SMTL ID : 4jds.1 (3 other biounits)

SETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 14 residues within 4Å: Chain A: I.115, A.118, G.119, E.120, G.156, N.157, H.185, K.186, A.187, N.188, H.189, Y.227, W.244 Ligands: 1L4.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:E.120, A:G.156, A:N.188, A:N.188, A:H.189, A:H.189 Water bridges: A:E.120, A:N.157, A:N.174, A:K.186, A:W.244 Salt bridges: A:K.186 pi-Stacking: A:W.244, A:W.244, A:W.244 SAM.17: 14 residues within 4Å: Chain B: I.115, A.118, G.119, E.120, G.156, N.157, H.185, K.186, A.187, N.188, H.189, Y.227, W.244 Ligands: 1L4.18 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:E.120, B:G.156, B:N.188, B:N.188, B:H.189, B:H.189 Water bridges: B:N.157, B:N.174, B:K.186, B:W.244, B:E.248 Salt bridges: B:K.186 pi-Stacking: B:W.244, B:W.244, B:W.244

2 x 1L4: N-[(2R)-3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl]-8-fluoro-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide(Non-covalent)

1L4.2: 17 residues within 4Å: Chain A: Y.137, H.144, V.147, D.148, N.155, G.156, N.157, T.158, L.159, S.160, V.166, Y.197, Y.227, G.228, Y.229 Ligands: SAM.1, UNX.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.227, A:Y.229 Hydrogen bonds: A:H.144, A:S.160, A:G.228 Water bridges: A:S.160 1L4.18: 17 residues within 4Å: Chain B: Y.137, H.144, V.147, D.148, N.155, G.156, N.157, T.158, L.159, S.160, V.166, Y.197, Y.227, G.228, Y.229 Ligands: SAM.17, UNX.24 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.227, B:Y.229 Hydrogen bonds: B:H.144, B:S.160, B:G.228 Water bridges: B:D.148, B:S.160

28 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.3: 2 residues within 4Å: Chain A: E.120, V.176 Ligand excluded by PLIP UNX.4: 2 residues within 4Å: Chain A: Y.109, K.125 Ligand excluded by PLIP UNX.5: 1 residues within 4Å: Chain A: P.16 Ligand excluded by PLIP UNX.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.7: 1 residues within 4Å: Chain A: P.16 Ligand excluded by PLIP UNX.8: 4 residues within 4Å: Chain A: L.159, Y.197, G.228 Ligands: 1L4.2 Ligand excluded by PLIP UNX.9: 2 residues within 4Å: Chain A: Q.246, L.249 Ligand excluded by PLIP UNX.10: 1 residues within 4Å: Chain A: S.177 Ligand excluded by PLIP UNX.11: 3 residues within 4Å: Chain A: L.249, Q.253 Chain B: A.216 Ligand excluded by PLIP UNX.12: 2 residues within 4Å: Chain B: G.129, A.216 Ligand excluded by PLIP UNX.13: 1 residues within 4Å: Chain A: P.78 Ligand excluded by PLIP UNX.14: 3 residues within 4Å: Chain A: Q.253 Chain B: R.215, A.216 Ligand excluded by PLIP UNX.15: 2 residues within 4Å: Chain A: F.85, P.207 Ligand excluded by PLIP UNX.16: 3 residues within 4Å: Chain A: V.247, K.250, A.251 Ligand excluded by PLIP UNX.19: 2 residues within 4Å: Chain B: E.120, V.176 Ligand excluded by PLIP UNX.20: 2 residues within 4Å: Chain B: Y.109, K.125 Ligand excluded by PLIP UNX.21: 1 residues within 4Å: Chain B: P.16 Ligand excluded by PLIP UNX.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.23: 1 residues within 4Å: Chain B: P.16 Ligand excluded by PLIP UNX.24: 4 residues within 4Å: Chain B: L.159, Y.197, G.228 Ligands: 1L4.18 Ligand excluded by PLIP UNX.25: 2 residues within 4Å: Chain B: Q.246, L.249 Ligand excluded by PLIP UNX.26: 1 residues within 4Å: Chain B: S.177 Ligand excluded by PLIP UNX.27: 3 residues within 4Å: Chain A: A.216 Chain B: L.249, Q.253 Ligand excluded by PLIP UNX.28: 2 residues within 4Å: Chain A: G.129, A.216 Ligand excluded by PLIP UNX.29: 1 residues within 4Å: Chain B: P.78 Ligand excluded by PLIP UNX.30: 3 residues within 4Å: Chain A: R.215, A.216 Chain B: Q.253 Ligand excluded by PLIP UNX.31: 2 residues within 4Å: Chain B: F.85, P.207 Ligand excluded by PLIP UNX.32: 3 residues within 4Å: Chain B: V.247, K.250, A.251 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, A. et al., SETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine. to be published

Release Date

2013-03-27

Peptides

Histone-lysine N-methyltransferase SETD7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Histone-lysine N-methyltransferase SETD7

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