SMTL ID : 9rkj.1 (1 other biounit)

Crystal Structure of compound 3-mediated ternary complex of KRAS G12R GCP with pVHL:ElonginC:ElonginB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

2 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 5 residues within 4Å: Chain B: R.67, S.71, S.72, T.73, E.74 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.72, B:S.72, B:T.73 Salt bridges: B:R.67, B:R.67 FLC.3: 3 residues within 4Å: Chain C: G.53, T.54, G.55 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.53, C:G.55

1 x 01: (2~{S},4~{R})-1-[(2~{S})-2-[[1-[4-[(3~{S})-4-[4-[5-[(4~{S})-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5~{H}-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butanoyl]cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide

01.2: 31 residues within 4Å: Chain C: N.16, R.18, W.37, F.40, Y.47, P.48, 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, R.103, V.104 Ligands: GOL.6 25 PLIP interactions: 10 interactions with chain D, 15 interactions with chain C Hydrophobic interactions: D:E.63, D:Y.65, D:Y.97, D:I.101, D:R.103, C:R.18, C:W.37, C:Y.47, C:Y.47, C:I.58, C:I.58, C:Y.61, C:Y.61, C:W.66 Hydrogen bonds: D:E.64, D:E.64, D:Q.100, D:R.103, C:Y.47, C:R.56, C:H.59, C:S.60, C:Y.61, C:H.64 Salt bridges: D:E.63

1 x GCP: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

GCP.4: 18 residues within 4Å: Chain D: A.12, R.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, A.60, G.61, N.117, K.118, D.120, S.146, A.147, K.148 Ligands: MG.5 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:R.13, D:R.13, D:G.14, D:V.15, D:G.16, D:K.17, D:K.17, D:S.18, D:A.19, D:N.117, D:K.118, D:K.118, D:A.147, D:K.148 Salt bridges: D:D.120

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain D: S.18, T.59, A.60 Ligands: GCP.4 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:S.18, D:T.59

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain C: W.37, Q.45 Chain D: Y.65, S.66, D.70, R.103 Ligands: 01.2 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.70, D:R.103, D:R.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vetma, V. et al., Identification of a Highly Cooperative PROTAC Degrader Targeting GTP-Loaded KRAS(On) Alleles. J.Am.Chem.Soc. (2025)

Release Date

2025-11-12

Peptides

Elongin-B: A
Elongin-C: B
von Hippel-Lindau disease tumor suppressor: C
Isoform 2B of GTPase KRas: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

Isoform 2B of GTPase KRas

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