SMTL ID : 5wcg.1

SET and MYND Domain Containing protein 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.52, C.55, C.74, C.78 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.52, A:C.55, A:C.74, A:C.78 ZN.2: 4 residues within 4Å: Chain A: C.209, C.262, C.264, C.267 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.209, A:C.262, A:C.264, A:C.267 ZN.3: 4 residues within 4Å: Chain A: C.65, C.68, H.86, C.90 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.65, A:C.68, A:H.86, A:C.90

1 x A4M: [3-(6-amino-2-methyl-9H-purin-9-yl)azetidin-1-yl]{5-[(4-cycloheptylpiperazin-1-yl)methyl]-1-methyl-1H-pyrazol-3-yl}methanone(Non-covalent)

A4M.4: 13 residues within 4Å: Chain A: G.16, K.17, H.137, C.181, N.182, G.183, F.184, A.203, N.206, H.207, Y.240, Y.258, F.260 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.240 Hydrogen bonds: A:H.207, A:H.207 Water bridges: A:E.263, A:E.263, A:E.263 pi-Stacking: A:Y.258, A:F.260, A:F.260

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 4 residues within 4Å: Chain A: Y.41, Y.54, C.55, T.220 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.220 Water bridges: A:T.220 pi-Cation interactions: A:Y.54

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 8 residues within 4Å: Chain A: E.104, T.105, L.108, V.179, N.180, G.183, F.184, S.196 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.104, A:E.104, A:T.105, A:V.179, A:G.183, A:F.184, A:S.196

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

UNX.7: 2 residues within 4Å: Chain A: S.208, C.210 No protein-ligand interaction detected (PLIP) UNX.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.9: 3 residues within 4Å: Chain A: D.168, N.169, D.170 No protein-ligand interaction detected (PLIP) UNX.10: 2 residues within 4Å: Chain A: S.239, I.241 No protein-ligand interaction detected (PLIP) UNX.11: 1 residues within 4Å: Chain A: W.83 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeng, H. et al., The crystal structure of SMYD2 in complex with compound MTF003. to be published

Release Date

2017-08-02

Peptides

N-lysine methyltransferase SMYD2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-lysine methyltransferase SMYD2

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