

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-hexamer

Ligands

6 x RN4: (7S)-7-phenyl-2-{[3-(piperidin-1-yl)propyl]sulfanyl}-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-amine(Non-covalent)

RN4.1: 13 residues within 4Å: Chain A: W.33, M.36, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, H.139, E.421, F.422 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.53, A:W.56, A:R.57, A:V.60, A:L.83, A:F.104, A:F.104, A:F.104 Hydrogen bonds: A:S.103, A:F.422 Salt bridges: A:D.46, A:E.421 pi-Stacking: A:W.33, A:W.56, A:W.56 RN4.14: 13 residues within 4Å: Chain B: W.33, M.36, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, H.139, E.421, F.422 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.53, B:W.56, B:R.57, B:V.60, B:L.83, B:F.104, B:F.104, B:F.104 Hydrogen bonds: B:S.103, B:S.103 Salt bridges: B:D.46, B:E.421 pi-Stacking: B:W.33, B:W.56, B:W.56 RN4.27: 13 residues within 4Å: Chain C: W.33, M.36, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, H.139, E.421, F.422 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:A.53, C:W.56, C:R.57, C:V.60, C:L.83, C:F.104, C:F.104, C:F.104 Hydrogen bonds: C:S.103, C:S.103 Salt bridges: C:D.46, C:E.421 pi-Stacking: C:W.33, C:W.56, C:W.56 RN4.40: 13 residues within 4Å: Chain D: W.33, M.36, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, H.139, E.421, F.422 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:A.53, D:W.56, D:R.57, D:V.60, D:L.83, D:F.104, D:F.104, D:F.104 Hydrogen bonds: D:S.103, D:F.422, D:F.422 Salt bridges: D:D.46, D:E.421 pi-Stacking: D:W.33, D:W.56, D:W.56 RN4.53: 13 residues within 4Å: Chain E: W.33, M.36, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, H.139, E.421, F.422 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:A.53, E:W.56, E:R.57, E:V.60, E:L.83, E:F.104, E:F.104, E:F.104 Hydrogen bonds: E:S.103, E:S.103, E:F.422 Salt bridges: E:D.46, E:E.421 pi-Stacking: E:W.33, E:W.56, E:W.56 RN4.66: 13 residues within 4Å: Chain F: W.33, M.36, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, H.139, E.421, F.422 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:A.53, F:W.56, F:R.57, F:V.60, F:L.83, F:F.104, F:F.104, F:F.104 Hydrogen bonds: F:S.103, F:S.103, F:F.422 Salt bridges: F:D.46, F:E.421 pi-Stacking: F:W.33, F:W.56, F:W.56

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

PEG.2: 8 residues within 4Å: Chain A: L.261, R.262, H.269, I.287, I.288, T.289, H.290, Q.417 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.261, A:R.262, A:I.288, A:T.289 PEG.3: 3 residues within 4Å: Chain A: T.58, P.61, D.86 No protein-ligand interaction detected (PLIP) PEG.15: 8 residues within 4Å: Chain B: L.261, R.262, H.269, I.287, I.288, T.289, H.290, Q.417 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.261, B:R.262, B:I.288, B:T.289 PEG.16: 3 residues within 4Å: Chain B: T.58, P.61, D.86 No protein-ligand interaction detected (PLIP) PEG.28: 8 residues within 4Å: Chain C: L.261, R.262, H.269, I.287, I.288, T.289, H.290, Q.417 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.261, C:R.262, C:I.288, C:T.289 PEG.29: 3 residues within 4Å: Chain C: T.58, P.61, D.86 No protein-ligand interaction detected (PLIP) PEG.41: 8 residues within 4Å: Chain D: L.261, R.262, H.269, I.287, I.288, T.289, H.290, Q.417 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.261, D:R.262, D:I.288 Water bridges: D:T.289 PEG.42: 3 residues within 4Å: Chain D: T.58, P.61, D.86 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.86 PEG.54: 8 residues within 4Å: Chain E: L.261, R.262, H.269, I.287, I.288, T.289, H.290, Q.417 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:L.261, E:R.262, E:I.288 Water bridges: E:T.289 PEG.55: 3 residues within 4Å: Chain E: T.58, P.61, D.86 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.86 PEG.67: 8 residues within 4Å: Chain F: L.261, R.262, H.269, I.287, I.288, T.289, H.290, Q.417 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:L.261, F:R.262, F:I.288 Water bridges: F:T.289 PEG.68: 3 residues within 4Å: Chain F: T.58, P.61, D.86 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.86

