SMTL ID : 2xb9.1

Structure of Helicobacter pylori type II dehydroquinase in complex with inhibitor compound (2R)-2-(4-methoxybenzyl)-3-dehydroquinic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-12-mer

Ligands

8 x XNW: (1R,2R,4S,5R)-1,4,5-TRIHYDROXY-2-(4-METHOXYBENZYL)-3-OXOCYCLOHEXANECARBOXYLIC ACID(Non-covalent)

XNW.1: 16 residues within 4Å: Chain A: N.10, L.11, L.14, R.17, 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 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:N.10, A:L.11, A:L.14, A:Y.22, A:I.106 Hydrogen bonds: A:N.76, A:G.78, A:A.79, A:H.82, A:H.102, A:L.103, A:T.104, A:T.104, A:R.113, C:D.89 Salt bridges: A:H.102 XNW.2: 16 residues within 4Å: Chain A: D.89, L.93 Chain B: N.10, L.11, L.14, R.17, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.113 19 PLIP interactions: 16 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:N.10, B:L.11, B:L.14, B:Y.22, B:Y.22, B:I.106, A:L.93 Hydrogen bonds: B:N.76, B:G.78, B:A.79, B:H.82, B:H.102, B:L.103, B:T.104, B:T.104, B:R.113, A:D.89, A:D.89 Salt bridges: B:H.102 XNW.4: 16 residues within 4Å: Chain D: N.10, L.11, L.14, R.17, 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 16 PLIP interactions: 14 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:N.10, D:L.11, D:L.14, D:Y.22, D:I.106 Hydrogen bonds: D:N.76, D:G.78, D:A.79, D:H.82, D:L.103, D:T.104, D:T.104, D:R.113, F:D.89, F:D.89 Salt bridges: D:H.102 XNW.5: 16 residues within 4Å: Chain D: D.89, L.93 Chain E: N.10, L.11, L.14, R.17, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.113 17 PLIP interactions: 15 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:N.10, E:L.11, E:L.14, E:Y.22, E:Y.22, E:I.106, D:L.93 Hydrogen bonds: E:N.76, E:G.78, E:A.79, E:H.82, E:L.103, E:T.104, E:T.104, E:R.113, D:D.89 Salt bridges: E:H.102 XNW.7: 16 residues within 4Å: Chain G: N.10, L.11, L.14, R.17, 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 16 PLIP interactions: 15 interactions with chain G, 1 interactions with chain I Hydrophobic interactions: G:N.10, G:L.11, G:L.14, G:Y.22, G:I.106 Hydrogen bonds: G:N.76, G:G.78, G:A.79, G:H.82, G:H.102, G:L.103, G:T.104, G:T.104, G:R.113, I:D.89 Salt bridges: G:H.102 XNW.8: 16 residues within 4Å: Chain G: D.89, L.93 Chain H: N.10, L.11, L.14, R.17, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.113 19 PLIP interactions: 16 interactions with chain H, 3 interactions with chain G Hydrophobic interactions: H:N.10, H:L.11, H:L.14, H:Y.22, H:Y.22, H:I.106, G:L.93 Hydrogen bonds: H:N.76, H:G.78, H:A.79, H:H.82, H:H.102, H:L.103, H:T.104, H:T.104, H:R.113, G:D.89, G:D.89 Salt bridges: H:H.102 XNW.10: 16 residues within 4Å: Chain J: N.10, L.11, L.14, R.17, 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 16 PLIP interactions: 14 interactions with chain J, 2 interactions with chain L Hydrophobic interactions: J:N.10, J:L.11, J:L.14, J:Y.22, J:I.106 Hydrogen bonds: J:N.76, J:G.78, J:A.79, J:H.82, J:L.103, J:T.104, J:T.104, J:R.113, L:D.89, L:D.89 Salt bridges: J:H.102 XNW.11: 16 residues within 4Å: Chain J: D.89, L.93 Chain K: N.10, L.11, L.14, R.17, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.113 17 PLIP interactions: 15 interactions with chain K, 2 interactions with chain J Hydrophobic interactions: K:N.10, K:L.11, K:L.14, K:Y.22, K:Y.22, K:I.106, J:L.93 Hydrogen bonds: K:N.76, K:G.78, K:A.79, K:H.82, K:L.103, K:T.104, K:T.104, K:R.113, J:D.89 Salt bridges: K:H.102

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 13 residues within 4Å: Chain C: L.11, R.17, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.109, R.113 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:I.106 Hydrogen bonds: C:N.76, C:N.76, C:A.79, C:L.103, C:T.104, C:R.109 Salt bridges: C:R.17, C:H.82, C:H.102, C:R.109, C:R.113 CIT.6: 13 residues within 4Å: Chain F: L.11, R.17, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.109, R.113 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:I.106 Hydrogen bonds: F:Y.22, F:N.76, F:N.76, F:A.79, F:H.102, F:L.103, F:T.104, F:R.109 Salt bridges: F:R.17, F:H.82, F:H.102, F:R.109, F:R.113 CIT.9: 13 residues within 4Å: Chain I: L.11, R.17, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.109, R.113 12 PLIP interactions: 12 interactions with chain I Hydrophobic interactions: I:I.106 Hydrogen bonds: I:N.76, I:N.76, I:A.79, I:L.103, I:T.104, I:R.109 Salt bridges: I:R.17, I:H.82, I:H.102, I:R.109, I:R.113 CIT.12: 13 residues within 4Å: Chain L: L.11, R.17, Y.22, N.76, G.78, A.79, H.82, H.102, L.103, T.104, I.106, R.109, R.113 14 PLIP interactions: 14 interactions with chain L Hydrophobic interactions: L:I.106 Hydrogen bonds: L:Y.22, L:N.76, L:N.76, L:A.79, L:H.102, L:L.103, L:T.104, L:R.109 Salt bridges: L:R.17, L:H.82, L:H.102, L:R.109, L:R.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peon, A. et al., Understanding the Key Factors that Control the Inhibition of Type II Dehydroquinase by (2R)-2- Benzyl-3-Dehydroquinic Acids. Chemmedchem (2010)

Release Date

2010-09-15

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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