SMTL ID : 4qev.3 (2 other biounits)

Crystal structure of BRD2(BD2) mutant with ligand ME bound (METHYL (2R)- 2-[(4S)-6-(4-CHLOROPHENYL)-8-METHOXY-1-METHYL-4H-[1,2,4]TRIAZOLO[4,3-A][1, 4]BENZODIAZEPIN-4-YL]PROPANOATE)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x 31O: methyl (2R)-2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]propanoate(Non-covalent)

31O.1: 9 residues within 4Å: Chain A: W.29, P.30, F.31, A.42, Y.45, Y.87, N.88, D.93, V.94 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.29, A:P.30, A:F.31, A:Y.45, A:Y.87, A:V.94 Hydrogen bonds: A:N.88 31O.5: 9 residues within 4Å: Chain B: W.29, P.30, F.31, A.42, Y.45, Y.87, N.88, D.93, V.94 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.29, B:P.30, B:F.31, B:Y.45, B:Y.87, B:V.94 Hydrogen bonds: B:N.88

2 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.2: 5 residues within 4Å: Chain A: S.6, K.10, M.62, E.63, R.65 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.6, A:K.10, A:R.65 Water bridges: A:N.13 2PE.6: 5 residues within 4Å: Chain B: S.6, K.10, M.62, E.63, R.65 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.6, B:K.10, B:R.65 Water bridges: B:N.13

2 x NI: NICKEL (II) ION(Non-covalent)

NI.3: 3 residues within 4Å: Chain A: R.78 Chain B: R.78 Ligands: NI.7 No protein-ligand interaction detected (PLIP) NI.7: 3 residues within 4Å: Chain A: R.78 Chain B: R.78 Ligands: NI.3 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: K.61, D.66, E.72 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.61, A:D.66, A:E.72 GOL.8: 3 residues within 4Å: Chain B: K.61, D.66, E.72 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.61, B:D.66, B:E.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baud, M.G. et al., Chemical biology. A bump-and-hole approach to engineer controlled selectivity of BET bromodomain chemical probes. Science (2014)

Release Date

2014-10-29

Peptides

Bromodomain-containing protein 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Bromodomain-containing protein 2

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