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

DMS.4: 6 residues within 4Å: Chain A: A.367, E.368, E.370, R.396, T.397, K.398 Ligand excluded by PLIP DMS.5: 4 residues within 4Å: Chain A: I.288, T.418, A.419, E.421 Ligand excluded by PLIP DMS.6: 3 residues within 4Å: Chain A: W.33, R.57, V.60 Ligand excluded by PLIP DMS.17: 6 residues within 4Å: Chain B: A.367, E.368, E.370, R.396, T.397, K.398 Ligand excluded by PLIP DMS.18: 4 residues within 4Å: Chain B: I.288, T.418, A.419, E.421 Ligand excluded by PLIP DMS.19: 3 residues within 4Å: Chain B: W.33, R.57, V.60 Ligand excluded by PLIP DMS.30: 6 residues within 4Å: Chain C: A.367, E.368, E.370, R.396, T.397, K.398 Ligand excluded by PLIP DMS.31: 4 residues within 4Å: Chain C: I.288, T.418, A.419, E.421 Ligand excluded by PLIP DMS.32: 3 residues within 4Å: Chain C: W.33, R.57, V.60 Ligand excluded by PLIP DMS.43: 6 residues within 4Å: Chain D: A.367, E.368, E.370, R.396, T.397, K.398 Ligand excluded by PLIP DMS.44: 4 residues within 4Å: Chain D: I.288, T.418, A.419, E.421 Ligand excluded by PLIP DMS.45: 3 residues within 4Å: Chain D: W.33, R.57, V.60 Ligand excluded by PLIP DMS.56: 6 residues within 4Å: Chain E: A.367, E.368, E.370, R.396, T.397, K.398 Ligand excluded by PLIP DMS.57: 4 residues within 4Å: Chain E: I.288, T.418, A.419, E.421 Ligand excluded by PLIP DMS.58: 3 residues within 4Å: Chain E: W.33, R.57, V.60 Ligand excluded by PLIP DMS.69: 6 residues within 4Å: Chain F: A.367, E.368, E.370, R.396, T.397, K.398 Ligand excluded by PLIP DMS.70: 4 residues within 4Å: Chain F: I.288, T.418, A.419, E.421 Ligand excluded by PLIP DMS.71: 3 residues within 4Å: Chain F: W.33, R.57, V.60 Ligand excluded by PLIP

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: E.159, T.161, L.255, R.257, R.284, S.286, T.308 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.257, A:R.257, A:R.284, A:S.286, A:S.286 Water bridges: A:E.159, A:T.308 GOL.8: 6 residues within 4Å: Chain A: W.56, R.212, L.216, E.219, E.223, F.420 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.212 GOL.20: 7 residues within 4Å: Chain B: E.159, T.161, L.255, R.257, R.284, S.286, T.308 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.257, B:R.257, B:R.284, B:S.286, B:S.286 Water bridges: B:E.159, B:T.308 GOL.21: 6 residues within 4Å: Chain B: W.56, R.212, L.216, E.219, E.223, F.420 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.212 GOL.33: 7 residues within 4Å: Chain C: E.159, T.161, L.255, R.257, R.284, S.286, T.308 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.257, C:R.257, C:R.284, C:S.286, C:S.286 Water bridges: C:E.159, C:T.308 GOL.34: 6 residues within 4Å: Chain C: W.56, R.212, L.216, E.219, E.223, F.420 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.212 GOL.46: 7 residues within 4Å: Chain D: E.159, T.161, L.255, R.257, R.284, S.286, T.308 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:T.161, D:R.257, D:R.257, D:R.284, D:S.286, D:S.286 Water bridges: D:E.159, D:T.308 GOL.47: 6 residues within 4Å: Chain D: W.56, R.212, L.216, E.219, E.223, F.420 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.212 GOL.59: 7 residues within 4Å: Chain E: E.159, T.161, L.255, R.257, R.284, S.286, T.308 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:T.161, E:R.257, E:R.257, E:R.284, E:S.286, E:S.286 Water bridges: E:E.159, E:T.308 GOL.60: 6 residues within 4Å: Chain E: W.56, R.212, L.216, E.219, E.223, F.420 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.212 GOL.72: 7 residues within 4Å: Chain F: E.159, T.161, L.255, R.257, R.284, S.286, T.308 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:T.161, F:R.257, F:R.257, F:R.284, F:S.286, F:S.286 Water bridges: F:E.159, F:T.308 GOL.73: 6 residues within 4Å: Chain F: W.56, R.212, L.216, E.219, E.223, F.420 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.212

