SMTL ID : 9isd.2 (1 other biounit)

Crystal structure of human secretory glutaminyl cyclase in complex with the inhibitor N-(1H-benzo[d]imidazol-5-yl)-1-phenylmethanesulfonamide (compound 5)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.159, E.202, L.249, W.329, H.330 Ligands: 01.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.159, A:E.202, A:H.330 ZN.4: 6 residues within 4Å: Chain B: D.159, E.202, L.249, W.329, H.330 Ligands: 01.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.159, B:E.202, B:E.202, B:H.330 ZN.6: 5 residues within 4Å: Chain C: D.159, E.202, W.329, H.330 Ligands: 01.7 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.159, C:E.202, C:E.202, C:H.330 ZN.9: 6 residues within 4Å: Chain D: D.159, E.202, L.249, W.329, H.330 Ligands: 01.10 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.159, D:E.202, D:E.202, D:H.330 ZN.12: 6 residues within 4Å: Chain E: D.159, E.202, L.249, W.329, H.330 Ligands: 01.13 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.159, E:E.202, E:E.202, E:H.330 ZN.15: 5 residues within 4Å: Chain F: D.159, E.202, W.329, H.330 Ligands: 01.16 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.159, F:D.159, F:E.202, F:E.202, F:H.330

6 x 01: N-(1H-benzo[d]imidazol-5-yl)-1-phenylmethanesulfonamide

01.2: 19 residues within 4Å: Chain A: H.140, D.159, E.201, E.202, W.207, D.248, L.249, I.303, Q.304, D.305, I.321, F.325, W.329, H.330 Chain B: N.263, L.311, G.314, V.315 Ligands: ZN.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.207, A:W.207, A:W.207, A:W.329 Hydrogen bonds: A:D.248, A:Q.304, A:Q.304, A:W.329 01.5: 18 residues within 4Å: Chain B: H.140, D.159, E.201, E.202, W.207, D.248, L.249, I.303, Q.304, D.305, I.321, F.325, W.329, H.330 Chain E: N.263, L.311, G.314 Ligands: ZN.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.207, B:W.207, B:W.207, B:W.329 Hydrogen bonds: B:D.248, B:Q.304, B:Q.304, B:W.329 01.7: 19 residues within 4Å: Chain C: H.140, D.159, E.201, E.202, W.207, D.248, L.249, I.303, Q.304, D.305, I.321, F.325, W.329, H.330 Chain D: P.262, N.263, L.311, G.314 Ligands: ZN.6 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.207, C:W.207, C:W.207, C:W.329, D:L.311 Hydrogen bonds: C:D.248, C:Q.304, C:Q.304, C:W.329 pi-Stacking: C:F.325 01.10: 19 residues within 4Å: Chain D: H.140, D.159, S.160, E.201, E.202, W.207, D.248, L.249, I.303, Q.304, D.305, I.321, F.325, W.329, H.330 Chain F: N.263, L.311, G.314 Ligands: ZN.9 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:W.207, D:W.207, D:W.329 Hydrogen bonds: D:D.248, D:Q.304, D:Q.304, D:W.329 Water bridges: F:N.263 01.13: 18 residues within 4Å: Chain A: N.263, L.311, G.314, V.315 Chain E: H.140, D.159, E.201, E.202, W.207, D.248, L.249, I.303, Q.304, D.305, F.325, W.329, H.330 Ligands: ZN.12 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:W.207, E:W.207, E:W.329, A:L.311 Hydrogen bonds: E:D.248, E:Q.304, E:Q.304, E:W.329 Water bridges: A:N.263 01.16: 19 residues within 4Å: Chain C: N.263, L.311, G.314, V.315 Chain F: H.140, D.159, E.201, E.202, W.207, D.248, L.249, I.303, Q.304, D.305, I.321, F.325, W.329, H.330 Ligands: ZN.15 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain C Hydrophobic interactions: F:W.207, F:W.207, F:W.329, C:L.311 Hydrogen bonds: F:D.248, F:Q.304, F:Q.304, F:W.329

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: Y.78, Y.115, R.118, Y.145, F.204 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.118, A:R.118 GOL.8: 8 residues within 4Å: Chain C: S.323, P.324, F.325 Chain D: N.259, F.261, P.262, A.265, S.298 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:F.325, D:S.298, D:S.298

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 8 residues within 4Å: Chain D: Y.78, P.79, G.80, Y.115, R.118, Y.145, F.204 Chain F: S.34 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:P.79, D:R.118, D:R.118 Water bridges: D:Y.115, D:Y.145 PEG.17: 12 residues within 4Å: Chain E: R.233 Chain F: P.79, G.80, S.81, P.82, S.84, Y.85, R.88, S.119, F.120, S.121, D.199 6 PLIP interactions: 1 interactions with chain E, 5 interactions with chain F Hydrogen bonds: E:R.233, F:G.80, F:R.88, F:R.88, F:S.119 Water bridges: F:S.119

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

DMS.14: 6 residues within 4Å: Chain E: I.47, L.48, R.270, A.273, I.274, E.277 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.270, E:R.270 Salt bridges: E:E.277

1 x DMF: DIMETHYLFORMAMIDE(Non-covalent)

DMF.18: 6 residues within 4Å: Chain F: Y.78, P.79, Y.115, R.118, Y.145, F.204 No protein-ligand interaction detected (PLIP)

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
F

B
H

C
I

D
J

E
B

F
E

Glutaminyl-peptide cyclotransferase

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