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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x F7D: (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5,8-di(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one(Non-covalent)

F7D.1: 18 residues within 4Å: Chain A: I.43, G.44, Q.45, I.51, L.53, V.69, K.71, E.83, P.111, M.131, D.132, R.133, F.134, G.135, D.137, L.184, V.196, D.197 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.43, A:I.43, A:Q.45, A:I.51, A:L.53, A:V.69, A:M.131, A:F.134, A:D.137 Hydrogen bonds: A:K.71, A:D.132, A:F.134, A:D.197

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

SO4.2: 3 residues within 4Å: Chain A: Q.95, K.98, H.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.95 Salt bridges: A:K.98, A:H.171 SO4.3: 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.4: 5 residues within 4Å: Chain A: H.169, E.170, Y.204, R.240, K.314 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.169, A:R.240, A:R.240 Water bridges: A:T.312, A:K.314

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

ACT.5: 4 residues within 4Å: Chain A: R.241, D.310, Y.311 Ligands: ACT.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.311 Salt bridges: A:R.241 ACT.6: 2 residues within 4Å: Chain A: K.85, R.203 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.173 Salt bridges: A:K.85, A:R.203 ACT.7: 4 residues within 4Å: Chain A: R.241, R.279, D.310 Ligands: ACT.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.310 Water bridges: A:R.279, A:R.279, A:R.279 Salt bridges: A:R.241, A:R.279

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

dos Reis, C.V. et al., Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropynyl-dihydropteridine inhibitor. To Be Published

Release Date

2018-03-21

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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