SMTL ID : 6npn.2 (3 other biounits)

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

Coordinates

PDB Format Compare

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: 14 residues within 4Å: Chain A: 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 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.51, A:V.69, A:M.131, A:F.134, A:L.184, A:V.196 Hydrogen bonds: A:D.132, A:F.134, A:D.197

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

SO4.2: 3 residues within 4Å: Chain A: Y.202, K.211, R.219 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.202 Salt bridges: A:K.211, A:R.219 SO4.3: 3 residues within 4Å: Chain A: K.85, R.89, R.203 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.203 Salt bridges: A:K.85, A:R.89 SO4.4: 2 residues within 4Å: Chain A: R.148, H.258 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.148, A:H.258

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

PEG.5: 8 residues within 4Å: Chain A: E.245, Y.249, Y.278, R.279, L.285, M.303, V.306, K.307 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.245, A:R.279

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

EDO.6: 5 residues within 4Å: Chain A: L.309, E.313, K.314, P.315, L.316 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.314, A:L.316 EDO.7: 3 residues within 4Å: Chain A: E.280, E.304, K.307 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.304, A:K.307 Water bridges: A:E.280, A:I.282, A:K.307 EDO.8: 2 residues within 4Å: Chain A: R.89, R.203 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.89, A:R.89, A:R.203 EDO.9: 2 residues within 4Å: Chain A: Q.95, H.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.95 Water bridges: A:H.171, A:H.171 EDO.10: 1 residues within 4Å: Chain A: R.241 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.241, A:R.279

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
B

Serine/threonine-protein kinase VRK1

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