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

Human Sirt5 in complex with stalled peptidylimidate intermediate of inhibitory compound 29

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.32 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.139, C.142, C.180, C.185 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.139, A:C.142, A:C.180, A:C.185

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)

BV8.2: 35 residues within 4Å: Chain A: G.31, A.32, G.33, A.36, E.37, T.42, F.43, R.44, Q.56, A.59, Y.75, R.78, Q.113, I.115, H.131, V.193, V.194, W.195, F.196, G.197, E.198, N.199, G.222, T.223, S.224, V.226, V.227, Y.228, N.248, T.249, E.250, G.264, P.265, C.266 Ligands: DMS.10 34 PLIP interactions: 34 interactions with chain A Hydrophobic interactions: A:V.193, A:V.194, A:N.199, A:V.227, A:V.227, A:Y.228 Hydrogen bonds: A:A.32, A:E.37, A:E.37, A:F.43, A:R.44, A:Y.75, A:Y.75, A:H.131, A:G.197, A:E.198, A:T.223, A:T.223, A:T.223, A:S.224, A:S.224, A:Y.228, A:Y.228, A:N.248, A:T.249, A:T.249, A:E.250, A:C.266 Water bridges: A:A.36, A:Q.56, A:R.78, A:Q.113, A:E.250 Salt bridges: A:R.78

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

EDO.3: 4 residues within 4Å: Chain A: V.40, P.41, R.78 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.78 EDO.4: 7 residues within 4Å: Chain A: P.41, T.42, F.43, G.47, A.55, R.78 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.78 Water bridges: A:P.41 EDO.5: 5 residues within 4Å: Chain A: H.76, G.159, K.160, A.162 Ligands: EDO.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.76, A:G.159 Water bridges: A:A.162 EDO.6: 7 residues within 4Å: Chain A: H.76, E.80, L.157, S.158, G.159, K.160 Ligands: EDO.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.80, A:L.157, A:G.159, A:K.160 EDO.7: 3 residues within 4Å: Chain A: A.183, G.184, G.186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.184 Water bridges: A:G.186

2 x BU2: 1,3-BUTANEDIOL(Non-covalent)

BU2.8: 8 residues within 4Å: Chain A: C.154, P.155, E.175, K.176, L.177, P.178, R.179, E.181 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.179 Hydrogen bonds: A:L.177, A:R.179, A:E.181, A:E.181 BU2.9: 1 residues within 4Å: Chain A: L.62 No protein-ligand interaction detected (PLIP)

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

DMS.10: 4 residues within 4Å: Chain A: F.43, R.44, V.226 Ligands: BV8.2 No protein-ligand interaction detected (PLIP) DMS.11: 4 residues within 4Å: Chain A: A.95, E.96, T.99, A.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.99

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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