SMTL ID : 3dp0.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 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.3: 3 residues within 4Å: Chain B: H.58, P.66, G.67 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain C: H.58, G.67 Chain D: F.101 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain D: H.58, P.66, G.67 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain E: H.58, G.67 Chain F: F.101 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain F: H.58, G.67 Ligand excluded by PLIP

7 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.2: 4 residues within 4Å: Chain A: M.131, M.154, I.155, A.156 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.131, A:A.156 BEN.4: 9 residues within 4Å: Chain B: I.20, L.21, P.22, H.23, F.83, A.94, K.97, I.98, V.99 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.20, B:L.21, B:F.83, B:F.83, B:I.98, B:V.99, B:V.99 Hydrogen bonds: B:V.99 BEN.7: 6 residues within 4Å: Chain C: A.38, T.84, S.85, L.86, W.87, G.88 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.85 BEN.10: 5 residues within 4Å: Chain E: R.110, T.138, V.145, E.148 Ligands: BEN.12 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:T.138, E:E.148 Hydrogen bonds: E:R.110, E:E.148 BEN.11: 4 residues within 4Å: Chain E: L.86, W.87, G.130, M.131 3 PLIP interactions: 3 interactions with chain E Water bridges: E:G.130, E:G.130, E:G.130 BEN.12: 6 residues within 4Å: Chain E: L.126, G.136, G.137, A.149, E.150 Ligands: BEN.10 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:E.150 Hydrogen bonds: E:E.150 BEN.13: 4 residues within 4Å: Chain E: Q.40, E.124, V.125, L.126 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:E.124, E:L.126 Hydrogen bonds: E:Q.40, E:E.124

1 x 2BC: N'-[(1E)-(3,5-dibromo-2,4-dihydroxyphenyl)methylidene]naphthalene-2-carbohydrazide(Non-covalent)

2BC.5: 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 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.98, B:Y.100, B:Y.100, A:F.59, A:F.109 Hydrogen bonds: B:E.159 pi-Stacking: B:Y.100

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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