SMTL ID : 6ykd.1

Human Pim-1 kinase in complex with an inhibitor identified by virtual screening

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

1 x OWB: ~{N}-[3-[6-[(3~{R})-piperidin-3-yl]-2-pyridin-4-yl-pyrimidin-4-yl]oxyphenyl]ethanamide(Non-covalent)

OWB.1: 12 residues within 4Å: Chain A: L.60, F.65, A.81, K.83, I.120, L.136, E.137, V.142, D.144, L.190, I.201, D.202 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.60, A:F.65, A:F.65, A:A.81, A:I.120, A:V.142, A:L.190, A:I.201 Hydrogen bonds: A:D.144, A:D.202

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: S.277, Q.280, R.284 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.280, A:R.284 Water bridges: A:Q.280 GOL.3: 2 residues within 4Å: Chain A: E.197, P.312 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.197

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

ACT.4: 3 residues within 4Å: Chain A: H.235, R.237, S.238 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.237, A:S.238 Water bridges: A:G.236 Salt bridges: A:R.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schneider, P. et al., Virtual Screening and Design with Machine Intelligence Applied to Pim-1 Kinase Inhibitors. Mol Inform (2020)

Release Date

2020-07-01

Peptides

Serine/threonine-protein kinase pim-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Serine/threonine-protein kinase pim-1