SMTL ID : 8qu8.1

PROTAC-mediated complex of KRAS with VHL/Elongin-B/Elongin-C/Cullin-2/Rbx1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.50 Å

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain E: C.41, C.44, H.79, C.82 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.41, E:C.44, E:H.79, E:C.82 ZN.2: 4 residues within 4Å: Chain E: C.52, C.55, C.67, H.81 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.52, E:C.55, E:C.67, E:H.81

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.3: 18 residues within 4Å: Chain F: V.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, D.31, E.32, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:G.14, F:V.15, F:G.16, F:K.17, F:S.18, F:A.19, F:E.32, F:N.117, F:K.118, F:K.118, F:A.147, F:K.148 Salt bridges: F:K.17, F:D.120 pi-Stacking: F:F.29, F:F.29

1 x WYL: (2S,4R)-1-[(2S)-2-[4-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2,3-triazol-1-yl]-3-methyl-butanoyl]-N-[(1R)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-2-oxidanyl-ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide(Non-covalent)

WYL.4: 24 residues within 4Å: Chain A: E.69, W.87, Y.97, P.98, L.100, R.106, I.108, S.110, Y.111, W.116 Chain F: V.10, G.61, Q.62, E.63, E.64, Y.65, R.69, D.70, M.73, D.93, H.96, Y.97, Q.100, R.103 17 PLIP interactions: 6 interactions with chain A, 11 interactions with chain F Hydrophobic interactions: A:Y.97, A:Y.97, A:P.98, A:I.108, A:W.116, F:V.10, F:E.63, F:Y.65, F:Y.97, F:Q.100 Hydrogen bonds: A:Y.111, F:E.64, F:D.70, F:D.70, F:Y.97, F:Q.100 Salt bridges: F:E.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Popow, J. et al., Targeting cancer with small molecule pan-KRAS degraders. Biorxiv (2023)

Release Date

2023-12-06

Peptides

von Hippel-Lindau disease tumor suppressor: A
Elongin-B: B
Elongin-C: C
Cullin-2: D
E3 ubiquitin-protein ligase RBX1, N-terminally processed: E
GTPase KRas: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

von Hippel-Lindau disease tumor suppressor

Elongin-B

Elongin-C

Cullin-2

E3 ubiquitin-protein ligase RBX1, N-terminally processed

GTPase KRas

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