SMTL ID : 7prt.1

Crystal structure of human heparanase in complex with covalent inhibitor CB678

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 5 residues within 4Å: Chain A: K.273, H.304, N.305, V.306, K.308 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.273, A:H.304, A:K.308, A:K.308 Water bridges: A:H.304

1 x 8I4- Z61: 2-deoxy-alpha-D-arabino-hexopyranose-(1-4)-(2R,3S,5R,6R)-2,3,4,5,6-pentakis(oxidanyl)cyclohexane-1-carboxylic acid(Post Translational Modification)

8I4-Z61.2: 13 residues within 4Å: Chain A: N.70, E.71, Y.144, E.189, Y.194, G.195, G.196, Q.229, G.235, Y.237 Chain B: D.27, G.61, T.62 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:E.189 Hydrogen bonds: A:N.70, A:G.195, A:G.196, A:Q.229, A:Y.237, B:T.62, B:T.62, B:T.62, A:G.235 Water bridges: B:K.63, A:A.234

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

NAG.3: 2 residues within 4Å: Chain A: F.6, N.8 No protein-ligand interaction detected (PLIP) NAG.4: 3 residues within 4Å: Chain A: T.40, N.46, S.48 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.40 Hydrogen bonds: A:S.48 NAG.5: 3 residues within 4Å: Chain A: D.29, N.63, F.104 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.104 Hydrogen bonds: A:D.29 NAG.6: 2 residues within 4Å: Chain A: N.84, Q.87 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.84 Water bridges: A:N.84, A:S.86

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

EDO.7: 6 residues within 4Å: Chain A: F.256, V.260, G.261, T.262 Chain B: V.17, S.18 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.22 EDO.8: 4 residues within 4Å: Chain A: R.153, H.332, L.334, L.335 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.153, A:L.334, A:L.335 EDO.9: 3 residues within 4Å: Chain A: R.278, V.279, Y.280 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.279, A:V.279

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

CL.10: 3 residues within 4Å: Chain A: G.233, A.234 Chain B: L.30 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: N.84, G.85, M.124, S.127 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Boer, C. et al., Mechanism-based heparanase inhibitors reduce cancer metastasis in vivo. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-08-03

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Heparanase 50 kDa subunit

Heparanase 8 kDa subunit

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