SMTL ID : 4x3t.2 (2 other biounits)

Crystal structure of chromobox homolog 7 (CBX7) chromodomain with MS37452

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-dimer

Ligands

2 x 45E: 1-[4-(2,3-dimethoxybenzoyl)piperazin-1-yl]-2-(3-methylphenoxy)ethanone(Non-covalent)

45E.1: 11 residues within 4Å: Chain A: M.4, F.9, V.11, W.30, W.33, Y.37, T.39, E.41, H.45 Chain B: E.44, L.47 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.11, A:W.30, A:Y.37, A:H.45, B:L.47 pi-Stacking: A:F.9, A:W.30, A:W.33, A:H.45 45E.4: 11 residues within 4Å: Chain A: E.44, L.47 Chain B: M.4, F.9, V.11, W.30, W.33, Y.37, T.39, E.41, H.45 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.11, B:W.30, B:Y.37, B:Y.37, B:H.45, A:L.47 pi-Stacking: B:F.9, B:W.33, B:H.45

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 2 residues within 4Å: Chain A: H.45 Chain B: H.45 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.45, B:H.45, H2O.1, H2O.1, H2O.3 ZN.3: 2 residues within 4Å: Chain A: H.3, M.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.3, H2O.1, H2O.3 ZN.5: 2 residues within 4Å: Chain B: H.3, M.4 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.3, H2O.1, H2O.2

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 7 residues within 4Å: Chain A: L.47 Chain B: V.11, H.45, I.46, L.47, D.48, L.51 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.47, B:D.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ren, C. et al., Small-Molecule Modulators of Methyl-Lysine Binding for the CBX7 Chromodomain. Chem.Biol. (2015)

Release Date

2015-03-04

Peptides

Chromobox protein homolog 7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
F

Chromobox protein homolog 7

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