SMTL ID : 6o0h.1

Cryo-EM structure of human ATP-citrate lyase in complex with inhibitor NDI-091143

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x LBG: methyl 3-chloro-5-[(4,6-difluoro[1,1'-biphenyl]-3-yl)sulfamoyl]-4-hydroxybenzoate(Non-covalent)

LBG.1: 20 residues within 4Å: Chain A: M.278, A.280, Y.307, T.316, I.340, G.341, G.342, S.343, I.344, F.347, N.349, V.350, T.353, F.354, I.357, V.377, R.378, R.379, G.380, P.382 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.307, A:T.316, A:F.354, A:F.354, A:I.357, A:V.377 Hydrogen bonds: A:G.342, A:T.353, A:R.378, A:G.380, A:G.380 pi-Stacking: A:F.347 Halogen bonds: A:P.382 LBG.3: 20 residues within 4Å: Chain B: M.278, A.280, Y.307, T.316, I.340, G.341, G.342, S.343, I.344, F.347, N.349, V.350, T.353, F.354, I.357, V.377, R.378, R.379, G.380, P.382 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.307, B:T.316, B:F.354, B:F.354, B:I.357, B:V.377 Hydrogen bonds: B:G.342, B:T.353, B:R.378, B:G.380, B:G.380 pi-Stacking: B:F.347 Halogen bonds: B:P.382 LBG.5: 20 residues within 4Å: Chain C: M.278, A.280, Y.307, T.316, I.340, G.341, G.342, S.343, I.344, F.347, N.349, V.350, T.353, F.354, I.357, V.377, R.378, R.379, G.380, P.382 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:Y.307, C:T.316, C:F.354, C:F.354, C:I.357, C:V.377 Hydrogen bonds: C:G.342, C:R.378, C:G.380, C:G.380 pi-Stacking: C:F.347 Halogen bonds: C:P.382 LBG.7: 20 residues within 4Å: Chain D: M.278, A.280, Y.307, T.316, I.340, G.341, G.342, S.343, I.344, F.347, N.349, V.350, T.353, F.354, I.357, V.377, R.378, R.379, G.380, P.382 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.307, D:T.316, D:F.354, D:F.354, D:I.357, D:V.377 Hydrogen bonds: D:G.342, D:R.378, D:G.380, D:G.380 pi-Stacking: D:F.347 Halogen bonds: D:P.382

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 14 residues within 4Å: Chain A: V.56, K.58, R.65, R.66, G.67, V.72, P.109, F.110, H.113, V.140, N.203, P.204, L.215, D.216 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.58, A:R.65, A:R.66, A:G.67, A:P.109, A:V.140, A:D.216 Salt bridges: A:R.66 ADP.4: 14 residues within 4Å: Chain B: V.56, K.58, R.65, R.66, G.67, V.72, P.109, F.110, H.113, V.140, N.203, P.204, L.215, D.216 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.58, B:R.65, B:R.66, B:G.67, B:P.109, B:V.140, B:D.216 Salt bridges: B:R.66 ADP.6: 14 residues within 4Å: Chain C: V.56, K.58, R.65, R.66, G.67, V.72, P.109, F.110, H.113, V.140, N.203, P.204, L.215, D.216 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:K.58, C:R.65, C:R.66, C:G.67, C:P.109, C:V.140 Salt bridges: C:R.66 ADP.8: 14 residues within 4Å: Chain D: V.56, K.58, R.65, R.66, G.67, V.72, P.109, F.110, H.113, V.140, N.203, P.204, L.215, D.216 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:K.58, D:R.65, D:R.66, D:G.67, D:P.109, D:V.140 Salt bridges: D:R.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, J. et al., An allosteric mechanism for potent inhibition of human ATP-citrate lyase. Nature (2019)

Release Date

2019-04-17

Peptides

ATP-citrate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

ATP-citrate synthase