SMTL ID : 9ivv.1

Crystal structure of human secretory glutaminyl cyclase in complex with the inhibitor 3-((2-(1H-imidazol-5-yl)ethyl)carbamoyl)-4-amino-1,2,5-oxadiazole 2-oxide (compound 13)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.96 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.127, E.170, H.298 Ligands: 01.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.127, A:D.127, A:E.170, A:H.298 ZN.10: 4 residues within 4Å: Chain B: D.127, E.170, H.298 Ligands: 01.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.127, B:D.127, B:E.170, B:H.298 ZN.19: 4 residues within 4Å: Chain C: D.127, E.170, H.298 Ligands: 01.20 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.127, C:D.127, C:E.170, C:H.298 ZN.28: 4 residues within 4Å: Chain D: D.127, E.170, H.298 Ligands: 01.29 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.127, D:D.127, D:E.170, D:H.298 ZN.37: 4 residues within 4Å: Chain E: D.127, E.170, H.298 Ligands: 01.38 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.127, E:D.127, E:E.170, E:H.298 ZN.46: 4 residues within 4Å: Chain F: D.127, E.170, H.298 Ligands: 01.47 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.127, F:D.127, F:E.170, F:H.298

6 x 01: 4-azanyl-~{N}-[2-(1~{H}-imidazol-4-yl)ethyl]-2-oxidanidyl-1,2,5-oxadiazol-2-ium-3-carboxamide

01.2: 12 residues within 4Å: Chain A: D.127, E.169, E.170, W.175, D.216, L.217, Q.272, W.297, H.298 Chain C: P.230, N.231 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:N.231, A:E.169 Water bridges: A:E.170 pi-Stacking: A:W.175, A:W.297 pi-Cation interactions: A:W.175 01.11: 12 residues within 4Å: Chain B: D.127, E.169, E.170, W.175, D.216, L.217, Q.272, W.297, H.298 Chain F: P.230, N.231 Ligands: ZN.10 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:E.169, F:N.231 Water bridges: B:E.170 pi-Stacking: B:W.175, B:W.297 pi-Cation interactions: B:W.175 01.20: 12 residues within 4Å: Chain C: D.127, E.169, E.170, W.175, D.216, L.217, Q.272, W.297, H.298 Chain E: P.230, N.231 Ligands: ZN.19 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:E.169, E:N.231 Water bridges: C:E.170 pi-Stacking: C:W.175, C:W.297 pi-Cation interactions: C:W.175 01.29: 12 residues within 4Å: Chain B: P.230, N.231 Chain D: D.127, E.169, E.170, W.175, D.216, L.217, Q.272, W.297, H.298 Ligands: ZN.28 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:E.169, B:N.231 Water bridges: D:E.170 pi-Stacking: D:W.175, D:W.297 pi-Cation interactions: D:W.175 01.38: 12 residues within 4Å: Chain A: P.230, N.231 Chain E: D.127, E.169, E.170, W.175, D.216, L.217, Q.272, W.297, H.298 Ligands: ZN.37 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:E.169, A:N.231 Water bridges: E:E.170 pi-Stacking: E:W.175, E:W.297 pi-Cation interactions: E:W.175 01.47: 12 residues within 4Å: Chain D: P.230, N.231 Chain F: D.127, E.169, E.170, W.175, D.216, L.217, Q.272, W.297, H.298 Ligands: ZN.46 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain F Hydrogen bonds: D:N.231, F:E.169 Water bridges: F:E.170 pi-Stacking: F:W.175, F:W.297 pi-Cation interactions: F:W.175

12 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 4 residues within 4Å: Chain A: Y.46, R.86, Y.113, F.172 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.86 pi-Cation interactions: A:Y.113 DMS.4: 4 residues within 4Å: Chain A: H.247, G.250, L.251, L.252 No protein-ligand interaction detected (PLIP) DMS.12: 4 residues within 4Å: Chain B: Y.46, R.86, Y.113, F.172 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.86 pi-Cation interactions: B:Y.113 DMS.13: 4 residues within 4Å: Chain B: H.247, G.250, L.251, L.252 No protein-ligand interaction detected (PLIP) DMS.21: 4 residues within 4Å: Chain C: Y.46, R.86, Y.113, F.172 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.86 pi-Cation interactions: C:Y.113 DMS.22: 4 residues within 4Å: Chain C: H.247, G.250, L.251, L.252 No protein-ligand interaction detected (PLIP) DMS.30: 4 residues within 4Å: Chain D: Y.46, R.86, Y.113, F.172 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.86 pi-Cation interactions: D:Y.113 DMS.31: 4 residues within 4Å: Chain D: H.247, G.250, L.251, L.252 No protein-ligand interaction detected (PLIP) DMS.39: 4 residues within 4Å: Chain E: Y.46, R.86, Y.113, F.172 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.86 pi-Cation interactions: E:Y.113 DMS.40: 4 residues within 4Å: Chain E: H.247, G.250, L.251, L.252 No protein-ligand interaction detected (PLIP) DMS.48: 4 residues within 4Å: Chain F: Y.46, R.86, Y.113, F.172 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.86 pi-Cation interactions: F:Y.113 DMS.49: 4 residues within 4Å: Chain F: H.247, G.250, L.251, L.252 No protein-ligand interaction detected (PLIP)

