SMTL ID : 6npn.4 (3 other biounits)

Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropynyl-dihydropteridine-3-hydroxyindazole inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x KWJ: (7R)-7-methyl-2-[(3-oxo-2,3-dihydro-1H-indazol-6-yl)amino]-5,8-di(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one(Non-covalent)

KWJ.1: 15 residues within 4Å: Chain A: I.43, I.51, V.69, K.71, E.83, Y.87, M.131, D.132, R.133, F.134, G.135, D.137, L.184, V.196, D.197 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.51, A:M.131, A:F.134, A:V.196 Hydrogen bonds: A:Y.87, A:D.132, A:F.134, A:D.197

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: K.85, R.89, R.203 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.85, A:R.89 SO4.3: 2 residues within 4Å: Chain A: R.89, R.203 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.89, A:R.203 SO4.4: 3 residues within 4Å: Chain A: Y.202, K.211, R.219 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.202 Water bridges: A:K.211 Salt bridges: A:K.211, A:R.219 SO4.5: 3 residues within 4Å: Chain A: Q.95, K.98, H.171 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.95 Water bridges: A:H.171 Salt bridges: A:K.98, A:H.171

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

EDO.6: 3 residues within 4Å: Chain A: L.308, D.310, E.313 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.310, A:D.310 Water bridges: A:L.308, A:E.313 EDO.7: 3 residues within 4Å: Chain A: T.305, N.319, I.323 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.305, A:N.319

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Counago, R.M. et al., Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropynyl-dihydropteridine-3-hydroxyindazole inhibitor. To Be Published

Release Date

2019-02-20

Peptides

Serine/threonine-protein kinase VRK1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Serine/threonine-protein kinase VRK1

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