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

NA.9: 4 residues within 4Å: Chain A: G.143, W.315 Chain E: T.300, T.302 Ligand excluded by PLIP NA.10: 4 residues within 4Å: Chain A: S.234, Y.246, R.247, S.259 Ligand excluded by PLIP NA.11: 4 residues within 4Å: Chain A: G.335, E.336, F.337, R.405 Ligand excluded by PLIP NA.12: 5 residues within 4Å: Chain A: R.187, P.188, E.233, S.234, F.235 Ligand excluded by PLIP NA.22: 4 residues within 4Å: Chain B: G.143, W.315 Chain D: T.300, T.302 Ligand excluded by PLIP NA.23: 4 residues within 4Å: Chain B: S.234, Y.246, R.247, S.259 Ligand excluded by PLIP NA.24: 4 residues within 4Å: Chain B: G.335, E.336, F.337, R.405 Ligand excluded by PLIP NA.25: 5 residues within 4Å: Chain B: R.187, P.188, E.233, S.234, F.235 Ligand excluded by PLIP NA.35: 4 residues within 4Å: Chain C: G.143, W.315 Chain F: T.300, T.302 Ligand excluded by PLIP NA.36: 4 residues within 4Å: Chain C: S.234, Y.246, R.247, S.259 Ligand excluded by PLIP NA.37: 4 residues within 4Å: Chain C: G.335, E.336, F.337, R.405 Ligand excluded by PLIP NA.38: 5 residues within 4Å: Chain C: R.187, P.188, E.233, S.234, F.235 Ligand excluded by PLIP NA.48: 4 residues within 4Å: Chain B: T.300, T.302 Chain D: G.143, W.315 Ligand excluded by PLIP NA.49: 4 residues within 4Å: Chain D: S.234, Y.246, R.247, S.259 Ligand excluded by PLIP NA.50: 4 residues within 4Å: Chain D: G.335, E.336, F.337, R.405 Ligand excluded by PLIP NA.51: 5 residues within 4Å: Chain D: R.187, P.188, E.233, S.234, F.235 Ligand excluded by PLIP NA.61: 4 residues within 4Å: Chain A: T.300, T.302 Chain E: G.143, W.315 Ligand excluded by PLIP NA.62: 4 residues within 4Å: Chain E: S.234, Y.246, R.247, S.259 Ligand excluded by PLIP NA.63: 4 residues within 4Å: Chain E: G.335, E.336, F.337, R.405 Ligand excluded by PLIP NA.64: 5 residues within 4Å: Chain E: R.187, P.188, E.233, S.234, F.235 Ligand excluded by PLIP NA.74: 4 residues within 4Å: Chain C: T.300, T.302 Chain F: G.143, W.315 Ligand excluded by PLIP NA.75: 4 residues within 4Å: Chain F: S.234, Y.246, R.247, S.259 Ligand excluded by PLIP NA.76: 4 residues within 4Å: Chain F: G.335, E.336, F.337, R.405 Ligand excluded by PLIP NA.77: 5 residues within 4Å: Chain F: R.187, P.188, E.233, S.234, F.235 Ligand excluded by PLIP

6 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 8 residues within 4Å: Chain A: A.154, G.377, S.378, L.379, Y.380, L.381, G.382, A.383 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:A.154, A:S.378 MG.26: 8 residues within 4Å: Chain B: A.154, G.377, S.378, L.379, Y.380, L.381, G.382, A.383 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:A.154, B:S.378 MG.39: 8 residues within 4Å: Chain C: A.154, G.377, S.378, L.379, Y.380, L.381, G.382, A.383 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:A.154, C:S.378 MG.52: 8 residues within 4Å: Chain D: A.154, G.377, S.378, L.379, Y.380, L.381, G.382, A.383 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:A.154, D:S.378 MG.65: 8 residues within 4Å: Chain E: A.154, G.377, S.378, L.379, Y.380, L.381, G.382, A.383 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:A.154, E:S.378 MG.78: 8 residues within 4Å: Chain F: A.154, G.377, S.378, L.379, Y.380, L.381, G.382, A.383 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:A.154, F:S.378

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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