SMTL ID : 4luc.1

Crystal Structure of small molecule disulfide 6 bound to K-Ras G12C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.29 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: S.18, Y.33, P.35 Ligands: GDP.4 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.18, H2O.1, H2O.1, H2O.1, H2O.1 CA.2: 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.1, H2O.1, H2O.2 CA.5: 5 residues within 4Å: Chain B: K.17, S.18, Y.33, P.35 Ligands: GDP.8 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.18, H2O.7, H2O.7, H2O.7, H2O.7 CA.6: 2 residues within 4Å: Chain B: G.139, I.140 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:G.139, H2O.7, H2O.7, H2O.7, H2O.10

2 x 20G: N-{1-[(2,4-dichlorophenoxy)acetyl]piperidin-4-yl}-4-sulfanylbutanamide(Non-covalent)

20G.3: 21 residues within 4Å: Chain A: V.8, V.10, G.11, A.12, C.13, G.14, K.17, P.35, T.59, G.61, Q.62, E.63, E.64, R.69, Y.72, M.73, F.79, Y.97, Q.100, I.101 Ligands: GDP.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.10, A:T.59, A:R.69 Hydrogen bonds: A:G.61, A:Q.100 Water bridges: A:G.11, A:C.13, A:C.13, A:E.63 Halogen bonds: A:Y.97 20G.7: 18 residues within 4Å: Chain B: V.8, V.10, G.11, A.12, C.13, K.17, P.35, T.59, G.61, Q.62, E.63, R.69, Y.72, M.73, F.79, Y.97, Q.100, I.101 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.10, B:T.59, B:E.63, B:R.69 Hydrogen bonds: B:G.61 Water bridges: B:G.11, B:C.13, B:C.13 Halogen bonds: B:Y.97

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

GDP.4: 22 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.1, 20G.3 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: 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:D.31, A:N.117, A:K.118, A:K.118, A:S.146, A:A.147, A:K.148 Water bridges: A:K.17, A:Y.33, A:T.59 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, A:F.29 GDP.8: 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.5 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:A.12, B:G.14, B:V.15, B:G.16, B:K.17, B:S.18, B:A.19, B:D.31, B:D.31, B:D.31, B:N.117, B:K.118, B:K.118, B:S.146, B:A.147, B:K.148 Water bridges: B:K.17, B:S.18, B:Y.33, B:K.148, B:K.148 Salt bridges: B:K.17, B:D.120 pi-Stacking: B:F.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ostrem, J.M. et al., K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions. Nature (2013)

Release Date

2013-11-27

Peptides

GTPase KRas: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GTPase KRas

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