SMTL ID : 5hi7.1

Co-crystal structure of human SMYD3 with an aza-SAH compound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.210, C.212, R.253, C.265, C.267, C.270 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.212, A:C.265, A:C.267, A:C.270 ZN.2: 4 residues within 4Å: Chain A: C.66, C.69, H.87, C.91 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.66, A:C.69, A:H.87, A:C.91 ZN.3: 6 residues within 4Å: Chain A: C.53, R.55, C.56, C.75, S.76, C.79 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.53, A:C.56, A:C.75, A:C.79

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: E.134, N.138, K.139 No protein-ligand interaction detected (PLIP) MG.5: 6 residues within 4Å: Chain A: M.194, D.336, D.340, Y.362, Q.376, K.379 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.336, H2O.1, H2O.1, H2O.1, H2O.5

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

DMS.6: 9 residues within 4Å: Chain A: C.190, N.191, A.192, M.194, V.219, P.371, V.372, V.375, H.408 No protein-ligand interaction detected (PLIP)

1 x 62X: 5'-{[(3S)-3-amino-3-carboxypropyl][3-(dimethylamino)propyl]amino}-5'-deoxyadenosine(Non-covalent)

62X.7: 18 residues within 4Å: Chain A: R.18, G.19, N.20, Y.128, E.134, N.136, C.184, N.185, S.186, F.187, S.206, L.207, L.208, N.209, H.210, Y.243, Y.261, F.263 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:R.18, A:N.20, A:N.20, A:N.20, A:Y.128, A:E.134, A:N.136, A:H.210, A:H.210, A:Y.261 Water bridges: A:R.18, A:K.139, A:K.139, A:N.185, A:S.206, A:D.266, A:D.266 pi-Stacking: A:F.263, A:F.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Van Aller, G.S. et al., Structure-Based Design of a Novel SMYD3 Inhibitor that Bridges the SAM-and MEKK2-Binding Pockets. Structure (2016)

Release Date

2016-03-30

Peptides

Histone-lysine N-methyltransferase SMYD3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase SMYD3

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