SMTL ID : 3dp2.1

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with compound 3j

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: H.58, P.66, G.67 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain B: H.58, P.66, G.67 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain C: H.58, G.67 Chain D: F.101 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain D: H.58, P.66, G.67 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain E: H.58, G.67 Chain F: F.101 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain E: F.101 Chain F: H.58, G.67 Ligand excluded by PLIP

6 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.2: 3 residues within 4Å: Chain A: Q.40, E.124, V.125 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.124 Hydrogen bonds: A:Q.40, A:E.124 BEN.3: 3 residues within 4Å: Chain A: M.131, M.154, I.155 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:M.131 BEN.4: 3 residues within 4Å: Chain A: G.137, T.138, E.148 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.138 Water bridges: A:E.124, A:E.124, A:G.136, A:T.138 BEN.6: 2 residues within 4Å: Chain B: W.87, G.88 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.87 Water bridges: B:D.90, B:D.90 BEN.11: 1 residues within 4Å: Chain D: Q.40 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Q.40 BEN.13: 4 residues within 4Å: Chain E: G.136, G.137, A.149, E.150 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:E.150 Hydrogen bonds: E:E.150

2 x 4BE: 4-bromo-N'-[(1E)-(3,5-dibromo-2,4-dihydroxyphenyl)methylidene]benzohydrazide(Non-covalent)

4BE.7: 11 residues within 4Å: Chain A: F.59, K.62, F.109, R.110, I.111, P.112 Chain B: P.22, I.98, Y.100, R.158, E.159 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.98, B:Y.100, A:F.59, A:P.112 Hydrogen bonds: B:R.158 pi-Stacking: B:Y.100 Halogen bonds: B:E.159, A:F.109 4BE.9: 13 residues within 4Å: Chain C: I.20, L.21, P.22, H.23, A.75, Q.76, G.79, I.98, V.99, F.101, R.158 Chain D: F.59, I.64 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:P.22, C:I.98, C:I.98, C:V.99 Hydrogen bonds: C:V.99 Halogen bonds: C:A.75 pi-Stacking: D:F.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, L. et al., Discovering potent inhibitors against the beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) of Helicobacter pylori: structure-based design, synthesis, bioassay, and crystal structure determination. J.Med.Chem. (2009)

Release Date

2009-05-05

Peptides

(3R)-hydroxymyristoyl-acyl carrier protein dehydratase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

(3R)-hydroxymyristoyl-acyl carrier protein dehydratase

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