SMTL ID : 7pi4.1

FAK Protac GSK215 in complex with FAK and pVHL:ElonginC:ElonginB

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x 7QB: (2S,4R)-4-hydroxy-1-((S)-2-(2-(4-(3-methoxy-4-((4-((2-(methylcarbamoyl)phenyl)amino)-5-(trifluoromethyl)pyridin-2-yl)amino)phenyl)piperazin-1-yl)acetamido)-3,3-dimethylbutanoyl)-N-((S)-1-(4-(4-methylthiazol-5-yl)phenyl)ethyl)pyrrolidine-2-carboxamide(Non-covalent)

7QB.1: 34 residues within 4Å: Chain A: W.30, F.33, Y.40, P.41, R.49, I.51, H.52, S.53, Y.54, H.57, W.59 Chain D: I.14, G.15, V.22, Q.24, A.38, V.70, M.85, E.86, L.87, C.88, T.89, G.91, S.95, Q.98, V.99, R.136, N.137, L.139, G.149, D.150, L.153, S.154 Ligands: PEG.16 22 PLIP interactions: 11 interactions with chain A, 11 interactions with chain D Hydrophobic interactions: A:W.30, A:W.30, A:I.51, A:I.51, A:H.52, A:W.59, D:I.14, D:V.22, D:A.38, D:Q.98, D:V.99, D:L.153 Hydrogen bonds: A:R.49, A:H.52, A:Y.54, A:H.57, D:C.88, D:C.88, D:R.136, D:D.150 pi-Stacking: A:Y.40 Water bridges: D:R.136

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain A: H.52 Chain D: R.94, S.95, Q.98, G.205 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.94 Water bridges: D:Q.210 PEG.14: 1 residues within 4Å: Chain D: N.215 No protein-ligand interaction detected (PLIP) PEG.15: 2 residues within 4Å: Chain D: S.125, K.126 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.126 PEG.16: 5 residues within 4Å: Chain D: Q.24, T.89, L.90 Ligands: 7QB.1, EDO.4 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.24

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

EDO.3: 3 residues within 4Å: Chain A: R.109, S.110, K.113 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.112 EDO.4: 5 residues within 4Å: Chain A: Q.38, P.39, Y.40 Ligands: EDO.6, PEG.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.39 EDO.5: 4 residues within 4Å: Chain A: R.24, R.103, S.110 Chain C: E.76 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.24, A:R.103, A:R.103, A:S.110, A:S.110 EDO.6: 3 residues within 4Å: Chain A: N.32, Q.38 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.32 Water bridges: A:N.32 EDO.7: 4 residues within 4Å: Chain A: T.42, P.44, R.49 Chain D: Y.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.42, A:R.49, A:R.49 Water bridges: A:T.42 EDO.9: 5 residues within 4Å: Chain B: D.2, F.4, D.17 Chain C: V.65, R.66 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.2 Water bridges: C:R.66 EDO.10: 4 residues within 4Å: Chain B: D.2, D.17, A.18, K.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.2, B:K.19 EDO.11: 2 residues within 4Å: Chain C: M.1, Y.2 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:M.1 Water bridges: C:M.1, C:E.18 EDO.12: 2 residues within 4Å: Chain B: I.34 Chain C: Y.2 No protein-ligand interaction detected (PLIP) EDO.13: 5 residues within 4Å: Chain A: L.71, Q.74 Chain C: T.68, N.69, S.70 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.69, C:S.70 EDO.17: 4 residues within 4Å: Chain D: S.250, R.252, P.253, E.257 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.250, D:E.257 EDO.18: 2 residues within 4Å: Chain D: F.182, R.184 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.184, D:R.184 EDO.19: 5 residues within 4Å: Chain D: E.16, G.17, Q.18, D.21, K.43 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.16, D:Q.18, D:D.21, D:D.21 EDO.20: 2 residues within 4Å: Chain D: E.124, S.125 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 2 residues within 4Å: Chain A: R.152, G.154 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:R.152, A:G.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Law, R.P. et al., Discovery and Characterisation of Highly Cooperative FAK-Degrading PROTACs. Angew.Chem.Int.Ed.Engl. (2021)

Release Date

2021-09-29

Peptides

von Hippel-Lindau disease tumor suppressor: A
Elongin-B: B
Isoform 2 of Elongin-C: C
Focal adhesion kinase 1: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
CCC

D
DDD

von Hippel-Lindau disease tumor suppressor

Elongin-B

Isoform 2 of Elongin-C

Focal adhesion kinase 1

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