SMTL ID : 4b6p.1

Structure of Mycobacterium tuberculosis Type II Dehydroquinase inhibited by (2S)-2-Perfluorobenzyl-3-dehydroquinic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-12-mer

Ligands

12 x 2HN: (1R,2S,4S,5R)-2-(2,3,4,5,6-pentafluorophenyl)methyl-1,4,5-trihydroxy-3-oxocyclohexane-1-carboxylic acid(Non-covalent)

2HN.1: 18 residues within 4Å: Chain A: P.11, N.12, L.13, R.15, L.16, R.19, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain B: V.84, D.88 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.24, A:V.105 Hydrogen bonds: A:N.75, A:N.75, A:N.75, A:G.77, A:H.81, A:I.102, A:S.103, A:R.112, B:D.88 Water bridges: A:G.78, A:G.78 Salt bridges: A:H.101 pi-Stacking: A:Y.24 Halogen bonds: B:D.88 2HN.4: 18 residues within 4Å: Chain B: P.11, N.12, L.13, R.15, L.16, R.19, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain K: V.84, D.88 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain K Hydrophobic interactions: B:Y.24, B:V.105 Hydrogen bonds: B:N.75, B:N.75, B:N.75, B:G.77, B:H.81, B:I.102, B:S.103, B:R.112, K:D.88 Water bridges: B:G.78, B:G.78 Salt bridges: B:H.101 pi-Stacking: B:Y.24 Halogen bonds: K:D.88 2HN.7: 18 residues within 4Å: Chain C: P.11, N.12, L.13, R.15, L.16, R.19, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain D: V.84, D.88 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Y.24, C:V.105 Hydrogen bonds: C:N.75, C:N.75, C:N.75, C:G.77, C:H.81, C:I.102, C:S.103, C:R.112, D:D.88 Water bridges: C:G.78, D:D.88 Salt bridges: C:H.101 pi-Stacking: C:Y.24 Halogen bonds: D:D.88 2HN.10: 18 residues within 4Å: Chain D: P.11, N.12, L.13, R.15, L.16, R.19, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain J: V.84, D.88 16 PLIP interactions: 14 interactions with chain D, 2 interactions with chain J Hydrophobic interactions: D:Y.24, D:V.105 Hydrogen bonds: D:N.75, D:N.75, D:N.75, D:G.77, D:H.81, D:I.102, D:S.103, D:R.112, J:D.88 Water bridges: D:G.78, D:G.78 Salt bridges: D:H.101 pi-Stacking: D:Y.24 Halogen bonds: J:D.88 2HN.13: 18 residues within 4Å: Chain E: P.11, N.12, L.13, R.15, L.16, R.19, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain H: V.84, D.88 17 PLIP interactions: 15 interactions with chain E, 2 interactions with chain H Hydrophobic interactions: E:Y.24, E:V.105 Hydrogen bonds: E:N.75, E:N.75, E:N.75, E:G.77, E:H.81, E:H.101, E:I.102, E:S.103, E:R.112, H:D.88 Water bridges: E:G.78, E:G.78 Salt bridges: E:H.101 pi-Stacking: E:Y.24 Halogen bonds: H:D.88 2HN.16: 18 residues within 4Å: Chain F: P.11, N.12, L.13, R.15, L.16, R.19, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain L: V.84, D.88 17 PLIP interactions: 15 interactions with chain F, 2 interactions with chain L Hydrophobic interactions: F:Y.24, F:V.105 Hydrogen bonds: F:N.75, F:N.75, F:N.75, F:G.77, F:H.81, F:H.101, F:I.102, F:S.103, F:R.112, L:D.88 Water bridges: F:G.78, F:G.78 Salt bridges: F:H.101 pi-Stacking: F:Y.24 Halogen bonds: L:D.88 2HN.19: 18 residues within 4Å: Chain E: V.84, D.88 Chain G: P.11, N.12, L.13, R.15, L.16, R.19, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 17 PLIP interactions: 3 interactions with chain E, 14 interactions with chain G Hydrogen bonds: E:D.88, G:N.75, G:N.75, G:N.75, G:G.77, G:H.81, G:H.101, G:I.102, G:S.103, G:R.112 Water bridges: E:D.88, G:G.78 Halogen bonds: E:D.88 Hydrophobic interactions: G:Y.24, G:V.105 Salt bridges: G:H.101 pi-Stacking: G:Y.24 2HN.22: 18 residues within 4Å: Chain G: V.84, D.88 Chain H: P.11, N.12, L.13, R.15, L.16, R.19, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 17 PLIP interactions: 14 interactions with chain H, 3 interactions with chain G Hydrophobic interactions: H:Y.24, H:V.105 Hydrogen bonds: H:N.75, H:N.75, H:N.75, H:G.77, H:H.81, H:H.101, H:I.102, H:S.103, H:R.112, G:D.88 Water bridges: H:G.78, G:D.88 Salt bridges: H:H.101 pi-Stacking: H:Y.24 Halogen bonds: G:D.88 2HN.25: 18 residues within 4Å: Chain F: V.84, D.88 Chain I: P.11, N.12, L.13, R.15, L.16, R.19, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 17 PLIP interactions: 14 interactions with chain I, 3 interactions with chain F Hydrophobic interactions: I:Y.24, I:V.105 Hydrogen bonds: I:N.75, I:N.75, I:N.75, I:G.77, I:H.81, I:H.101, I:I.102, I:S.103, I:R.112, F:D.88 Water bridges: I:G.78, F:D.88 Salt bridges: I:H.101 pi-Stacking: I:Y.24 Halogen bonds: F:D.88 2HN.28: 18 residues within 4Å: Chain C: V.84, D.88 Chain J: P.11, N.12, L.13, R.15, L.16, R.19, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 16 PLIP interactions: 2 interactions with chain C, 14 interactions with chain J Hydrogen bonds: C:D.88, J:N.75, J:N.75, J:N.75, J:G.77, J:H.81, J:I.102, J:S.103, J:R.112 Halogen bonds: C:D.88 Hydrophobic interactions: J:Y.24, J:V.105 Water bridges: J:G.78, J:G.78 Salt bridges: J:H.101 pi-Stacking: J:Y.24 2HN.31: 18 residues within 4Å: Chain A: V.84, D.88 Chain K: P.11, N.12, L.13, R.15, L.16, R.19, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 16 PLIP interactions: 13 interactions with chain K, 3 interactions with chain A Hydrophobic interactions: K:Y.24, K:V.105 Hydrogen bonds: K:N.75, K:N.75, K:N.75, K:G.77, K:H.81, K:I.102, K:S.103, K:R.112, A:D.88 Water bridges: K:G.78, A:D.88 Salt bridges: K:H.101 pi-Stacking: K:Y.24 Halogen bonds: A:D.88 2HN.34: 18 residues within 4Å: Chain I: V.84, D.88 Chain L: P.11, N.12, L.13, R.15, L.16, R.19, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 17 PLIP interactions: 14 interactions with chain L, 3 interactions with chain I Hydrophobic interactions: L:Y.24, L:V.105 Hydrogen bonds: L:N.75, L:N.75, L:N.75, L:G.77, L:H.81, L:H.101, L:I.102, L:S.103, L:R.112, I:D.88 Water bridges: L:G.78, I:D.88 Salt bridges: L:H.101 pi-Stacking: L:Y.24 Halogen bonds: I:D.88

