SMTL ID : 5qir.1

Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0102305

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

monomer

Ligands

1 x J5D: N-[(4-fluoro-3-methylphenyl)methyl]acetamide(Covalent)

J5D.1: 10 residues within 4Å: Chain A: G.42, D.43, R.44, N.45, C.46, F.47, E.169, T.217, S.218, H.219 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.43, A:D.43, A:R.44, A:C.46, A:S.218

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 3 residues within 4Å: Chain A: D.195, T.196, A.197 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.195 Water bridges: A:R.25, A:R.25

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

EDO.3: 4 residues within 4Å: Chain A: R.33, Q.187, H.200, Y.212 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.33, A:Q.187, A:H.200 EDO.4: 8 residues within 4Å: Chain A: F.1, N.2, L.3, I.4, S.5, K.39, T.40, K.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.3 EDO.5: 5 residues within 4Å: Chain A: K.7, C.8, D.9, T.35, A.36 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.7 EDO.6: 2 residues within 4Å: Chain A: N.95, S.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.99, A:S.99 Water bridges: A:S.99 EDO.7: 4 residues within 4Å: Chain A: A.83, G.84, F.85, R.139 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.139, A:T.160, A:T.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sethi, R. et al., Covalent fragment group deposition. To Be Published

Release Date

2019-12-18

Peptides

Ubiquitin thioesterase OTUB2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ubiquitin thioesterase OTUB2

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