SMTL ID : 8xbk.1

Crystal Structure of Human Liver Fructose-1,6-bisphosphatase Complexed with a Covalent Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

homo-tetramer

Ligands

4 x YR9: N-[2-[4-[(3-bromophenyl)carbamoylsulfamoyl]phenyl]ethyl]ethanamide(Covalent)(Non-covalent)

YR9.1: 17 residues within 4Å: Chain A: M.19, E.21, G.22, R.23, A.25, G.27, T.28, G.29, E.30, L.31, T.32, M.178, C.180 Chain C: T.28 Ligands: EDO.4, EDO.7, YR9.18 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:R.23, A:A.25, A:M.178 Hydrogen bonds: A:E.21, A:E.21, A:G.27, A:G.27, A:G.27, A:T.28, A:G.29, A:L.31, A:T.32, A:T.32 Water bridges: A:E.30 YR9.9: 18 residues within 4Å: Chain B: V.18, M.19, E.21, G.22, R.23, A.25, G.27, T.28, G.29, E.30, L.31, T.32, M.178, C.180 Chain D: M.19, T.28, G.29 Ligands: YR9.21 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:E.21, B:R.23, B:A.25, B:M.178 Hydrogen bonds: B:E.21, B:G.27, B:G.27, B:T.28, B:G.29, B:L.31, B:T.32, B:T.32 Water bridges: B:E.30, B:Y.114 YR9.18: 15 residues within 4Å: Chain A: G.29 Chain C: V.18, M.19, E.21, G.22, R.23, G.27, T.28, G.29, E.30, L.31, T.32, M.178, C.180 Ligands: YR9.1 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:V.18, C:R.23, C:M.178 Hydrogen bonds: C:E.21, C:E.21, C:G.22, C:G.22, C:G.27, C:T.28, C:G.29, C:L.31, C:T.32, C:T.32 Water bridges: C:Y.114 YR9.21: 16 residues within 4Å: Chain B: T.28 Chain D: V.18, M.19, E.21, G.22, R.23, A.25, G.27, T.28, G.29, E.30, L.31, T.32, M.178, C.180 Ligands: YR9.9 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:V.18, D:E.21, D:R.23, D:R.23, D:A.25, D:M.178 Hydrogen bonds: D:G.27, D:T.28, D:G.29, D:L.31, D:T.32, D:T.32, D:T.32 Water bridges: D:E.30, D:E.30

18 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: N.213, G.215, Y.216 Chain B: P.240, G.242 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: R.141, K.143, N.159, V.161 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: F.17, C.180, N.183, K.199, D.200 Ligands: YR9.1 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: T.297, G.299, K.300, E.301, A.302, L.329 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: P.234, P.235, D.236 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: F.17, L.176, M.178, C.180, G.181, N.183 Ligands: YR9.1 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: L.196, V.197, K.199 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain B: T.297, K.300, E.301, A.302, L.329 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: Y.241, G.242 Chain B: N.213, G.215, Y.216 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain B: F.17, C.180, G.181, V.182, N.183, D.200 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain B: E.98, D.100, K.101, R.277, H.312 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain B: D.75, E.98, E.99 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: L.196, V.197, D.198, K.199 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain B: T.28, E.30 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain C: T.297, K.300, E.301, A.302, L.329 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain C: P.240, Y.241, G.242 Chain D: N.213, G.215, Y.216 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain D: D.80, M.83, N.84 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain C: Y.58 Chain D: L.196, V.197, D.198, K.199 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-covalent)

MG.17: 4 residues within 4Å: Chain B: E.98, D.119, D.122, E.281 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.119, B:D.122, B:E.281, H2O.8 MG.20: 4 residues within 4Å: Chain C: E.98, D.119, D.122, E.281 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.98, C:E.98, C:D.119, C:D.122, C:E.281 MG.25: 4 residues within 4Å: Chain D: E.98, D.119, D.122, E.281 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.119, D:E.281

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, H. et al., Structure-Guided Design of Affinity/Covalent-Bond Dual-Driven Inhibitors Targeting the AMP Site of FBPase. J.Med.Chem. (2024)

Release Date

2024-11-20

Peptides

Fructose-1,6-bisphosphatase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Fructose-1,6-bisphosphatase 1

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