SMTL ID : 2zir.1

Crystal Structure of rat protein farnesyltransferase complexed with a benzofuran inhibitor and FPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: Y.100, F.103, R.104, L.107, N.130 Chain B: P.147, G.148, Q.149 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:Q.149, A:Q.80 Hydrogen bonds: A:R.104, A:N.130, A:N.130 GOL.2: 6 residues within 4Å: Chain A: K.198 Chain B: T.47, E.50, N.296, K.297, L.298 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.296 Water bridges: B:K.297, B:K.297, B:K.297 GOL.6: 8 residues within 4Å: Chain B: W.331, I.375, H.378, F.379, G.380, P.399, T.400, P.408 No protein-ligand interaction detected (PLIP) GOL.7: 4 residues within 4Å: Chain A: Y.166 Chain B: C.98, L.99 Ligands: NH7.5 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:C.98 Water bridges: A:Y.166 GOL.8: 3 residues within 4Å: Chain B: D.40, S.42, E.44 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.42, B:S.42, B:E.44

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain B: D.300, C.302, Y.364, H.365 Ligands: NH7.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.300, B:D.300, B:C.302, B:H.365

1 x FPP: FARNESYL DIPHOSPHATE(Non-covalent)

FPP.4: 15 residues within 4Å: Chain A: K.164, Y.166, H.201 Chain B: R.205, Y.208, H.251, G.253, Y.254, C.257, R.294, K.297, Y.303, W.306, Y.364 Ligands: NH7.5 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.208, B:W.306, B:W.306 Hydrogen bonds: B:Y.303 Water bridges: B:G.293, B:R.294, B:R.294, B:K.297 Salt bridges: B:H.251, B:R.294, B:R.294, B:K.297, B:K.297, A:K.164

1 x NH7: 2-[(S)-(4-chlorophenyl)(hydroxy)(1-methyl-1H-imidazol-5-yl)methyl]-N-morpholin-4-yl-7-phenyl-1-benzofuran-5-carboxamide(Non-covalent)

NH7.5: 18 residues within 4Å: Chain A: Y.166 Chain B: A.95, Y.96, L.99, S.102, W.105, W.109, R.205, D.300, C.302, Y.303, R.361, D.362, Y.364, H.365 Ligands: ZN.3, FPP.4, GOL.7 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.109, B:Y.364, B:Y.364, A:Y.166 Water bridges: B:Y.96 Salt bridges: B:D.362 pi-Stacking: B:W.105, B:W.109, B:Y.364

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Asoh, K. et al., Synthesis and structure-activity relationships of novel benzofuran farnesyltransferase inhibitors. Bioorg.Med.Chem.Lett. (2009)

Release Date

2009-02-24

Peptides

Protein farnesyltransferase subunit alpha: A
Protein farnesyltransferase subunit beta: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein farnesyltransferase subunit alpha

Protein farnesyltransferase subunit beta

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