SMTL ID : 5v6v.1

Crystal structure of small molecule aziridine 3 covalently bound to K-Ras G12C

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

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

GDP.1: 21 residues within 4Å: Chain A: A.12, C.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, E.32, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: CA.2 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:A.12, A:G.14, A:V.15, A:G.16, A:K.17, A:S.18, A:S.18, A:A.19, A:V.30, A:E.32, A:N.117, A:K.118, A:K.118, A:S.146, A:S.146, A:A.147, A:K.148 Water bridges: A:K.17, A:Y.33 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, A:F.29 GDP.6: 21 residues within 4Å: Chain B: A.12, C.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, E.32, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: CA.7 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:G.14, B:V.15, B:G.16, B:K.17, B:S.18, B:A.19, B:Y.33, B:N.117, B:K.118, B:K.118, B:S.146, B:S.146, B:A.147, B:K.148 Water bridges: B:K.17, B:S.18, B:S.18, B:Y.33 Salt bridges: B:K.17, B:D.120 pi-Stacking: B:F.29, B:F.29

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: S.18, Y.33, P.35, A.60 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.18, H2O.1, H2O.2, H2O.2, H2O.5 CA.3: 1 residues within 4Å: Chain A: G.139 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.139, H2O.1, H2O.4, H2O.4, H2O.6 CA.5: 1 residues within 4Å: Chain B: E.64 No protein-ligand interaction detected (PLIP) CA.7: 5 residues within 4Å: Chain B: S.18, Y.33, P.35, A.60 Ligands: GDP.6 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.18, H2O.7, H2O.8, H2O.8, H2O.8 CA.8: 2 residues within 4Å: Chain B: G.139, I.140 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.139, H2O.9, H2O.11 CA.9: 4 residues within 4Å: Chain B: E.4, Y.5, K.6, E.77 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.4, B:E.77, B:E.77

2 x 8YA: 3-amino-1-{4-[6-chloro-8-fluoro-7-(5-methyl-1H-indazol-4-yl)quinazolin-4-yl]piperazin-1-yl}propan-1-one(Covalent)

8YA.4: 23 residues within 4Å: Chain A: V.10, G.11, A.12, C.13, K.17, E.38, T.59, A.60, G.61, Q.62, E.63, E.64, Y.65, S.66, R.69, D.70, M.73, H.96, Y.97, Q.100, I.101, R.103, V.104 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.97, A:Q.100, A:I.101, A:V.104 Hydrogen bonds: A:C.13, A:G.61, A:R.69, A:R.69, A:D.70, A:D.70, A:R.103 Water bridges: A:E.63, A:Y.97 8YA.11: 21 residues within 4Å: Chain B: V.10, G.11, A.12, C.13, E.38, T.59, A.60, G.61, Q.62, E.63, E.64, Y.65, R.69, D.70, M.73, H.96, Y.97, Q.100, I.101, R.103, V.104 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.97, B:Y.97, B:Q.100, B:V.104 Hydrogen bonds: B:C.13, B:R.69, B:R.69, B:D.70, B:R.103

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 3 residues within 4Å: Chain B: Q.26, N.27, H.28 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.26, B:N.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McGregor, L.M. et al., Expanding the Scope of Electrophiles Capable of Targeting K-Ras Oncogenes. Biochemistry (2017)

Release Date

2017-06-28

Peptides

GTPase KRas: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GTPase KRas

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