SMTL ID : 7pr7.1

Crystal structure of human heparanase in complex with covalent inhibitor VL166

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 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.272, H.300, N.301, V.302, K.304 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.272, A:H.300, A:K.304, A:K.272, A:N.301 Water bridges: A:N.301

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

8I4-NDG.2: 22 residues within 4Å: Chain A: F.2, 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.60, G.61, T.62, K.63 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:E.185, A:V.226, A:Y.233, B:D.27 Hydrogen bonds: A:N.66, A:N.66, A:Y.140, A:G.191, A:G.192, A:Q.225, A:Y.233, B:R.58, B:T.62, A:Q.225, A:A.230, A:Y.233, A:Y.233, B:N.29, B:T.62 Water bridges: B:N.29, A:G.191, A:G.191

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

NAG.3: 7 residues within 4Å: Chain A: F.2, K.3, N.4, L.34 Chain B: F.66, I.68 Ligands: NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.4 NAG.4: 5 residues within 4Å: Chain A: T.36, A.37, N.42, S.44 Ligands: NAG.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.36 Hydrogen bonds: A:N.42, A:S.44 NAG.5: 5 residues within 4Å: Chain A: D.38, L.39, N.80, S.82, Q.83 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.80

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

EDO.6: 9 residues within 4Å: Chain A: F.252, K.253, V.256, G.257, T.258 Chain B: V.17, S.18, P.19, F.21 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:V.256, A:N.281, B:L.22 EDO.7: 5 residues within 4Å: Chain A: R.149, H.328, G.329, L.330, L.331 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.149, A:R.149, A:L.330, A:L.331 EDO.8: 7 residues within 4Å: Chain A: D.237, D.241, P.242, L.243, P.244, K.333, S.334 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.247 EDO.9: 8 residues within 4Å: Chain A: Y.16, A.19, N.20, L.24, D.25, L.26, N.59, I.60 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.20, A:L.26 Water bridges: A:N.59, A:N.59 EDO.10: 10 residues within 4Å: Chain A: L.50, C.53, S.54, Y.58, I.60, W.62, L.95, S.98, F.100, A.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.98, A:S.98 EDO.11: 8 residues within 4Å: Chain A: T.303, Y.305, K.319, L.321, R.323, G.365, L.366, P.367 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.303, A:K.319 EDO.12: 8 residues within 4Å: Chain A: F.228, G.229, A.230, H.234, E.238 Chain B: L.30, D.33, L.39 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.229 Water bridges: A:G.229, A:H.234

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

CL.13: 6 residues within 4Å: Chain A: F.78, N.80, G.81, K.119, M.120, S.123 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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