SMTL ID : 8hen.1

Crystal structure of CTSB in complex with 212-148

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: R.44, H.48, N.170, P.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.44 Water bridges: A:I.47, A:H.48 GOL.2: 11 residues within 4Å: Chain A: E.22, R.24, V.38, S.42, E.56, V.57, S.58, A.59, G.94, G.95, L.96 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.22, A:R.24, A:S.42, A:S.42, A:E.56, A:V.57, A:A.59

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

DMS.3: 4 residues within 4Å: Chain A: R.11, D.230, N.231, K.235 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.11, A:R.11 Salt bridges: A:D.230

1 x L4F: 2-[4-[[(2~{S})-1-oxidanylidene-3-phenyl-1-[[(3~{S})-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]amino]propan-2-yl]carbamoyl]piperazin-1-yl]ethyl 4-carbamimidamidobenzoate(Covalent)

L4F.4: 17 residues within 4Å: Chain A: Q.26, G.30, C.32, W.33, D.72, N.75, G.76, G.77, Y.78, P.79, G.124, A.176, M.199, G.201, H.202, W.224, E.248 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.75, A:Y.78, A:A.176, A:M.199 Hydrogen bonds: A:N.75, A:G.77, A:G.77, A:G.124, A:G.201 Water bridges: A:G.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Structure-based discovery of dual pathway inhibitors for SARS-CoV-2 entry. Nat Commun (2023)

Release Date

2023-12-13

Peptides

Cathepsin B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cathepsin B

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