SMTL ID : 7rni.1

Discovery of an Anion-Dependent Farnesyltransferase Inhibitor from a Phenotypic Screen

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

hetero-1-1-mer

Ligands

2 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.1: 5 residues within 4Å: Chain A: R.67, R.97, D.98, D.101, Y.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.67 ACE.2: 6 residues within 4Å: Chain B: V.260, I.261, R.313, H.398, V.400, Y.401 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.261, B:Y.401 Hydrogen bonds: B:R.313, B:R.313, B:H.398

1 x 60I: [4-[[3-(2,2-dimethylpropyl)-1~{H}-benzimidazol-2-yl]methyl]piperazin-1-yl]-(1,3,5-trimethylpyrazol-4-yl)methanone(Non-covalent)

60I.3: 21 residues within 4Å: Chain A: A.129, Y.166 Chain B: C.95, L.96, S.99, W.102, W.106, A.151, Y.154, M.193, R.202, Y.205, C.206, H.248, G.250, Y.251, C.254, Y.300, W.303, Y.361 Ligands: DMA.6 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.106, B:Y.154, B:Y.205, B:W.303, A:A.129 Hydrogen bonds: B:S.99, B:R.202 Water bridges: B:W.102 pi-Stacking: B:W.102, B:W.102

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain B: D.297, C.299, D.352, Y.361, H.362 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.297, B:D.297, B:C.299, B:H.362, H2O.15

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: Y.131, Q.167 Chain B: H.194 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.194, H2O.6, H2O.7

1 x DMA: DIMETHYLALLYL DIPHOSPHATE(Non-covalent)

DMA.6: 11 residues within 4Å: Chain A: K.164, Y.166, Y.200, H.201 Chain B: H.248, Y.251, G.290, R.291, K.294, Y.300 Ligands: 60I.3 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:H.248, B:Y.300, B:Y.300 Water bridges: B:G.290, B:R.291, B:R.291, A:K.164, A:K.164 Salt bridges: B:R.291, B:R.291, B:K.294, B:K.294, A:K.164 Hydrophobic interactions: A:Y.200, A:Y.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bukhtiyarova, M. et al., Discovery of an Anion-Dependent Farnesyltransferase Inhibitor from a Phenotypic Screen. ACS Med Chem Lett (2021)

Release Date

2021-09-08

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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