SMTL ID : 6qux.1

Crystal Structure of KRAS-G12D in Complex with Natural Product-Like Compound 15

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-dimer

Ligands

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

GCP.1: 27 residues within 4Å: Chain A: A.12, D.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, E.32, Y.33, D.34, P.35, T.36, A.60, G.61, Q.62, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.2 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:A.12, A:D.13, A:G.14, A:V.15, A:G.16, A:K.17, A:K.17, A:S.18, A:A.19, A:V.30, A:D.31, A:T.36, A:G.61, A:N.117, A:K.118, A:K.118, A:S.146, A:A.147, A:K.148 Water bridges: A:S.18, A:D.34, A:Q.62, A:Q.62 Salt bridges: A:D.120 pi-Stacking: A:F.29 GCP.5: 27 residues within 4Å: Chain B: A.12, D.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, E.32, Y.33, D.34, P.35, T.36, A.60, G.61, Q.62, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.6 28 PLIP interactions: 28 interactions with chain B Hydrogen bonds: B:A.12, B:D.13, B:G.14, B:V.15, B:G.16, B:K.17, B:K.17, B:S.18, B:A.19, B:V.30, B:D.31, B:Y.33, B:T.36, B:G.61, B:Q.62, B:N.117, B:K.118, B:K.118, B:S.146, B:A.147, B:K.148 Water bridges: B:S.18, B:D.34, B:Q.62, B:K.148 Salt bridges: B:D.120 pi-Stacking: B:F.29, B:F.29

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.17, S.18, T.36 Ligands: GCP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.18, A:T.36, H2O.1, H2O.1 MG.6: 4 residues within 4Å: Chain B: K.17, S.18, T.36 Ligands: GCP.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.18, B:T.36, H2O.6, H2O.6

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain B: E.4, K.6 Ligands: JJN.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.4, B:K.6 Water bridges: B:D.55, B:D.55 EDO.4: 8 residues within 4Å: Chain A: S.40, R.42 Chain B: E.38, D.39, S.40, L.57, M.68 Ligands: JJN.7 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.40, A:R.42, A:R.42, B:E.38, B:E.38 Water bridges: A:S.40, A:Y.41

1 x JJN: (6~{a}~{R},11~{b}~{S})-6~{a}-(1,4-dimethylpiperidin-4-yl)-7,11~{b}-dihydro-6~{H}-indolo[2,3-c]isoquinolin-5-one(Non-covalent)

JJN.7: 12 residues within 4Å: Chain B: K.6, L.7, V.8, S.40, R.42, D.55, L.57, Y.72, T.75, G.76 Ligands: EDO.3, EDO.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:K.6, B:V.8, B:L.57, B:L.57, B:L.57, B:T.75 Water bridges: B:R.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bergner, A. et al., KRAS Binders Hidden in Nature. Chemistry (2019)

Release Date

2019-07-31

Peptides

GTPase KRas: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GTPase KRas

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