SMTL ID : 4b6o.1

Structure of Mycobacterium tuberculosis Type II Dehydroquinase inhibited by (2S)-2-(4-methoxy)benzyl-3-dehydroquinic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-12-mer

Ligands

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

3DQ.1: 16 residues within 4Å: Chain A: P.11, N.12, R.15, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain C: V.84, D.88, E.92 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:N.12, A:Y.24, A:V.105, C:D.88 Hydrogen bonds: A:N.75, A:N.75, A:G.77, A:H.81, A:H.101, A:I.102, A:S.103, A:R.112, C:D.88 Salt bridges: A:H.101 Water bridges: C:D.88, C:D.88 3DQ.6: 16 residues within 4Å: Chain B: P.11, N.12, R.15, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain G: V.84, D.88, E.92 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain G Hydrophobic interactions: B:N.12, B:Y.24, B:V.105, G:D.88 Hydrogen bonds: B:N.75, B:N.75, B:G.77, B:H.81, B:H.101, B:I.102, B:S.103, B:R.112, G:D.88 Water bridges: B:G.78, B:G.78 Salt bridges: B:H.101 3DQ.11: 16 residues within 4Å: Chain C: P.11, N.12, R.15, 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, E.92 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain H Hydrophobic interactions: C:N.12, C:Y.24, C:V.105, H:D.88 Hydrogen bonds: C:N.75, C:N.75, C:G.77, C:H.81, C:H.101, C:I.102, C:S.103, C:R.112, H:D.88 Salt bridges: C:H.101 Water bridges: H:D.88, H:D.88 3DQ.16: 16 residues within 4Å: Chain D: P.11, N.12, R.15, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain I: V.84, D.88, E.92 15 PLIP interactions: 11 interactions with chain D, 4 interactions with chain I Hydrophobic interactions: D:N.12, D:Y.24, D:V.105, I:D.88 Hydrogen bonds: D:N.75, D:N.75, D:G.77, D:H.81, D:I.102, D:S.103, D:R.112, I:D.88 Salt bridges: D:H.101 Water bridges: I:D.88, I:D.88 3DQ.21: 16 residues within 4Å: Chain E: P.11, N.12, R.15, 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, E.92 15 PLIP interactions: 13 interactions with chain E, 2 interactions with chain J Hydrophobic interactions: E:N.12, E:Y.24, E:V.105, J:D.88 Hydrogen bonds: E:N.75, E:N.75, E:G.77, E:H.81, E:I.102, E:S.103, E:R.112, J:D.88 Water bridges: E:G.78, E:G.78 Salt bridges: E:H.101 3DQ.26: 16 residues within 4Å: Chain B: V.84, D.88, E.92 Chain F: P.11, N.12, R.15, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 16 PLIP interactions: 12 interactions with chain F, 4 interactions with chain B Hydrophobic interactions: F:N.12, F:Y.24, F:V.105, B:D.88 Hydrogen bonds: F:N.75, F:N.75, F:G.77, F:H.81, F:H.101, F:I.102, F:S.103, F:R.112, B:D.88 