SMTL ID : 5vs6.1

Structure of DUB complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

homo-dimer

Ligands

2 x 9QD: N-[3-({4-hydroxy-1-[(3R)-3-phenylbutanoyl]piperidin-4-yl}methyl)-4-oxo-3,4-dihydroquinazolin-7-yl]-3-(4-methylpiperazin-1-yl)propanamide(Non-covalent)

9QD.1: 16 residues within 4Å: Chain A: Y.17, D.88, V.89, Q.90, Q.144, L.199, M.200, R.201, F.202, K.213, H.249, N.253, H.254, Y.258, Y.307 Ligands: ACT.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Q.144, A:M.200, A:R.201, A:F.202, A:F.202, A:K.213, A:H.249, A:Y.307, A:Y.307 Hydrogen bonds: A:D.88, A:V.89, A:Q.90, A:R.201, A:F.202 9QD.3: 18 residues within 4Å: Chain B: Y.17, D.88, V.89, Q.90, Q.144, Q.198, L.199, M.200, R.201, F.202, K.213, H.249, N.253, H.254, Y.258, Y.307 Ligands: ACT.4, GOL.5 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Q.144, B:M.200, B:R.201, B:F.202, B:F.202, B:K.213, B:H.249, B:Y.307, B:Y.307 Hydrogen bonds: B:D.88, B:D.88, B:V.89, B:Q.90, B:F.202, B:Y.258

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 4 residues within 4Å: Chain A: D.88, F.202, N.211 Ligands: 9QD.1 No protein-ligand interaction detected (PLIP) ACT.4: 6 residues within 4Å: Chain B: D.88, F.202, M.203, N.211 Ligands: 9QD.3, GOL.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.202

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 10 residues within 4Å: Chain B: F.84, M.85, Q.86, H.87, D.88, F.202, N.211, H.254 Ligands: 9QD.3, ACT.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.85, B:H.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lamberto, I. et al., Structure-Guided Development of a Potent and Selective Non-covalent Active-Site Inhibitor of USP7. Cell Chem Biol (2017)

Release Date

2017-12-20

Peptides

Ubiquitin carboxyl-terminal hydrolase 7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ubiquitin carboxyl-terminal hydrolase 7

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