SMTL ID : 7wjv.1

Crystal structure of human liver FBPase complexed with an covalent inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-tetramer

Ligands

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 15 residues within 4Å: Chain A: V.18, E.21, G.22, A.25, G.27, T.28, G.29, E.30, L.31, T.32, K.113, Y.114, R.141, V.161, M.178 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:T.28, A:T.28, A:G.29, A:E.30, A:L.31, A:T.32, A:Y.114, A:Y.114 Water bridges: A:G.27, A:T.32, A:T.32 Salt bridges: A:K.113 AMP.5: 15 residues within 4Å: Chain B: V.18, E.21, G.22, A.25, G.27, T.28, G.29, E.30, L.31, T.32, K.113, Y.114, R.141, V.161, M.178 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:T.28, B:T.28, B:G.29, B:E.30, B:L.31, B:T.32, B:Y.114, B:Y.114, B:R.141 Water bridges: B:G.27, B:T.32, B:T.32 Salt bridges: B:K.113 AMP.8: 14 residues within 4Å: Chain C: V.18, E.21, G.22, A.25, G.27, T.28, G.29, E.30, L.31, T.32, K.113, Y.114, V.161, M.178 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:T.28, C:T.28, C:T.28, C:G.29, C:E.30, C:L.31, C:T.32, C:T.32, C:Y.114, C:Y.114, C:R.141 Water bridges: C:T.32, C:T.32, C:K.113 Salt bridges: C:K.113 AMP.10: 15 residues within 4Å: Chain D: V.18, E.21, G.22, A.25, G.27, T.28, G.29, E.30, L.31, T.32, K.113, Y.114, R.141, V.161, M.178 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:T.28, D:T.28, D:G.29, D:E.30, D:L.31, D:T.32, D:T.32, D:Y.114, D:Y.114, D:R.141 Water bridges: D:G.27, D:T.32, D:T.32, D:K.113, D:K.113 Salt bridges: D:K.113

1 x LSA: 1,2-BENZISOTHIAZOL-3(2H)-ONE 1,1-DIOXIDE(Non-covalent)

LSA.2: 10 residues within 4Å: Chain A: K.51, I.54, Y.58, V.71, I.127, D.128, L.130 Chain B: M.186, V.197, D.198 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.197, B:V.197 Hydrogen bonds: A:K.51, A:K.51

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: E.98, E.99, D.119, L.121 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.98, A:D.119, A:L.121, H2O.3, H2O.6 MG.7: 4 residues within 4Å: Chain B: E.98, E.99, D.119, L.121 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.98, B:E.99, B:L.121, H2O.15, H2O.20

1 x PMQ: benzylcarbamic acid(Covalent)

PMQ.4: 9 residues within 4Å: Chain A: H.254, R.255, V.258, Y.259 Chain B: V.71, I.127, D.128, C.129, L.130 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.255, A:V.258, B:L.130 Water bridges: A:S.170 pi-Stacking: A:Y.259

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain B: N.273, T.298, V.306, Q.313, R.314, A.315, P.316 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.273, B:T.298, B:T.298, B:Q.313 Water bridges: B:R.314 GOL.9: 7 residues within 4Å: Chain C: N.273, T.298, V.306, Q.313, R.314, A.315, P.316 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.273, C:T.298, C:T.298, C:Q.313 Water bridges: C:K.300, C:K.300, C:R.314 GOL.11: 8 residues within 4Å: Chain D: N.273, T.298, E.301, V.306, Q.313, R.314, A.315, P.316 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.301, D:Q.313 Water bridges: D:N.273, D:R.314

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wen, W. et al., N -Acylamino Saccharin as an Emerging Cysteine-Directed Covalent Warhead and Its Application in the Identification of Novel FBPase Inhibitors toward Glucose Reduction. J.Med.Chem. (2022)

Release Date

2022-07-13

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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