SMTL ID : 8qw7.1 (1 other biounit)

Crystal Structure of compound 4 in complex with KRAS G12V C118S GDP and pVHL:ElonginC:ElonginB

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x X53: (2S,4R)-1-[(2R)-2-[3-[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-oxazol-5-yl]-3-methyl-butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide(Non-covalent)

X53.1: 36 residues within 4Å: Chain C: N.16, R.18, P.35, W.37, F.40, Y.47, P.48, T.49, L.50, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 Chain D: V.10, G.61, Q.62, E.63, E.64, Y.65, R.69, D.70, M.73, D.93, H.96, Y.97, E.99, Q.100, I.101, K.102, R.103, V.104, S.107, E.108 27 PLIP interactions: 16 interactions with chain D, 11 interactions with chain C Hydrophobic interactions: D:V.10, D:E.63, D:Y.65, D:D.93, D:H.96, D:Y.97, D:I.101, D:R.103, C:W.37, C:I.58, C:Y.61, C:Y.61, C:W.66 Hydrogen bonds: D:E.64, D:E.64, D:Y.97, D:Q.100, D:R.103, C:R.56, C:H.59, C:Y.61, C:Y.61, C:H.64 Salt bridges: D:E.63 pi-Stacking: D:Y.97, C:Y.47 pi-Cation interactions: D:K.102

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

GDP.2: 17 residues within 4Å: Chain D: V.13, G.14, V.15, G.16, K.17, S.18, A.19, D.31, E.32, Y.33, N.117, K.118, D.120, S.146, A.147, K.148 Ligands: MG.3 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:G.14, D:G.16, D:K.17, D:S.18, D:S.18, D:A.19, D:D.31, D:N.117, D:K.118, D:A.147, D:K.148 Salt bridges: D:K.17, D:D.120

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain D: S.18, D.34, P.35, A.60 Ligands: GDP.2 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.18

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

Elongin-B: A
Elongin-C: B
von Hippel-Lindau disease tumor suppressor: C
GTPase KRas: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

C
B

D
A

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

GTPase KRas

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