SMTL ID : 4b6q.1

Structure of Mycobacterium tuberculosis Type II Dehydroquinase inhibited by (2R)-2-(benzothiophen-5-yl)methyl-3-dehydroquinic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-12-mer

Ligands

12 x BZ5: (1R,2R,4S,5R)-2-(benzo[b]thiophen-5-yl)methyl-1,4,5-trihydroxy-3-oxocyclohexane-1-carboxylic acid(Non-covalent)

BZ5.1: 15 residues within 4Å: Chain A: N.12, L.13, R.15, L.16, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain J: V.84, D.88 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain J Hydrophobic interactions: A:L.13, A:V.105 Hydrogen bonds: A:N.75, A:N.75, A:N.75, A:G.77, A:G.78, A:H.81, A:I.102, A:S.103, A:R.112, J:D.88 Salt bridges: A:H.101 BZ5.9: 15 residues within 4Å: Chain B: N.12, L.13, R.15, L.16, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain G: V.84, D.88 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain G Hydrophobic interactions: B:L.13, B:V.105 Hydrogen bonds: B:N.75, B:N.75, B:N.75, B:G.77, B:G.78, B:H.81, B:I.102, B:S.103, B:R.112, G:D.88 Salt bridges: B:H.101 Water bridges: G:D.88, G:D.88 BZ5.17: 15 residues within 4Å: Chain B: V.84, D.88 Chain C: N.12, L.13, R.15, L.16, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.13, C:V.105 Hydrogen bonds: C:N.75, C:N.75, C:N.75, C:G.77, C:G.78, C:H.81, C:I.102, C:S.103, C:R.112, B:D.88 Salt bridges: C:H.101 BZ5.25: 15 residues within 4Å: Chain D: N.12, L.13, R.15, L.16, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain H: V.84, D.88 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain H Hydrophobic interactions: D:L.13, D:V.105 Hydrogen bonds: D:N.75, D:N.75, D:N.75, D:G.77, D:G.78, D:H.81, D:H.101, D:I.102, D:S.103, D:R.112, H:D.88 Salt bridges: D:H.101 BZ5.33: 15 residues within 4Å: Chain E: N.12, L.13, R.15, L.16, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain L: V.84, D.88 16 PLIP interactions: 13 interactions with chain E, 3 interactions with chain L Hydrophobic interactions: E:L.13, E:V.105 Hydrogen bonds: E:N.75, E:N.75, E:N.75, E:G.77, E:G.78, E:H.81, E:H.101, E:I.102, E:S.103, E:R.112, L:D.88 Salt bridges: E:H.101 Water bridges: L:D.88, L:D.88 BZ5.41: 15 residues within 4Å: Chain D: V.84, D.88 Chain F: N.12, L.13, R.15, L.16, 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 F, 3 interactions with chain D Hydrophobic interactions: F:L.13, F:V.105 Hydrogen bonds: F:N.75, F:N.75, F:N.75, F:G.77, F:G.78, F:H.81, F:H.101, F:I.102, F:S.103, F:R.112, D:D.88 Salt bridges: F:H.101 Water bridges: D:D.88, D:D.88 BZ5.49: 15 residues within 4Å: Chain C: V.84, D.88 Chain G: N.12, L.13, R.15, L.16, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 13 PLIP interactions: 12 interactions with chain G, 1 interactions with chain C Hydrophobic interactions: G:L.13, G:V.105 Hydrogen bonds: G:N.75, G:N.75, G:N.75, G:G.77, G:G.78, G:H.81, G:I.102, G:S.103, G:R.112, C:D.88 Salt bridges: G:H.101 BZ5.57: 15 residues within 4Å: Chain F: V.84, D.88 Chain H: N.12, L.13, R.15, L.16, 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 H, 3 interactions with chain F Hydrophobic interactions: H:L.13, H:V.105 Hydrogen bonds: H:N.75, H:N.75, H:N.75, H:G.77, H:G.78, H:H.81, H:H.101, H:I.102, H:S.103, H:R.112, F:D.88 Salt bridges: H:H.101 Water bridges: F:D.88, F:D.88 BZ5.65: 15 residues within 4Å: Chain E: V.84, D.88 Chain I: N.12, L.13, R.15, L.16, 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 I, 3 interactions with chain E Hydrophobic interactions: I:L.13, I:V.105 Hydrogen bonds: I:N.75, I:N.75, I:N.75, I:G.77, I:G.78, I:H.81, I:H.101, I:I.102, I:S.103, I:R.112, E:D.88 Salt bridges: I:H.101 Water bridges: E:D.88, E:D.88 BZ5.73: 15 residues within 4Å: Chain J: N.12, L.13, R.15, L.16, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 Chain K: V.84, D.88 13 PLIP interactions: 12 interactions with chain J, 1 interactions with chain K Hydrophobic interactions: J:L.13, J:V.105 Hydrogen bonds: J:N.75, J:N.75, J:N.75, J:G.77, J:G.78, J:H.81, J:I.102, J:S.103, J:R.112, K:D.88 Salt bridges: J:H.101 BZ5.81: 15 residues within 4Å: Chain A: V.84, D.88 Chain K: N.12, L.13, R.15, L.16, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 15 PLIP interactions: 12 interactions with chain K, 3 interactions with chain A Hydrophobic interactions: K:L.13, K:V.105 Hydrogen bonds: K:N.75, K:N.75, K:N.75, K:G.77, K:G.78, K:H.81, K:I.102, K:S.103, K:R.112, A:D.88 Salt bridges: K:H.101 Water bridges: A:D.88, A:D.88 BZ5.89: 15 residues within 4Å: Chain I: V.84, D.88 Chain L: N.12, L.13, R.15, L.16, N.75, G.77, G.78, H.81, H.101, I.102, S.103, V.105, R.112 14 PLIP interactions: 13 interactions with chain L, 1 interactions with chain I Hydrophobic interactions: L:L.13, L:V.105 Hydrogen bonds: L:N.75, L:N.75, L:N.75, L:G.77, L:G.78, L:H.81, L:H.101, L:I.102, L:S.103, L:R.112, I:D.88 Salt bridges: L:H.101

