SMTL ID : 8bac.1

Crystal structure of human heparanase in complex with competitive inhibitor GD05

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.305 No protein-ligand interaction detected (PLIP) NAG.2: 3 residues within 4Å: Chain A: T.40, N.46, S.48 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.46, A:S.48

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

EDO.3: 4 residues within 4Å: Chain A: R.274, R.278, V.279, Y.280 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.274, A:V.279, A:V.279

1 x SJ5: (3S,4R,5R)-4,5-dihydroxypiperidine-3-carboxylic acid(Non-covalent)

SJ5.4: 11 residues within 4Å: Chain A: E.71, Y.144, E.189, Y.194, G.195, G.196, Q.229, Y.237 Chain B: D.27, G.61, T.62 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:D.27, B:T.62, B:T.62, A:E.189, A:G.195, A:G.196, A:Q.229, A:Y.237, A:Y.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Doherty, G.G. et al., Synthesis of Uronic Acid 1-Azasugars as Putative Inhibitors of alpha-Iduronidase, beta-Glucuronidase and Heparanase. Chembiochem (2023)

Release Date

2023-03-01

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

Related Entries With Identical Sequence