SMTL ID : 8uct.1

Crystal structure of TcPINK1 in complex with PRT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.93 Å

Oligo State

homo-dimer

Ligands

2 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.1: 6 residues within 4Å: Chain A: K.26, P.130, H.212, H.216, C.433, R.434 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.26, A:H.212 Water bridges: A:H.212 DTT.5: 6 residues within 4Å: Chain B: K.26, P.130, H.212, H.216, C.433, R.434 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.26, B:H.212 Water bridges: B:H.212

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

SO4.2: 6 residues within 4Å: Chain A: Y.29, Y.30, D.33, R.107, A.137, F.139 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.29, A:D.33 Salt bridges: A:R.107 SO4.3: 7 residues within 4Å: Chain A: G.56, T.57, N.58, K.224 Chain B: Q.89, S.90, N.91 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.58, B:S.90, B:S.90 Salt bridges: A:K.224 SO4.6: 6 residues within 4Å: Chain B: Y.29, Y.30, D.33, R.107, A.137, F.139 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.33 Salt bridges: B:R.107 SO4.7: 7 residues within 4Å: Chain A: Q.89, S.90, N.91 Chain B: G.56, T.57, N.58, K.224 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.90, A:S.90, B:N.58 Salt bridges: B:K.224

2 x 3YT: 2-{[(1R,2S)-2-aminocyclohexyl]amino}-4-{[3-(2H-1,2,3-triazol-2-yl)phenyl]amino}pyrimidine-5-carboxamide(Non-covalent)

3YT.4: 18 residues within 4Å: Chain A: I.53, A.54, K.55, V.61, A.79, K.81, M.179, K.180, R.181, Y.182, D.183, C.184, N.185, D.226, N.227, L.229, S.243, D.244 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.54, A:L.229, A:L.229 Hydrogen bonds: A:K.180, A:Y.182, A:N.227, A:D.244 3YT.8: 18 residues within 4Å: Chain B: I.53, A.54, K.55, V.61, A.79, K.81, M.179, K.180, R.181, Y.182, D.183, C.184, N.185, D.226, N.227, L.229, S.243, D.244 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.54, B:L.229, B:L.229 Hydrogen bonds: B:K.180, B:Y.182, B:N.227, B:D.244

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shomali, T. et al., Characterization of a new family of PINK1 inhibitors. To Be Published

Release Date

2024-05-08

Peptides

Serine/threonine-protein kinase Pink1, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Serine/threonine-protein kinase Pink1, mitochondrial