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

SO4.2: 8 residues within 4Å: Chain A: S.54, A.56 Chain J: S.54, A.56 Chain K: S.54, A.56 Ligands: SO4.74, SO4.82 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.4: 6 residues within 4Å: Chain A: R.87, P.119 Chain G: E.110, R.113 Chain K: E.109, F.111 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: H.63 Chain K: R.15, R.18 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: H.29, V.49, R.50, Q.51, W.61 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: K.46, V.48, R.50 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: A.56, Q.57 Ligand excluded by PLIP SO4.10: 8 residues within 4Å: Chain B: S.54, A.56 Chain C: S.54, A.56 Chain G: S.54, A.56 Ligands: SO4.18, SO4.50 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain B: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.12: 6 residues within 4Å: Chain B: R.87, P.119 Chain C: E.109, F.111 Chain D: E.110, R.113 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: H.63 Chain C: R.15, R.18 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain B: H.29, V.49, R.50, Q.51, W.61 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: K.46, V.48, R.50 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain B: A.56, Q.57 Ligand excluded by PLIP SO4.18: 8 residues within 4Å: Chain B: S.54, A.56 Chain C: S.54, A.56 Chain G: S.54, A.56 Ligands: SO4.10, SO4.50 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain C: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.20: 6 residues within 4Å: Chain C: R.87, P.119 Chain E: E.110, R.113 Chain G: E.109, F.111 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain C: H.63 Chain G: R.15, R.18 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain C: H.29, V.49, R.50, Q.51, W.61 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain C: K.46, V.48, R.50 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain C: A.56, Q.57 Ligand excluded by PLIP SO4.26: 8 residues within 4Å: Chain D: S.54, A.56 Chain F: S.54, A.56 Chain H: S.54, A.56 Ligands: SO4.42, SO4.58 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain D: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.28: 6 residues within 4Å: Chain B: E.110, R.113 Chain D: R.87, P.119 Chain F: E.109, F.111 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain D: H.63 Chain F: R.15, R.18 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain D: H.29, V.49, R.50, Q.51, W.61 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain D: K.46, V.48, R.50 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain D: A.56, Q.57 Ligand excluded by PLIP SO4.34: 8 residues within 4Å: Chain E: S.54, A.56 Chain I: S.54, A.56 Chain L: S.54, A.56 Ligands: SO4.66, SO4.90 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain E: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.36: 6 residues within 4Å: Chain C: E.110, R.113 Chain E: R.87, P.119 Chain I: E.109, F.111 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain E: H.63 Chain I: R.15, R.18 Ligand excluded by PLIP SO4.38: 5 residues within 4Å: Chain E: H.29, V.49, R.50, Q.51, W.61 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain E: K.46, V.48, R.50 Ligand excluded by PLIP SO4.40: 2 residues within 4Å: Chain E: A.56, Q.57 Ligand excluded by PLIP SO4.42: 8 residues within 4Å: Chain D: S.54, A.56 Chain F: S.54, A.56 Chain H: S.54, A.56 Ligands: SO4.26, SO4.58 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain F: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.44: 6 residues within 4Å: Chain F: R.87, P.119 Chain H: E.109, F.111 Chain J: E.110, R.113 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain F: H.63 Chain H: R.15, R.18 Ligand excluded by PLIP SO4.46: 5 residues within 4Å: Chain F: H.29, V.49, R.50, Q.51, W.61 Ligand excluded by PLIP SO4.47: 3 residues within 4Å: Chain F: K.46, V.48, R.50 Ligand excluded by PLIP SO4.48: 2 residues within 4Å: Chain F: A.56, Q.57 Ligand excluded by PLIP SO4.50: 8 residues within 4Å: Chain B: S.54, A.56 Chain C: