SMTL ID : 5wbn.1

Crystal structure of fragment 3-(3-Benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.39, C.42, H.58, H.64 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.39, A:C.42, A:H.58, A:H.64 ZN.2: 4 residues within 4Å: Chain A: C.27, C.30, C.47, H.54 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.27, A:C.30, A:C.47, A:H.54 ZN.3: 4 residues within 4Å: Chain A: C.7, H.9, C.77, C.80 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.7, A:H.9, A:C.77, A:C.80

1 x 9ZV: 3-(3-benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid(Non-covalent)

9ZV.4: 7 residues within 4Å: Chain A: W.37, G.48, R.49, L.56, W.76, Y.78, Y.83 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.37, A:W.76, A:W.76, A:W.76, A:Y.83 Hydrogen bonds: A:R.49, A:L.56 Water bridges: A:R.49, A:R.49 pi-Stacking: A:W.76, A:W.76, A:W.76 pi-Cation interactions: A:R.49

8 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.5: 2 residues within 4Å: Chain A: C.14 Ligands: UNX.9 No protein-ligand interaction detected (PLIP) UNX.6: 3 residues within 4Å: Chain A: Y.50, I.51 Ligands: UNX.7 No protein-ligand interaction detected (PLIP) UNX.7: 3 residues within 4Å: Chain A: I.51, N.52 Ligands: UNX.6 No protein-ligand interaction detected (PLIP) UNX.8: 3 residues within 4Å: Chain A: D.72, L.73, H.97 No protein-ligand interaction detected (PLIP) UNX.9: 5 residues within 4Å: Chain A: V.13, C.14, I.16, Y.43 Ligands: UNX.5 No protein-ligand interaction detected (PLIP) UNX.10: 3 residues within 4Å: Chain A: V.11, A.12 Ligands: UNX.11 No protein-ligand interaction detected (PLIP) UNX.11: 2 residues within 4Å: Chain A: A.12 Ligands: UNX.10 No protein-ligand interaction detected (PLIP) UNX.12: 2 residues within 4Å: Chain A: G.28, D.29 No protein-ligand interaction detected (PLIP)

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.13: 5 residues within 4Å: Chain A: E.35, W.37, G.48, S.69, I.71 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.49, A:S.69 FMT.14: 4 residues within 4Å: Chain A: P.3, S.74, Y.83, H.85 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.75 FMT.15: 6 residues within 4Å: Chain A: V.84, H.85, H.86, L.89, L.90, K.93 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.85, A:H.86, A:H.86

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.16: 3 residues within 4Å: Chain A: P.17, A.18, A.19 Ligand excluded by PLIP

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

ACT.17: 4 residues within 4Å: Chain A: W.6, L.10, V.11, H.86 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.11 Water bridges: A:V.11 Salt bridges: A:H.86 ACT.18: 6 residues within 4Å: Chain A: D.29, Y.46, H.54, Q.57, H.58, N.61 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.46, A:H.58 Hydrogen bonds: A:H.54, A:Q.57, A:N.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harding, R.J. et al., Crystal structure of fragment 3-(3-Benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain. To be published

Release Date

2017-08-02

Peptides

Histone deacetylase 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 6

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