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

Crystal Structure of ACBI4-mediated ternary complex of KRAS G12D C118S GDP with pVHL:ElonginC:ElonginB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x 01: (2~{S},4~{R})-1-[(2~{S})-2-[(5~{S})-5-[3-[(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]propyl]-4,5,6,7-tetrahydrobenzotriazol-1-yl]-3-methyl-butanoyl]-~{N}-[(1-methylindazol-6-yl)methyl]-4-oxidanyl-pyrrolidine-2-carboxamide

01.1: 28 residues within 4Å: Chain C: R.18, F.25, W.37, F.40, Y.47, P.48, I.58, H.59, S.60, Y.61, H.64, W.66 Chain D: V.10, 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 28 PLIP interactions: 11 interactions with chain C, 17 interactions with chain D Hydrophobic interactions: C:R.18, C:Y.47, C:Y.61, C:Y.61, C:W.66, D:V.10, D:E.63, D:Y.65, D:M.73, D:D.93, D:H.96, D:Q.100, D:I.101, D:K.102 Hydrogen bonds: C:Y.47, C:H.59, C:Y.61, C:H.64, D:E.64, D:Y.65, D:Y.65, D:D.70, D:Q.100, D:R.103 Water bridges: C:R.56, D:Y.97 pi-Stacking: C:Y.61 Salt bridges: D:E.63

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

GDP.2: 20 residues within 4Å: Chain D: A.12, D.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.3 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:A.12, D:G.14, D:V.15, D:G.16, D:K.17, D:S.18, D:A.19, D:D.31, D:N.117, D:K.118, D:K.118, D:S.146, D:A.147, D:K.148 Water bridges: D:S.18, D:S.18 Salt bridges: D:K.17, D:D.120 pi-Stacking: D:F.29, D:F.29

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain D: S.18 Ligands: GDP.2 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:S.18, H2O.1, H2O.1, H2O.1, H2O.1

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
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

GTPase KRas

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