SMTL ID : 9isd.1 (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 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.159, A:E.202, 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 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.159, B:D.159, B:E.202, B:E.202, B:H.330 ZN.7: 6 residues within 4Å: Chain C: D.159, E.202, L.249, W.329, H.330 Ligands: 01.8 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.159, C:E.202, C:E.202, C:H.330 ZN.11: 6 residues within 4Å: Chain D: D.159, E.202, L.249, W.329, H.330 Ligands: 01.12 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.159, D:E.202, D:E.202, D:H.330 ZN.13: 6 residues within 4Å: Chain E: D.159, E.202, L.249, W.329, H.330 Ligands: 01.14 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.159, E:D.159, E:E.202, E:E.202, E:H.330 ZN.15: 6 residues within 4Å: Chain F: D.159, E.202, L.249, W.329, H.330 Ligands: 01.16 4 PLIP interactions: 4 interactions with chain F Metal complexes: 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: 20 residues within 4Å: Chain A: 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 B: P.262, N.263, L.311, G.314 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 D: 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.329 Hydrogen bonds: B:D.248, B:Q.304, B:Q.304, B:W.329 Water bridges: B:I.303 01.8: 19 residues within 4Å: Chain C: 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 E: N.263, L.311, G.314 Ligands: ZN.7 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:W.207, C:W.207, C:W.329 Hydrogen bonds: C:D.248, C:Q.304, C:Q.304, C:W.329, E:N.263 pi-Stacking: C:W.207 01.12: 20 residues within 4Å: Chain A: P.262, N.263, L.311, G.314 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 Ligands: ZN.11 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:W.207, D:W.329, A:L.311 Hydrogen bonds: D:D.248, D:Q.304, D:Q.304, D:W.329 01.14: 19 residues within 4Å: Chain E: 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.13 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:W.207, E:W.207, E:W.329 Hydrogen bonds: E:D.248, E:Q.304, E:Q.304 01.16: 19 residues within 4Å: Chain C: P.262, N.263, L.311, G.314 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 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:W.207, F:W.207, F:Q.304, F:W.329 Hydrogen bonds: F:D.248, F:Q.304, F:Q.304, F:W.329 pi-Stacking: F:W.207

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: Y.78, Y.115, R.118, Y.145, F.204 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.118, A:R.118, A:Y.145

1 x DMF: DIMETHYLFORMAMIDE(Non-covalent)

DMF.6: 5 residues within 4Å: Chain B: Y.78, Y.115, R.118, Y.145, F.204 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.118

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

DMS.9: 6 residues within 4Å: Chain C: H.279, G.282, L.284, K.285, D.286, H.287 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.284

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

PEG.10: 8 residues within 4Å: Chain C: E.105, D.107, I.124, Q.194, L.219, K.222, M.223, Q.237 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.105, C:Q.194, C:K.222 Water bridges: C:Q.237, C:Q.237

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
C

C
D

D
G

E
K

F
L

Glutaminyl-peptide cyclotransferase

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