- 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: 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)
- 1 x DMF: DIMETHYLFORMAMIDE(Non-covalent)
- 1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 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
AB
CC
DD
GE
KF
L
- 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
- 1 x GOL: GLYCEROL(Non-functional Binders)
- 1 x DMF: DIMETHYLFORMAMIDE(Non-covalent)
- 1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 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
AB
CC
DD
GE
KF
L