S.54, A.56 Chain G: S.54, A.56 Ligands: SO4.10, SO4.18 Ligand excluded by PLIP SO4.51: 3 residues within 4Å: Chain G: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.52: 6 residues within 4Å: Chain A: E.110, R.113 Chain B: E.109, F.111 Chain G: R.87, P.119 Ligand excluded by PLIP SO4.53: 3 residues within 4Å: Chain B: R.15, R.18 Chain G: H.63 Ligand excluded by PLIP SO4.54: 5 residues within 4Å: Chain G: H.29, V.49, R.50, Q.51, W.61 Ligand excluded by PLIP SO4.55: 3 residues within 4Å: Chain G: K.46, V.48, R.50 Ligand excluded by PLIP SO4.56: 2 residues within 4Å: Chain G: A.56, Q.57 Ligand excluded by PLIP SO4.58: 8 residues within 4Å: Chain D: S.54, A.56 Chain F: S.54, A.56 Chain H: S.54, A.56 Ligands: SO4.26, SO4.42 Ligand excluded by PLIP SO4.59: 3 residues within 4Å: Chain H: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.60: 6 residues within 4Å: Chain D: E.109, F.111 Chain H: R.87, P.119 Chain I: E.110, R.113 Ligand excluded by PLIP SO4.61: 3 residues within 4Å: Chain D: R.15, R.18 Chain H: H.63 Ligand excluded by PLIP SO4.62: 5 residues within 4Å: Chain H: H.29, V.49, R.50, Q.51, W.61 Ligand excluded by PLIP SO4.63: 3 residues within 4Å: Chain H: K.46, V.48, R.50 Ligand excluded by PLIP SO4.64: 2 residues within 4Å: Chain H: A.56, Q.57 Ligand excluded by PLIP SO4.66: 8 residues within 4Å: Chain E: S.54, A.56 Chain I: S.54, A.56 Chain L: S.54, A.56 Ligands: SO4.34, SO4.90 Ligand excluded by PLIP SO4.67: 3 residues within 4Å: Chain I: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.68: 6 residues within 4Å: Chain H: E.110, R.113 Chain I: R.87, P.119 Chain L: E.109, F.111 Ligand excluded by PLIP SO4.69: 3 residues within 4Å: Chain I: H.63 Chain L: R.15, R.18 Ligand excluded by PLIP SO4.70: 5 residues within 4Å: Chain I: H.29, V.49, R.50, Q.51, W.61 Ligand excluded by PLIP SO4.71: 3 residues within 4Å: Chain I: K.46, V.48, R.50 Ligand excluded by PLIP SO4.72: 2 residues within 4Å: Chain I: A.56, Q.57 Ligand excluded by PLIP SO4.74: 8 residues within 4Å: Chain A: S.54, A.56 Chain J: S.54, A.56 Chain K: S.54, A.56 Ligands: SO4.2, SO4.82 Ligand excluded by PLIP SO4.75: 3 residues within 4Å: Chain J: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.76: 6 residues within 4Å: Chain A: E.109, F.111 Chain F: E.110, R.113 Chain J: R.87, P.119 Ligand excluded by PLIP SO4.77: 3 residues within 4Å: Chain A: R.15, R.18 Chain J: H.63 Ligand excluded by PLIP SO4.78: 5 residues within 4Å: Chain J: H.29, V.49, R.50, Q.51, W.61 Ligand excluded by PLIP SO4.79: 3 residues within 4Å: Chain J: K.46, V.48, R.50 Ligand excluded by PLIP SO4.80: 2 residues within 4Å: Chain J: A.56, Q.57 Ligand excluded by PLIP SO4.82: 8 residues within 4Å: Chain A: S.54, A.56 Chain J: S.54, A.56 Chain K: S.54, A.56 Ligands: SO4.2, SO4.74 Ligand excluded by PLIP SO4.83: 3 residues within 4Å: Chain K: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.84: 6 residues within 4Å: Chain J: E.109, F.111 Chain K: R.87, P.119 Chain L: E.110, R.113 Ligand excluded by PLIP SO4.85: 3 residues within 4Å: Chain J: R.15, R.18 Chain K: H.63 Ligand excluded by PLIP SO4.86: 5 residues within 4Å: Chain K: H.29, V.49, R.50, Q.51, W.61 Ligand excluded by PLIP SO4.87: 3 residues within 4Å: Chain K: K.46, V.48, R.50 Ligand excluded by PLIP SO4.88: 2 residues within 4Å: Chain K: A.56, Q.57 Ligand excluded by PLIP SO4.90: 8 residues within 4Å: Chain E: S.54, A.56 Chain I: S.54, A.56 Chain L: S.54, A.56 Ligands: SO4.34, SO4.66 Ligand excluded by PLIP SO4.91: 3 residues within 4Å: Chain L: R.50, W.61, Q.64 Ligand excluded by PLIP SO4.92: 6 residues within 4Å: Chain E: E.109, F.111 Chain K: E.110, R.113 Chain L: R.87, P.119 Ligand excluded by PLIP SO4.93: 3 residues within 4Å: Chain E: R.15, R.18 Chain L: H.63 Ligand excluded by PLIP SO4.94: 5 residues within 4Å: Chain L: H.29, V.49, R.50, Q.51, W.61 Ligand excluded by PLIP SO4.95: 3 residues within 4Å: Chain L: K.46, V.48, R.50 Ligand excluded by PLIP SO4.96: 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

Related Entries With Identical Sequence