SMTL ID : 8b0b.1

Crystal structure of human heparanase in complex with covalent inhibitor VB151

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: T.36, A.37, N.42, S.44 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.36 Hydrogen bonds: A:A.37, A:S.44 NAG.2: 5 residues within 4Å: Chain A: L.39, F.78, N.80, S.82, Q.83 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.80 NAG.3: 2 residues within 4Å: Chain A: N.301, V.302 No protein-ligand interaction detected (PLIP)

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

EDO.4: 5 residues within 4Å: Chain A: L.213, L.273, R.274, V.275, Y.276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.275, A:V.275

1 x OUU: (1~{S},2~{R},3~{R},4~{S},6~{S})-2-(2-acetamidoethoxy)-3,4,6-tris(oxidanyl)cyclohexane-1-carboxylic acid(Covalent)

OUU.5: 19 residues within 4Å: Chain A: N.66, E.67, H.138, Y.140, E.185, Y.190, G.191, G.192, Q.225, V.226, G.229, A.230, G.231, Y.233 Chain B: D.27, N.29, R.58, G.61, T.62 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:E.185, A:A.230 Hydrogen bonds: A:N.66, A:Y.140, A:G.191, A:G.192, A:Q.225, A:A.230, A:G.231, A:Y.233, B:D.27, B:T.62 Water bridges: B:D.27, B:N.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borlandelli, V. et al., 4-O-Substituted Glucuronic Cyclophellitols are Selective Mechanism-Based Heparanase Inhibitors. Chemmedchem (2023)

Release Date

2022-12-28

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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