- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.37 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x ZN: ZINC ION(Non-covalent)
- 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)
- 1 x DMF: DIMETHYLFORMAMIDE(Non-covalent)
- 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
FB
HC
ID
JE
BF
E
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.37 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x ZN: ZINC ION(Non-covalent)
- 6 x 01: N-(1H-benzo[d]imidazol-5-yl)-1-phenylmethanesulfonamide
- 2 x GOL: GLYCEROL(Non-functional Binders)
- 2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 1 x DMF: DIMETHYLFORMAMIDE(Non-covalent)
- 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
FB
HC
ID
JE
BF
E