SMTL ID : 8e9e.1

Rat protein farnesyltransferase in complex with FPP and inhibitor 2f

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.84 Å

Oligo State

hetero-1-1-mer

Ligands

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 3 residues within 4Å: Chain A: K.164, Q.195, D.196 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.164, A:Q.195, A:D.196 TRS.2: 1 residues within 4Å: Chain A: T.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.248 TRS.3: 3 residues within 4Å: Chain A: E.111, S.113, R.115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.111 TRS.11: 5 residues within 4Å: Chain A: Q.285 Chain B: Q.233, N.234, N.269, S.272 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.285, B:Q.233, B:N.269, B:S.272, B:S.272

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: L.144, Q.145, K.146, D.147 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.147 EDO.5: 1 residues within 4Å: Chain A: L.269 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.228 EDO.6: 3 residues within 4Å: Chain A: I.156, E.160, D.191 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.160, A:E.160 EDO.10: 3 residues within 4Å: Chain B: A.92, S.357, R.358 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.357, B:S.357 EDO.12: 5 residues within 4Å: Chain A: Y.166, Q.167 Chain B: H.149, E.198, R.202 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.198, B:R.202, A:Q.167 EDO.13: 3 residues within 4Å: Chain A: P.271 Chain B: D.38, S.39 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.38 EDO.14: 6 residues within 4Å: Chain A: W.169, H.170, R.173, Q.204 Chain B: E.198, V.199 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.170, B:V.199 Water bridges: A:Q.204 EDO.15: 1 residues within 4Å: Chain B: Y.182 No protein-ligand interaction detected (PLIP) EDO.16: 2 residues within 4Å: Chain B: N.170, I.172 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.170

1 x FPP: FARNESYL DIPHOSPHATE(Non-covalent)

FPP.7: 15 residues within 4Å: Chain A: K.164, Y.166, Y.200 Chain B: W.102, R.202, Y.205, H.248, G.250, Y.251, C.254, R.291, K.294, Y.300, W.303 Ligands: XMY.9 20 PLIP interactions: 16 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.102, B:R.202, B:Y.205, B:Y.251, A:Y.200 Hydrogen bonds: B:Y.300, B:Y.300 Water bridges: B:R.291, B:R.291, B:R.291, B:K.294, B:L.295, A:K.164, A:K.198 Salt bridges: B:H.248, B:R.291, B:R.291, B:K.294, B:K.294, A:K.164

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 5 residues within 4Å: Chain B: D.297, C.299, Y.361, H.362 Ligands: XMY.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.297, B:D.297, B:C.299, B:H.362

1 x XMY: (5S)-4-({1-[(4-bromophenyl)methyl]-1H-imidazol-5-yl}methyl)-5-butyl-1-[3-(trifluoromethoxy)phenyl]piperazin-2-one(Non-covalent)

XMY.9: 15 residues within 4Å: Chain A: Y.166 Chain B: L.96, S.99, W.102, W.106, D.297, C.299, Y.300, W.303, D.359, Y.361, H.362, Y.365 Ligands: FPP.7, ZN.8 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.96, B:L.96, B:D.359, B:Y.361 Hydrogen bonds: B:Y.361 Water bridges: B:Y.300 pi-Stacking: B:W.102, B:W.102, B:W.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Structure-Guided Discovery of Potent Antifungals that Prevent Ras Signaling by Inhibiting Protein Farnesyltransferase. J.Med.Chem. (2022)

Release Date

2022-10-26

Peptides

Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha: A
Protein farnesyltransferase subunit beta: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha

Protein farnesyltransferase subunit beta

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