Salt bridges: F:H.101 Water bridges: B:D.88, B:D.88 3DQ.31: 16 residues within 4Å: Chain F: V.84, D.88, E.92 Chain G: P.11, N.12, R.15, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 16 PLIP interactions: 12 interactions with chain G, 4 interactions with chain F Hydrophobic interactions: G:N.12, G:Y.24, G:V.105, F:D.88 Hydrogen bonds: G:N.75, G:N.75, G:G.77, G:H.81, G:H.101, G:I.102, G:S.103, G:R.112, F:D.88 Salt bridges: G:H.101 Water bridges: F:D.88, F:D.88 3DQ.36: 16 residues within 4Å: Chain A: V.84, D.88, E.92 Chain H: P.11, N.12, R.15, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 16 PLIP interactions: 14 interactions with chain H, 2 interactions with chain A Hydrophobic interactions: H:N.12, H:Y.24, H:V.105, A:D.88 Hydrogen bonds: H:N.75, H:N.75, H:G.77, H:H.81, H:H.101, H:I.102, H:S.103, H:R.112, A:D.88 Water bridges: H:G.78, H:G.78 Salt bridges: H:H.101 3DQ.41: 16 residues within 4Å: Chain I: P.11, N.12, R.15, 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, E.92 15 PLIP interactions: 13 interactions with chain I, 2 interactions with chain L Hydrophobic interactions: I:N.12, I:Y.24, I:V.105, L:D.88 Hydrogen bonds: I:N.75, I:N.75, I:G.77, I:H.81, I:I.102, I:S.103, I:R.112, L:D.88 Water bridges: I:G.78, I:G.78 Salt bridges: I:H.101 3DQ.46: 16 residues within 4Å: Chain J: P.11, N.12, R.15, 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, E.92 15 PLIP interactions: 13 interactions with chain J, 2 interactions with chain K Hydrophobic interactions: J:N.12, J:Y.24, J:V.105, K:D.88 Hydrogen bonds: J:N.75, J:N.75, J:G.77, J:H.81, J:I.102, J:S.103, J:R.112, K:D.88 Water bridges: J:G.78, J:G.78 Salt bridges: J:H.101 3DQ.51: 16 residues within 4Å: Chain E: V.84, D.88, E.92 Chain K: P.11, N.12, R.15, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 15 PLIP interactions: 4 interactions with chain E, 11 interactions with chain K Hydrophobic interactions: E:D.88, K:N.12, K:Y.24, K:V.105 Hydrogen bonds: E:D.88, K:N.75, K:N.75, K:G.77, K:H.81, K:I.102, K:S.103, K:R.112 Water bridges: E:D.88, E:D.88 Salt bridges: K:H.101 3DQ.56: 16 residues within 4Å: Chain D: V.84, D.88, E.92 Chain L: P.11, N.12, R.15, Y.24, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 15 PLIP interactions: 13 interactions with chain L, 2 interactions with chain D Hydrophobic interactions: L:N.12, L:Y.24, L:V.105, D:D.88 Hydrogen bonds: L:N.75, L:N.75, L:G.77, L:H.81, L:I.102, L:S.103, L:R.112, D:D.88 Water bridges: L:G.78, L:G.78 Salt bridges: L:H.101

