SMTL ID : 8ohr.1

Crystal structure of human heparanase in complex with glucuronic acid configured 3-geminal diol iminosugar inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x VP5: (3~{S},4~{R})-4,5,5-tris(oxidanyl)piperidine-3-carboxylic acid(Non-covalent)

VP5.1: 12 residues within 4Å: Chain A: N.66, E.67, Y.140, E.185, Y.190, G.191, G.192, Q.225, Y.233 Chain B: D.27, G.61, T.62 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.140, A:Y.140, A:E.185, A:G.191, A:G.192, A:Q.225, A:Y.233, B:D.27, B:T.62, B:T.62 Water bridges: B:K.63

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

EDO.2: 5 residues within 4Å: Chain A: F.252, V.256, G.257, T.258 Chain B: S.18 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.22 EDO.3: 7 residues within 4Å: Chain A: L.337, L.340, L.342, P.351, P.352, L.353, M.354 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.354 Water bridges: A:L.337, A:M.354 EDO.5: 4 residues within 4Å: Chain A: R.149, H.328, L.330, L.331 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.149, A:L.330, A:L.331

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 1 residues within 4Å: Chain A: N.301 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: G.229, A.230 Chain B: L.30 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y. et al., Molecular Basis for Inhibition of Heparanases and beta-Glucuronidases by Siastatin B. J.Am.Chem.Soc. (2024)

Release Date

2024-01-10

Peptides

Heparanase 50 kDa subunit: A
Heparanase 8 kDa subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Heparanase 50 kDa subunit

Heparanase 8 kDa subunit

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