SMTL ID : 8cqi.1

Human heparanase in complex with inhibitor R3794

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: T.40, N.46, S.48 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.48 NAG.2: 3 residues within 4Å: Chain A: D.29, N.63, F.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.63 NAG.3: 4 residues within 4Å: Chain A: L.43, N.84, S.86, Q.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.43, A:N.84 NAG.4: 2 residues within 4Å: Chain A: N.8, L.38 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain A: N.305 Ligands: LYY.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.305

1 x VGO: (3~{S},4~{S})-4,5,5-tris(oxidanyl)piperidine-3-carboxylic acid

VGO.5: 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.30, G.64, T.65 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:Y.144, A:Y.144, A:E.189, A:G.195, A:G.196, B:T.65, B:T.65, B:T.65 Water bridges: B:D.30, B:D.30, B:N.32, B:T.65

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

EDO.6: 5 residues within 4Å: Chain A: G.261, T.262, T.284, N.285, T.286 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.262, A:N.285, A:T.286 Water bridges: A:T.262 EDO.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x LYY: 1,5-anhydro-D-arabinitol

LYY.7: 5 residues within 4Å: Chain A: H.304, N.305, V.306, K.308 Ligands: NAG.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.304, A:K.308

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

CL.10: 4 residues within 4Å: Chain A: G.233, A.234 Chain B: D.30, L.33 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: N.84, G.85, M.124 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: G.115, Q.116, H.142 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: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Heparanase 50 kDa subunit

Heparanase

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