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: N.9, N.231, R.234 Chain E: W.297, H.298 Ligand excluded by PLIP GOL.6: 2 residues within 4Å: Chain A: S.31, E.309 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain A: P.221, E.305, L.307, D.308 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: D.75, T.76, H.186, K.190 Chain B: K.190, S.193, T.194 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain B: N.9, N.231, R.234 Chain D: W.297, H.298 Ligand excluded by PLIP GOL.15: 2 residues within 4Å: Chain B: S.31, E.309 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain B: P.221, E.305, L.307, D.308 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain A: K.190, S.193, T.194 Chain B: D.75, T.76, H.186, K.190 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain A: W.297, H.298 Chain C: N.9, N.231, R.234 Ligand excluded by PLIP GOL.24: 2 residues within 4Å: Chain C: S.31, E.309 Ligand excluded by PLIP GOL.25: 4 residues within 4Å: Chain C: P.221, E.305, L.307, D.308 Ligand excluded by PLIP GOL.26: 7 residues within 4Å: Chain C: D.75, T.76, H.186, K.190 Chain D: K.190, S.193, T.194 Ligand excluded by PLIP GOL.32: 5 residues within 4Å: Chain D: N.9, N.231, R.234 Chain F: W.297, H.298 Ligand excluded by PLIP GOL.33: 2 residues within 4Å: Chain D: S.31, E.309 Ligand excluded by PLIP GOL.34: 4 residues within 4Å: Chain D: P.221, E.305, L.307, D.308 Ligand excluded by PLIP GOL.35: 7 residues within 4Å: Chain C: K.190, S.193, T.194 Chain D: D.75, T.76, H.186, K.190 Ligand excluded by PLIP GOL.41: 5 residues within 4Å: Chain C: W.297, H.298 Chain E: N.9, N.231, R.234 Ligand excluded by PLIP GOL.42: 2 residues within 4Å: Chain E: S.31, E.309 Ligand excluded by PLIP GOL.43: 4 residues within 4Å: Chain E: P.221, E.305, L.307, D.308 Ligand excluded by PLIP GOL.44: 7 residues within 4Å: Chain E: D.75, T.76, H.186, K.190 Chain F: K.190, S.193, T.194 Ligand excluded by PLIP GOL.50: 5 residues within 4Å: Chain B: W.297, H.298 Chain F: N.9, N.231, R.234 Ligand excluded by PLIP GOL.51: 2 residues within 4Å: Chain F: S.31, E.309 Ligand excluded by PLIP GOL.52: 4 residues within 4Å: Chain F: P.221, E.305, L.307, D.308 Ligand excluded by PLIP GOL.53: 7 residues within 4Å: Chain E: K.190, S.193, T.194 Chain F: D.75, T.76, H.186, K.190 Ligand excluded by PLIP

6 x DMF: DIMETHYLFORMAMIDE(Non-covalent)

DMF.9: 6 residues within 4Å: Chain A: P.221, N.222, D.254, Y.261, D.308, T.311 No protein-ligand interaction detected (PLIP) DMF.18: 6 residues within 4Å: Chain B: P.221, N.222, D.254, Y.261, D.308, T.311 No protein-ligand interaction detected (PLIP) DMF.27: 6 residues within 4Å: Chain C: P.221, N.222, D.254, Y.261, D.308, T.311 No protein-ligand interaction detected (PLIP) DMF.36: 6 residues within 4Å: Chain D: P.221, N.222, D.254, Y.261, D.308, T.311 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.261 DMF.45: 6 residues within 4Å: Chain E: P.221, N.222, D.254, Y.261, D.308, T.311 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.261 DMF.54: 6 residues within 4Å: Chain F: P.221, N.222, D.254, Y.261, D.308, T.311 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, G.-B. et al., Knowledge-Guided Diffusion Model for 3D Ligand-Pharmacophore Mapping. Nat Commun (2025)

Release Date

2025-03-12

Peptides

Glutaminyl-peptide cyclotransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Glutaminyl-peptide cyclotransferase

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