- 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)
- 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 PLIPEDO.3: 6 residues within 4Å:- Chain A: F.253, K.254, V.257, G.258, T.259
- Ligands: EDO.24
Ligand excluded by PLIPEDO.4: 5 residues within 4Å:- Chain A: L.214, R.272, R.275, V.276, Y.277
Ligand excluded by PLIPEDO.5: 7 residues within 4Å:- Chain A: L.338, L.341, L.343, P.352, P.353, L.354, M.355
Ligand excluded by PLIPEDO.6: 4 residues within 4Å:- Chain A: R.287, Y.288, K.289, R.378
Ligand excluded by PLIPEDO.7: 4 residues within 4Å:- Chain A: K.334, S.335
- Ligands: EDO.8, EDO.16
Ligand excluded by PLIPEDO.8: 6 residues within 4Å:- Chain A: L.197, H.329, L.332, S.333, K.334
- Ligands: EDO.7
Ligand excluded by PLIPEDO.9: 6 residues within 4Å:- Chain A: F.170, V.173, E.174, P.178, G.179, K.180
Ligand excluded by PLIPEDO.10: 3 residues within 4Å:- Chain A: L.322, N.339, K.357
Ligand excluded by PLIPEDO.11: 5 residues within 4Å:- Chain A: Y.306, K.320, L.322, G.366, P.368
Ligand excluded by PLIPEDO.12: 5 residues within 4Å:- Chain A: Q.113, P.114, R.115, I.161, S.165
Ligand excluded by PLIPEDO.13: 3 residues within 4Å:- Chain A: L.143, T.147, D.152
Ligand excluded by PLIPEDO.14: 6 residues within 4Å:- Chain A: Y.107, D.134, S.135, K.181, W.183, E.221
Ligand excluded by PLIPEDO.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 PLIPEDO.16: 5 residues within 4Å:- Chain A: D.238, D.242, P.243, K.334
- Ligands: EDO.7
Ligand excluded by PLIPEDO.19: 6 residues within 4Å:- Chain A: E.68, P.69, N.70, S.71, V.111, G.112
Ligand excluded by PLIPEDO.20: 2 residues within 4Å:- Chain A: Q.167, Q.171
Ligand excluded by PLIPEDO.21: 2 residues within 4Å:- Chain A: N.144, T.147
Ligand excluded by PLIPEDO.22: 3 residues within 4Å:- Chain A: R.177, P.178, K.180
Ligand excluded by PLIPEDO.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 PLIPEDO.24: 5 residues within 4Å:- Chain A: K.254, V.257, N.282
- Chain B: P.21
- Ligands: EDO.3
Ligand excluded by PLIPEDO.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)
- 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
AB
B
- 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)
- 22 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 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
AB
B