SMTL ID : 4j4o.1

Crystal structure of FK506 binding domain of plasmodium VIVAX FKBP35 in complex with D44

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-dimer

Ligands

2 x D44: N-(2-ethylphenyl)-2-(3H-imidazo[4,5-b]pyridin-2-ylsulfanyl)acetamide(Non-covalent)

D44.1: 18 residues within 4Å: Chain A: Y.43, F.54, D.55, F.64, E.72, V.73, I.74, W.77, Y.100, C.105, S.108, I.109, F.117 Ligands: GOL.2, GOL.5, D44.6, GOL.7, GOL.10 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.64, A:V.73, A:W.77, A:Y.100, A:I.109 Hydrogen bonds: A:D.55, A:I.74 pi-Stacking: A:F.54, A:F.54 D44.6: 18 residues within 4Å: Chain B: Y.43, F.54, D.55, F.64, E.72, V.73, I.74, W.77, Y.100, C.105, S.108, I.109, F.117 Ligands: D44.1, GOL.2, GOL.5, GOL.7, GOL.10 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.64, B:V.73, B:W.77, B:Y.100, B:I.109 Hydrogen bonds: B:D.55, B:D.55, B:I.74, B:Y.100 pi-Stacking: B:F.54, B:F.54

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: E.72, V.73, I.74, Y.100 Ligands: D44.1, GOL.5, D44.6, GOL.10 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.72, A:V.73 Water bridges: A:K.75, B:E.107 GOL.3: 4 residues within 4Å: Chain A: T.12, E.13, D.14, Y.98 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.13, A:D.14, A:D.14 Water bridges: A:E.13 GOL.4: 5 residues within 4Å: Chain A: E.30, N.31, K.86, S.123, F.124 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.30, A:F.124, A:F.124 Water bridges: A:K.86, A:K.86 GOL.5: 7 residues within 4Å: Chain A: Y.100 Chain B: Y.100 Ligands: D44.1, GOL.2, D44.6, GOL.7, GOL.10 No protein-ligand interaction detected (PLIP) GOL.7: 8 residues within 4Å: Chain B: E.72, V.73, I.74, Y.100 Ligands: D44.1, GOL.5, D44.6, GOL.10 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.72, B:V.73 Water bridges: B:K.75, A:E.107 GOL.8: 4 residues within 4Å: Chain B: T.12, E.13, D.14, Y.98 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.13, B:D.14, B:D.14, B:Y.98 Water bridges: B:E.13, B:E.13 GOL.9: 5 residues within 4Å: Chain B: E.30, N.31, K.86, S.123, F.124 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.30, B:F.124, B:F.124 Water bridges: B:K.86, B:K.86 GOL.10: 7 residues within 4Å: Chain A: Y.100 Chain B: Y.100 Ligands: D44.1, GOL.2, GOL.5, D44.6, GOL.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harikishore, A. et al., Small molecule Plasmodium FKBP35 inhibitor as a potential antimalaria agent. Sci Rep (2013)

Release Date

2013-09-11

Peptides

70 kDa peptidylprolyl isomerase, putative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

70 kDa peptidylprolyl isomerase, putative

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