SMTL ID : 6bsk.1

Human PIM1 kinase in complex with compound 12b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

monomer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: R.107, A.109, L.110, Q.111, L.114 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.107, A:R.107, A:Q.111 EDO.2: 4 residues within 4Å: Chain A: R.192, T.251, F.252 Ligands: SO4.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.252 Water bridges: A:P.250, A:T.251, A:T.251 EDO.3: 3 residues within 4Å: Chain A: S.232, Q.235, R.239 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.232, A:R.239, A:R.239 Water bridges: A:V.224 EDO.4: 4 residues within 4Å: Chain A: L.5, V.11, I.37, H.39 No protein-ligand interaction detected (PLIP)

1 x MVG: 4-{6-[6-(propan-2-ylamino)-1H-indazol-1-yl]pyrazin-2-yl}benzoic acid(Non-covalent)

MVG.5: 15 residues within 4Å: Chain A: L.15, F.20, V.23, A.36, K.38, I.75, L.91, E.92, R.93, P.94, V.97, D.99, L.145, I.156, D.157 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.20, A:F.20, A:V.23, A:V.23, A:A.36, A:I.75, A:L.91, A:I.156 Hydrogen bonds: A:D.99, A:D.99, A:D.157 Water bridges: A:K.38, A:F.158 Salt bridges: A:K.38

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

SO4.6: 5 residues within 4Å: Chain A: R.127, N.131, F.252, E.253 Ligands: EDO.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.253 Water bridges: A:R.127, A:R.127, A:F.252, A:F.252 Salt bridges: A:R.127 SO4.7: 3 residues within 4Å: Chain A: D.79, W.80, F.81 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gingipalli, L. et al., Discovery of 2,6-disubstituted pyrazine derivatives as inhibitors of CK2 and PIM kinases. Bioorg. Med. Chem. Lett. (2018)

Release Date

2018-03-21

Peptides

Serine/threonine-protein kinase pim-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Serine/threonine-protein kinase pim-1

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