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

SO4.2: 3 residues within 4Å: Chain A: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.3: 8 residues within 4Å: Chain A: S.54, A.56 Chain C: S.54, A.56 Chain H: S.54, A.56 Ligands: SO4.13, SO4.38 Ligand excluded by PLIP SO4.4: 7 residues within 4Å: Chain A: R.87, H.114, S.115, Y.116, P.119 Chain G: R.113 Chain H: F.111 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: A.56, Q.57 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain B: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.8: 8 residues within 4Å: Chain B: S.54, A.56 Chain F: S.54, A.56 Chain G: S.54, A.56 Ligands: SO4.28, SO4.33 Ligand excluded by PLIP SO4.9: 7 residues within 4Å: Chain B: R.87, H.114, S.115, Y.116, P.119 Chain D: R.113 Chain F: F.111 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain B: A.56, Q.57 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain C: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.13: 8 residues within 4Å: Chain A: S.54, A.56 Chain C: S.54, A.56 Chain H: S.54, A.56 Ligands: SO4.3, SO4.38 Ligand excluded by PLIP SO4.14: 7 residues within 4Å: Chain A: F.111 Chain C: R.87, H.114, S.115, Y.116, P.119 Chain L: R.113 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain C: A.56, Q.57 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain D: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.18: 8 residues within 4Å: Chain D: S.54, A.56 Chain I: S.54, A.56 Chain L: S.54, A.56 Ligands: SO4.43, SO4.58 Ligand excluded by PLIP SO4.19: 7 residues within 4Å: Chain B: R.113 Chain D: R.87, H.114, S.115, Y.116, P.119 Chain L: F.111 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain D: A.56, Q.57 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain E: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.23: 8 residues within 4Å: Chain E: S.54, A.56 Chain J: S.54, A.56 Chain K: S.54, A.56 Ligands: SO4.48, SO4.53 Ligand excluded by PLIP SO4.24: 7 residues within 4Å: Chain E: R.87, H.114, S.115, Y.116, P.119 Chain I: R.113 Chain K: F.111 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain E: A.56, Q.57 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain F: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.28: 8 residues within 4Å: Chain B: S.54, A.56 Chain F: S.54, A.56 Chain G: S.54, A.56 Ligands: SO4.8, SO4.33 Ligand excluded by PLIP SO4.29: 7 residues within 4Å: Chain F: R.87, H.114, S.115, Y.116, P.119 Chain G: F.111 Chain J: R.113 Ligand excluded by PLIP SO4.30: 2 residues within 4Å: Chain F: A.56, Q.57 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain G: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.33: 8 residues within 4Å: Chain B: S.54, A.56 Chain F: S.54, A.56 Chain G: S.54, A.56 Ligands: SO4.8, SO4.28 Ligand excluded by PLIP SO4.34: 7 residues within 4Å: Chain A: R.113 Chain B: F.111 Chain G: R.87, H.114, S.115, Y.116, P.119 Ligand excluded by PLIP SO4.35: 2 residues within 4Å: Chain G: A.56, Q.57 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain H: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.38: 8 residues within 4Å: Chain A: S.54, A.56 Chain C: S.54, A.56 Chain H: S.54, A.56 Ligands: SO4.3, SO4.13 Ligand excluded by PLIP SO4.39: 7 residues within 4Å: Chain C: F.111 Chain H: R.87, H.114, S.115, Y.116, P.119 Chain K: R.113 Ligand excluded by PLIP SO4.40: 2 residues within 4Å: Chain H: A.56, Q.57 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain I: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.43: 8 residues within 4Å: Chain D: S.54, A.56 Chain I: S.54, A.56 Chain L: S.54, A.56 Ligands: SO4.18, SO4.58 Ligand excluded by PLIP SO4.44: 7 residues within 4Å: Chain D: F.111 Chain E: R.113 Chain I: R.87, H.114, S.115, Y.116, P.119 Ligand excluded by PLIP SO4.45: 2 residues within 4Å: Chain I: A.56, Q.57 Ligand excluded by PLIP SO4.47: 3 residues within 4Å: Chain J: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.48: 8 residues within 4Å: Chain E: S.54, A.56 Chain J: S.54, A.56 Chain K: S.54, A.56 Ligands: SO4.23, SO4.53 Ligand excluded by PLIP SO4.49: 7 residues within 4Å: Chain E: F.111 Chain F: R.113 Chain J: R.87, H.114, S.115, Y.116, P.119 Ligand excluded by PLIP SO4.50: 2 residues within 4Å: Chain J: A.56, Q.57 Ligand excluded by PLIP SO4.52: 3 residues within 4Å: Chain K: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.53: 8 residues within 4Å: Chain E: S.54, A.56 Chain J: S.54, A.56 Chain K: S.54, A.56 Ligands: SO4.23, SO4.48 Ligand excluded by PLIP SO4.54: 7 residues within 4Å: Chain H: R.113 Chain J: F.111 Chain K: R.87, H.114, S.115, Y.116, P.119 Ligand excluded by PLIP SO4.55: 2 residues within 4Å: Chain K: A.56, Q.57 Ligand excluded by PLIP SO4.57: 3 residues within 4Å: Chain L: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.58: 8 residues within 4Å: Chain D: S.54, A.56 Chain I: S.54, A.56 Chain L: S.54, A.56 Ligands: SO4.18, SO4.43 Ligand excluded by PLIP SO4.59: 7 residues within 4Å: Chain C: R.113 Chain I: F.111 Chain L: R.87, H.114, S.115, Y.116, P.119 Ligand excluded by PLIP SO4.60: 2 residues within 4Å: Chain L: A.56, Q.57 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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