SMTL ID : 6eqs.2 (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: 34 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.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, P.265, C.266 Ligands: BU2.9, BU2.10 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:N.199, A:V.227, A:V.227 Hydrogen bonds: A:A.32, A:G.33, 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:E.37, 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: 3 residues within 4Å: Chain A: V.40, R.78 Ligands: BU2.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.78 EDO.4: 3 residues within 4Å: Chain A: E.80, K.160 Ligands: EDO.6 No protein-ligand interaction detected (PLIP) EDO.5: 3 residues within 4Å: Chain A: Y.49, P.163, E.164 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.49 EDO.6: 9 residues within 4Å: Chain A: H.76, E.80, S.151, P.152, L.157, S.158, G.159, K.160 Ligands: EDO.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.151, A:L.157, A:G.159, A:K.160 Water bridges: A:S.151 EDO.7: 3 residues within 4Å: Chain A: K.18, F.19, K.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.22, A:K.22

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

BU2.8: 9 residues within 4Å: Chain A: P.41, T.42, F.43, G.47, G.48, Y.49, A.55, F.74 Ligands: EDO.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.43, A:A.55 Hydrogen bonds: A:Y.49, A:R.78 BU2.9: 2 residues within 4Å: Chain A: N.199 Ligands: BV8.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.199 BU2.10: 6 residues within 4Å: Chain A: R.44, Q.56, S.224, V.226, V.227 Ligands: BV8.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.226, A:V.227 Hydrogen bonds: A:R.44, A:R.44, A:Q.56, A:S.224

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
B

NAD-dependent protein deacylase sirtuin-5, mitochondrial

Related Entries With Identical Sequence