SMTL ID : 6eo0.1 (3 other biounits)

Zebrafish Sirt5 in complex with stalled peptidylimidate and bicyclic intermediate of inhibitory compound 29

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.141, C.144, C.182, C.187 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.141, A:C.144, A:C.182, A:C.187

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

EDO.2: 1 residues within 4Å: Chain A: E.265 No protein-ligand interaction detected (PLIP)

1 x BV8: 3-[[(~{Z})-~{C}-[(2~{R},3~{R},4~{S},5~{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]-3,4-bis(oxidanyl)oxolan-2-yl]sulfanyl-~{N}-[(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]carbonimidoyl]amino]propanoic acid(Non-covalent)

BV8.3: 33 residues within 4Å: Chain A: G.33, A.34, G.35, A.38, E.39, T.44, F.45, R.46, A.61, Y.77, R.80, Q.115, I.117, H.133, V.196, W.197, F.198, G.199, E.200, T.201, L.202, G.224, T.225, S.226, I.228, V.229, Y.230, N.250, M.251, E.252, P.267, C.268 Ligands: BVT.4 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:F.198, A:T.201, A:L.202, A:V.229 Hydrogen bonds: A:A.34, A:G.35, A:E.39, A:E.39, A:F.45, A:Y.77, A:Y.77, A:Q.115, A:Q.115, A:H.133, A:G.199, A:E.200, A:T.225, A:S.226, A:S.226, A:Y.230, A:N.250, A:M.251, A:E.252, A:C.268 Salt bridges: A:R.80

1 x BVT: 3-[[(2~{S},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]amino]propanoic acid(Non-covalent)

BVT.4: 33 residues within 4Å: Chain A: G.33, A.34, G.35, A.38, E.39, T.44, F.45, R.46, A.61, Y.77, R.80, Q.115, I.117, H.133, V.195, V.196, F.198, G.199, E.200, T.201, L.202, G.224, T.225, S.226, I.228, V.229, Y.230, N.250, M.251, E.252, P.267, C.268 Ligands: BV8.3 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:V.195, A:V.196, A:F.198, A:T.201, A:L.202, A:V.229 Hydrogen bonds: A:A.34, A:G.35, A:E.39, A:E.39, A:F.45, A:Y.77, A:H.133, A:V.196, A:G.199, A:E.200, A:T.225, A:S.226, A:S.226, A:Y.230, A:Y.230, A:N.250, A:M.251, A:E.252, A:C.268 Salt bridges: A:R.80

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

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