SMTL ID : 6enx.1

Zebrafish Sirt5 in complex with stalled bicyclic intermediate of inhibitory compound 10

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.135, C.138, C.176, C.181 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.135, A:C.138, A:C.176, A:C.181

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 6 residues within 4Å: Chain A: S.221, Y.224, A.227, P.249, A.250, R.253 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.224

1 x BJW: 4-[(2~{R},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2-[[(5~{S})-6-[[(2~{S})-3-(1~{H}-indol-3-yl)-1-oxidanylidene-1-(propan-2-ylamino)propan-2-yl]amino]-6-oxidanylidene-5-(phenylmethoxycarbonylamino)hexyl]amino]-6-oxidanyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]butanoic acid(Non-covalent)

BJW.3: 31 residues within 4Å: Chain A: G.27, A.28, G.29, T.38, F.39, R.40, W.46, Y.71, R.74, Q.109, I.111, H.127, V.189, V.190, W.191, F.192, G.193, E.194, T.195, G.218, T.219, S.220, I.222, V.223, Y.224, N.244, M.245, E.246, G.260, P.261, C.262 34 PLIP interactions: 34 interactions with chain A Hydrophobic interactions: A:V.189, A:V.190, A:T.195, A:I.222, A:V.223, A:V.223 Hydrogen bonds: A:A.28, A:G.29, A:F.39, A:R.40, A:R.40, A:R.40, A:Y.71, A:Y.71, A:Q.109, A:H.127, A:V.190, A:G.193, A:E.194, A:T.219, A:S.220, A:S.220, A:Y.224, A:Y.224, A:N.244, A:M.245, A:E.246, A:C.262 Water bridges: A:G.29, A:E.33, A:G.263 Salt bridges: A:R.40, A:R.40, A:R.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rajabi, N. et al., Mechanism-Based Inhibitors of the Human Sirtuin 5 Deacylase: Structure-Activity Relationship, Biostructural, and Kinetic Insight. Angew. Chem. Int. Ed. Engl. (2017)

Release Date

2017-11-01

Peptides

NAD-dependent protein deacylase sirtuin-5, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NAD-dependent protein deacylase sirtuin-5, mitochondrial