SMTL ID : 7yuz.1

Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor AP8784

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

hetero-1-1-mer

Ligands

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

GDP.1: 21 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, E.36, Y.37, N.121, K.122, D.124, L.125, S.150, A.151, K.152 Ligands: MG.2 23 PLIP interactions: 23 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:V.34, A:E.36, A:N.121, A:K.122, A:K.122, A:A.151, A:K.152 Water bridges: A:K.21, A:S.22, A:S.22, A:Y.37, A:D.62, A:T.63 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.1, H2O.1

1 x IOD: IODIDE ION(Non-functional Binders)

IOD.3: 1 residues within 4Å: Chain A: Q.48 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ohta, A. et al., Validation of a New Methodology to Create Oral Drugs beyond the Rule of 5 for Intracellular Tough Targets. J.Am.Chem.Soc. (2023)

Release Date

2023-07-26

Peptides

Isoform 2B of GTPase KRas: A
AP8784: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
I

Isoform 2B of GTPase KRas

AP8784

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