SMTL ID : 7m0x.1

Crystal structure of the BRAF:MEK1 kinases in complex with AMPPNP and PD0325901

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

hetero-1-1-mer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 23 residues within 4Å: Chain A: I.23, G.24, S.25, G.26, S.27, F.28, G.29, V.31, A.41, K.43, L.74, T.89, Q.90, W.91, C.92, D.136, K.138, N.140, N.141, F.143, D.154 Chain B: E.106 Ligands: MG.2 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.27, A:F.28, A:K.43, A:T.89, A:Q.90, A:C.92, A:D.136, A:N.140, A:N.141, B:E.106 Water bridges: A:K.138, A:K.138, B:E.106 Salt bridges: A:K.43 ANP.4: 21 residues within 4Å: Chain B: L.78, G.79, A.80, G.81, N.82, V.86, A.99, K.101, M.147, E.148, H.149, M.150, S.154, Q.157, K.196, S.198, N.199, L.201, D.212 Ligands: MG.5, 4BM.6 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.81, B:N.82, B:N.82, B:N.82, B:E.148, B:M.150, B:S.154, B:S.154, B:S.154, B:K.196, B:S.198, B:S.198 Water bridges: B:A.80, B:N.199, B:N.199 Salt bridges: B:K.101

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.43, N.141, D.154 Ligands: ANP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.154, H2O.1 MG.5: 5 residues within 4Å: Chain B: K.101, N.199, D.212 Ligands: ANP.4, 4BM.6 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.212, H2O.4, H2O.5

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

1 x 4BM: N-{[(2R)-2,3-dihydroxypropyl]oxy}-3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]benzamide(Non-covalent)

4BM.6: 21 residues within 4Å: Chain B: G.81, N.82, G.83, G.84, K.101, L.119, L.122, V.131, I.145, M.147, C.211, D.212, F.213, G.214, V.215, S.216, L.219, I.220, M.223 Ligands: ANP.4, MG.5 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.122, B:I.145, B:L.219, B:I.220 Hydrogen bonds: B:N.82, B:N.82, B:G.83, B:G.84, B:K.101, B:K.101 Water bridges: B:N.199 pi-Stacking: B:F.213 Halogen bonds: B:V.131

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

SO4.7: 3 residues within 4Å: Chain B: R.185, S.245, V.246 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.245, B:S.245, B:V.246 Salt bridges: B:R.185 SO4.8: 4 residues within 4Å: Chain B: M.191, R.193, R.238, H.243 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.193, B:R.238, B:H.243

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain B: E.66, L.67, Q.120, H.123, G.135, A.136 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.67, B:L.67, B:Q.120, B:Q.120, B:A.136, B:A.136 GOL.10: 3 residues within 4Å: Chain B: A.351, E.352, Q.358 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.358 Water bridges: B:E.352, B:Q.358

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gonzalez-Del Pino, G.L. et al., Allosteric MEK inhibitors act on BRAF/MEK complexes to block MEK activation. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-04-21

Peptides

Serine/threonine-protein kinase B-raf: A
Dual specificity mitogen-activated protein kinase kinase 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine/threonine-protein kinase B-raf

Dual specificity mitogen-activated protein kinase kinase 1

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