SMTL ID : 8jjs.1

Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor AP10343

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

hetero-1-1-mer

Ligands

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

GDP.1: 20 residues within 4Å: Chain A: A.16, D.17, G.18, V.19, G.20, K.21, S.22, A.23, F.33, V.34, D.35, Y.37, N.121, K.122, D.124, L.125, S.150, A.151, K.152 Ligands: MG.2 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:G.18, A:V.19, A:G.20, A:K.21, A:S.22, A:A.23, A:D.35, A:N.121, A:K.122, A:A.151, A:K.152 Water bridges: A:D.17, A:D.17, A:D.17, A:K.21, A:S.22, A:S.22, A:S.22, A:Y.37, A:K.122, A:K.122 Salt bridges: A:K.21, A:D.124 pi-Stacking: A:F.33, A:F.33

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.22 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.22, H2O.1, H2O.1, H2O.2, H2O.2

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 6 residues within 4Å: Chain A: A.64, G.65, R.73, Y.101 Chain B: F.7, L.8 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Water bridges: A:D.17, A:T.63, A:T.63, A:R.73, A:R.73 Salt bridges: A:R.73 Hydrogen bonds: B:L.8 SO4.4: 2 residues within 4Å: Chain A: H.32, F.33 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.27, A:F.33, A:F.33 Salt bridges: A:H.32 SO4.5: 3 residues within 4Å: Chain A: S.70, A.71, M.72 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.71, A:M.72 Water bridges: A:Q.66, A:Y.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanada, M. et al., Development of Orally Bioavailable Peptides Targeting an Intracellular Protein: From a Hit to a Clinical KRAS Inhibitor. J.Am.Chem.Soc. (2023)

Release Date

2023-07-26

Peptides

Isoform 2B of GTPase KRas: A
MAA-ILE-SAR-SAR-7T2-SAR-IAE-LEU-MEA-MLE-7TK: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
I

Isoform 2B of GTPase KRas

MAA-ILE-SAR-SAR-7T2-SAR-IAE-LEU-MEA-MLE-7TK

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