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

SO4.2: 8 residues within 4Å: Chain A: S.54, A.56 Chain B: S.54, A.56 Chain K: S.54, A.56 Ligands: SO4.5, SO4.32 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.5: 8 residues within 4Å: Chain A: S.54, A.56 Chain B: S.54, A.56 Chain K: S.54, A.56 Ligands: SO4.2, SO4.32 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain B: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.8: 8 residues within 4Å: Chain C: S.54, A.56 Chain D: S.54, A.56 Chain J: S.54, A.56 Ligands: SO4.11, SO4.29 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain C: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.11: 8 residues within 4Å: Chain C: S.54, A.56 Chain D: S.54, A.56 Chain J: S.54, A.56 Ligands: SO4.8, SO4.29 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain D: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.14: 8 residues within 4Å: Chain E: S.54, A.56 Chain G: S.54, A.56 Chain H: S.54, A.56 Ligands: SO4.20, SO4.23 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain E: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.17: 8 residues within 4Å: Chain F: S.54, A.56 Chain I: S.54, A.56 Chain L: S.54, A.56 Ligands: SO4.26, SO4.35 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain F: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.20: 8 residues within 4Å: Chain E: S.54, A.56 Chain G: S.54, A.56 Chain H: S.54, A.56 Ligands: SO4.14, SO4.23 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain G: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.23: 8 residues within 4Å: Chain E: S.54, A.56 Chain G: S.54, A.56 Chain H: S.54, A.56 Ligands: SO4.14, SO4.20 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain H: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.26: 8 residues within 4Å: Chain F: S.54, A.56 Chain I: S.54, A.56 Chain L: S.54, A.56 Ligands: SO4.17, SO4.35 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain I: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.29: 8 residues within 4Å: Chain C: S.54, A.56 Chain D: S.54, A.56 Chain J: S.54, A.56 Ligands: SO4.8, SO4.11 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain J: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.32: 8 residues within 4Å: Chain A: S.54, A.56 Chain B: S.54, A.56 Chain K: S.54, A.56 Ligands: SO4.2, SO4.5 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain K: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.35: 8 residues within 4Å: Chain F: S.54, A.56 Chain I: S.54, A.56 Chain L: S.54, A.56 Ligands: SO4.17, SO4.26 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain L: R.50, W.61, Q.64 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lence, E. et al., Mechanistic basis of the inhibition of type II dehydroquinase by (2S)- and (2R)-2-benzyl-3-dehydroquinic acids. ACS Chem. Biol. (2013)

Release Date

2012-12-19

Peptides

3-DEHYDROQUINATE DEHYDRATASE: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

3-DEHYDROQUINATE DEHYDRATASE

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