SMTL ID : 8jyg.1

Crystal structure of Human HPSE1 in complex with inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

1 x V8R: (5~{S},6~{R},7~{S},8~{S})-6,7,8-tris(oxidanyl)-2-[2-(3-phenoxyphenyl)ethyl]-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-5-carboxylic acid(Non-covalent)

V8R.1: 16 residues within 4Å: Chain A: N.67, E.68, Q.113, R.115, Y.141, Y.142, E.186, Y.191, G.192, G.193, Q.226, Y.234 Chain B: D.29, G.63, T.64 Ligands: EDO.23 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Q.113, A:Y.141, A:Y.191 Hydrogen bonds: A:N.67, A:E.68, A:G.192, A:G.193, A:Q.226, A:Y.234, A:Y.234, A:Y.234, B:D.29, B:T.64 Water bridges: B:K.65

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

EDO.2: 4 residues within 4Å: Chain A: K.255, P.352, P.353, L.354 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: F.253, K.254, V.257, G.258, T.259 Ligands: EDO.24 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: L.214, R.272, R.275, V.276, Y.277 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: L.338, L.341, L.343, P.352, P.353, L.354, M.355 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: R.287, Y.288, K.289, R.378 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: K.334, S.335 Ligands: EDO.8, EDO.16 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: L.197, H.329, L.332, S.333, K.334 Ligands: EDO.7 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: F.170, V.173, E.174, P.178, G.179, K.180 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: L.322, N.339, K.357 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: Y.306, K.320, L.322, G.366, P.368 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: Q.113, P.114, R.115, I.161, S.165 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: L.143, T.147, D.152 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: Y.107, D.134, S.135, K.181, W.183, E.221 Ligand excluded by PLIP EDO.15: 11 residues within 4Å: Chain A: L.309, F.313, S.314, N.315, K.316, V.318, R.360, P.361, G.362, S.363, L.365 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: D.238, D.242, P.243, K.334 Ligands: EDO.7 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: E.68, P.69, N.70, S.71, V.111, G.112 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain A: Q.167, Q.171 Ligand excluded by PLIP EDO.21: 2 residues within 4Å: Chain A: N.144, T.147 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: R.177, P.178, K.180 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: G.230, A.231, G.232, Y.234 Chain B: D.29 Ligands: V8R.1 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain A: K.254, V.257, N.282 Chain B: P.21 Ligands: EDO.3 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain A: F.229, G.230, A.231, E.239 Chain B: L.32, D.35 Ligand excluded by PLIP

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

NAG.17: 2 residues within 4Å: Chain A: N.81, Q.84 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.81 NAG.18: 1 residues within 4Å: Chain A: N.302 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Imai, Y. et al., Structure-based lead optimization to improve potency and selectivity of a novel tetrahydroimidazo[1,2-a]pyridine-5-carboxylic acid series of heparanase-1 inhibitor. Bioorg.Med.Chem. (2023)

Release Date

2023-09-20

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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