SMTL ID : 8d0h.1

Human SARM1 TIR domain bound to NB-3-GDPR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

homo-dimer

Ligands

2 x Q1O: [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-[4-[(1~{S})-1-[methyl-[2,2,2-tris(fluoranyl)ethylcarbamoyl]amino]ethyl]pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

Q1O.1: 12 residues within 4Å: Chain A: S.10, Y.11, R.12, R.13, D.37, V.38, L.41, F.46, L.50, K.71, W.81, E.85 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.46 Hydrogen bonds: A:Y.11, A:R.13, A:R.13, A:R.13, A:D.37 Water bridges: A:W.81 Salt bridges: A:R.12, A:R.13, A:K.71, A:K.71 pi-Cation interactions: A:R.13 Halogen bonds: A:L.41 Q1O.2: 13 residues within 4Å: Chain A: E.129 Chain B: S.10, Y.11, R.12, R.13, D.37, V.38, L.41, F.46, L.50, W.81, V.82, E.85 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.46, B:L.50 Hydrogen bonds: B:Y.11, B:R.13, B:R.13, B:R.13 Water bridges: B:I.9, B:D.37 Salt bridges: B:R.12, A:E.129 pi-Cation interactions: B:R.13 Halogen bonds: B:L.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bratkowski, M. et al., Uncompetitive, adduct-forming SARM1 inhibitors are neuroprotective in preclinical models of nerve injury and disease. Neuron (2022)

Release Date

2022-09-21

Peptides

NAD(+) hydrolase SARM1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NAD(+) hydrolase SARM1

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