SMTL ID : 4b6s.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 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: 17 residues within 4Å: Chain A: P.9, N.10, L.11, M.13, L.14, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.113 Chain C: D.89, L.93 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:Y.22, A:I.106 Hydrogen bonds: A:N.76, A:N.76, A:N.76, A:G.78, A:H.82, A:L.103, A:T.104, A:R.113, C:D.89, C:D.89 Water bridges: A:A.79, A:A.79 Salt bridges: A:H.102 pi-Stacking: A:Y.22 Halogen bonds: C:D.89 2HN.3: 16 residues within 4Å: Chain A: D.89, L.93 Chain B: P.9, N.10, L.11, M.13, L.14, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, R.113 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.22 Hydrogen bonds: B:N.76, B:N.76, B:N.76, B:G.78, B:A.79, B:H.82, B:L.103, B:T.104, B:R.113, A:D.89 Salt bridges: B:H.102 pi-Stacking: B:Y.22 Halogen bonds: A:D.89 2HN.4: 16 residues within 4Å: Chain B: D.89, L.93 Chain C: P.9, N.10, L.11, M.13, L.14, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, R.113 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:Y.22 Hydrogen bonds: C:N.76, C:N.76, C:N.76, C:G.78, C:A.79, C:H.82, C:H.102, C:L.103, C:T.104, C:R.113, B:D.89 Salt bridges: C:H.102 pi-Stacking: C:Y.22 Halogen bonds: B:D.89, B:D.89 2HN.5: 17 residues within 4Å: Chain D: P.9, N.10, L.11, M.13, L.14, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.113 Chain F: D.89, L.93 17 PLIP interactions: 2 interactions with chain F, 15 interactions with chain D Hydrogen bonds: F:D.89, D:N.76, D:N.76, D:N.76, D:G.78, D:H.82, D:H.102, D:L.103, D:T.104, D:R.113 Halogen bonds: F:D.89 Hydrophobic interactions: D:Y.22, D:I.106 Water bridges: D:A.79, D:A.79 Salt bridges: D:H.102 pi-Stacking: D:Y.22 2HN.7: 16 residues within 4Å: Chain D: D.89, L.93 Chain E: P.9, N.10, L.11, M.13, L.14, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, R.113 16 PLIP interactions: 13 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:Y.22 Hydrogen bonds: E:N.76, E:N.76, E:N.76, E:G.78, E:A.79, E:H.82, E:H.102, E:L.103, E:T.104, E:R.113, D:D.89, D:D.89 Salt bridges: E:H.102 pi-Stacking: E:Y.22 Halogen bonds: D:D.89 2HN.8: 16 residues within 4Å: Chain E: D.89, L.93 Chain F: P.9, N.10, L.11, M.13, L.14, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, R.113 16 PLIP interactions: 12 interactions with chain F, 4 interactions with chain E Hydrophobic interactions: F:Y.22 Hydrogen bonds: F:N.76, F:N.76, F:N.76, F:G.78, F:A.79, F:H.82, F:L.103, F:T.104, F:R.113, E:D.89, E:D.89 Salt bridges: F:H.102 pi-Stacking: F:Y.22 Halogen bonds: E:D.89, E:D.89 2HN.9: 17 residues within 4Å: Chain G: P.9, N.10, L.11, M.13, L.14, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.113 Chain I: D.89, L.93 17 PLIP interactions: 14 interactions with chain G, 3 interactions with chain I Hydrophobic interactions: G:Y.22, G:I.106 Hydrogen bonds: G:N.76, G:N.76, G:N.76, G:G.78, G:H.82, G:L.103, G:T.104, G:R.113, I:D.89, I:D.89 Water bridges: G:A.79, G:A.79 Salt bridges: G:H.102 pi-Stacking: G:Y.22 Halogen bonds: I:D.89 2HN.11: 16 residues within 4Å: Chain G: D.89, L.93 Chain H: P.9, N.10, L.11, M.13, L.14, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, R.113 14 PLIP interactions: 12 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:Y.22 Hydrogen bonds: H:N.76, H:N.76, H:N.76, H:G.78, H:A.79, H:H.82, H:L.103, H:T.104, H:R.113, G:D.89 Salt bridges: H:H.102 pi-Stacking: H:Y.22 Halogen bonds: G:D.89 2HN.12: 16 residues within 4Å: Chain H: D.89, L.93 Chain I: P.9, N.10, L.11, M.13, L.14, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, R.113 16 PLIP interactions: 13 interactions with chain I, 3 interactions with chain H Hydrophobic interactions: I:Y.22 Hydrogen bonds: I:N.76, I:N.76, I:N.76, I:G.78, I:A.79, I:H.82, I:H.102, I:L.103, I:T.104, I:R.113, H:D.89 Salt bridges: I:H.102 pi-Stacking: I:Y.22 Halogen bonds: H:D.89, H:D.89 2HN.13: 17 residues within 4Å: Chain J: P.9, N.10, L.11, M.13, L.14, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.113 Chain L: D.89, L.93 17 PLIP interactions: 15 interactions with chain J, 2 interactions with chain L Hydrophobic interactions: J:Y.22, J:I.106 Hydrogen bonds: J:N.76, J:N.76, J:N.76, J:G.78, J:H.82, J:H.102, J:L.103, J:T.104, J:R.113, L:D.89 Water bridges: J:A.79, J:A.79 Salt bridges: J:H.102 pi-Stacking: J:Y.22 Halogen bonds: L:D.89 2HN.15: 16 residues within 4Å: Chain J: D.89, L.93 Chain K: P.9, N.10, L.11, M.13, L.14, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, R.113 16 PLIP interactions: 13 interactions with chain K, 3 interactions with chain J Hydrophobic interactions: K:Y.22 Hydrogen bonds: K:N.76, K:N.76, K:N.76, K:G.78, K:A.79, K:H.82, K:H.102, K:L.103, K:T.104, K:R.113, J:D.89, J:D.89 Salt bridges: K:H.102 pi-Stacking: K:Y.22 Halogen bonds: J:D.89 2HN.16: 16 residues within 4Å: Chain K: D.89, L.93 Chain L: P.9, N.10, L.11, M.13, L.14, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, R.113 16 PLIP interactions: 4 interactions with chain K, 12 interactions with chain L Hydrogen bonds: K:D.89, K:D.89, L:N.76, L:N.76, L:N.76, L:G.78, L:A.79, L:H.82, L:L.103, L:T.104, L:R.113 Halogen bonds: K:D.89, K:D.89 Hydrophobic interactions: L:Y.22 Salt bridges: L:H.102 pi-Stacking: L:Y.22

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: F.54, E.57 Chain B: F.54, E.57 Chain C: E.57 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:E.57, C:E.57, C:E.57 PO4.6: 5 residues within 4Å: Chain D: F.54, E.57 Chain E: F.54, E.57 Chain F: E.57 4 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D, 1 interactions with chain F Hydrogen bonds: E:E.57, D:E.57, D:E.57, F:E.57 PO4.10: 5 residues within 4Å: Chain G: F.54, E.57 Chain H: F.54, E.57 Chain I: E.57 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain G Hydrogen bonds: I:E.57, I:E.57, G:E.57 PO4.14: 5 residues within 4Å: Chain J: F.54, E.57 Chain K: F.54, E.57 Chain L: E.57 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain L, 2 interactions with chain J Hydrogen bonds: K:E.57, L:E.57, J:E.57, J:E.57

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
B

C
C

D
A

E
B

F
C

G
A

H
B

I
C

J
A

K
B

L
C

3-DEHYDROQUINATE DEHYDRATASE

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