SMTL ID : 9kmb.1

Crystal structure of human glutaminyl cyclase in complex with N-(2-(1H-imidazol-5-yl)ethyl)-4-methoxybenzenesulfonamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.127, E.170, L.217, W.297, H.298 Ligands: 01.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.127, A:E.170, A:H.298 ZN.3: 6 residues within 4Å: Chain B: D.127, E.170, L.217, W.297, H.298 Ligands: 01.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.127, B:E.170, B:H.298 ZN.5: 6 residues within 4Å: Chain C: D.127, E.170, L.217, W.297, H.298 Ligands: 01.6 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.127, C:E.170, C:E.170, C:H.298 ZN.7: 6 residues within 4Å: Chain D: D.127, E.170, L.217, W.297, H.298 Ligands: 01.8 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.127, D:E.170, D:H.298 ZN.9: 6 residues within 4Å: Chain E: D.127, E.170, L.217, W.297, H.298 Ligands: 01.10 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.127, E:E.170, E:H.298 ZN.11: 6 residues within 4Å: Chain F: D.127, E.170, L.217, W.297, H.298 Ligands: 01.12 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.127, F:E.170, F:E.170, F:H.298

6 x 01: ~{N}-[2-(1~{H}-imidazol-5-yl)ethyl]-4-methoxy-benzenesulfonamide

01.2: 18 residues within 4Å: Chain A: H.108, D.127, E.169, E.170, W.175, D.216, L.217, I.271, Q.272, D.273, I.289, F.293, W.297, H.298 Chain C: P.230, N.231, G.282 Ligands: ZN.1 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:W.297 Hydrogen bonds: A:D.216, A:Q.272, A:Q.272, C:N.231 pi-Stacking: A:W.175 01.4: 20 residues within 4Å: Chain A: P.230, N.231, L.279, G.282, V.283 Chain B: H.108, D.127, E.169, E.170, W.175, D.216, L.217, I.271, Q.272, D.273, I.289, F.293, W.297, H.298 Ligands: ZN.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.216, B:Q.272, B:Q.272, B:W.297 pi-Stacking: B:W.175, B:W.175 01.6: 18 residues within 4Å: Chain B: P.230, N.231, L.279, G.282 Chain C: H.108, D.127, E.169, E.170, W.175, D.216, L.217, I.271, Q.272, D.273, F.293, W.297, H.298 Ligands: ZN.5 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.216, C:Q.272, C:Q.272, C:W.297 pi-Stacking: C:W.175, C:W.175 01.8: 18 residues within 4Å: Chain D: H.108, D.127, E.169, E.170, W.175, D.216, L.217, I.271, Q.272, D.273, I.289, F.293, W.297, H.298 Chain F: P.230, N.231, G.282 Ligands: ZN.7 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:W.297 Hydrogen bonds: D:D.216, D:Q.272, D:Q.272, F:N.231 pi-Stacking: D:W.175 01.10: 20 residues within 4Å: Chain D: P.230, N.231, L.279, G.282, V.283 Chain E: H.108, D.127, E.169, E.170, W.175, D.216, L.217, I.271, Q.272, D.273, I.289, F.293, W.297, H.298 Ligands: ZN.9 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:D.216, E:Q.272, E:Q.272, E:W.297 pi-Stacking: E:W.175, E:W.175 01.12: 18 residues within 4Å: Chain E: P.230, N.231, L.279, G.282 Chain F: H.108, D.127, E.169, E.170, W.175, D.216, L.217, I.271, Q.272, D.273, F.293, W.297, H.298 Ligands: ZN.11 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:D.216, F:Q.272, F:Q.272, F:W.297 pi-Stacking: F:W.175, F:W.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, J.W. et al., Deciphering Glutaminyl Cyclase Catalytic Pathways Enables Recognition of Anchor Pharmacophores for Inhibitor Discovery. J.Chem.Inf.Model. (2025)

Release Date

2025-06-25

Peptides

Glutaminyl-peptide cyclotransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Glutaminyl-peptide cyclotransferase

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