SMTL ID : 9g0v.1 (1 other biounit)

Human LTC4 synthase in complex with compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.78 Å

Oligo State

homo-trimer

Ligands

6 x PLM: PALMITIC ACID(Non-covalent)

PLM.1: 7 residues within 4Å: Chain A: A.72, W.75, I.79 Chain C: L.71, W.75 Ligands: PLM.6, PLM.11 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.71, C:W.75, C:W.75, A:W.75, A:I.79 PLM.3: 4 residues within 4Å: Chain A: L.21, L.24, Y.28 Ligands: 01.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.21, A:L.24, A:Y.28, A:Y.28 PLM.6: 7 residues within 4Å: Chain A: L.71, W.75 Chain B: A.72, W.75, I.79 Ligands: PLM.1, PLM.11 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.71, A:W.75, A:W.75, B:W.75, B:I.79 PLM.8: 4 residues within 4Å: Chain B: L.21, L.24, Y.28 Ligands: 01.15 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.21, B:L.24, B:Y.28, B:Y.28 PLM.11: 7 residues within 4Å: Chain B: L.71, W.75 Chain C: A.72, W.75, I.79 Ligands: PLM.1, PLM.6 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:W.75, C:I.79, B:L.71, B:W.75, B:W.75 PLM.13: 4 residues within 4Å: Chain C: L.21, L.24, Y.28 Ligands: 01.5 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.21, C:L.24, C:Y.28, C:Y.28

3 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-functional Binders)

LMT.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) LMT.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) LMT.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

3 x VDW: [(2~{S})-5-[[(2~{R})-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-3-sulfanyl-propan-2-yl]amino]-1-oxidanyl-1,5-bis(oxidanylidene)pentan-2-yl]azanium(Non-covalent)

VDW.4: 16 residues within 4Å: Chain A: R.58, N.62, E.65, Y.66, Y.100, Y.104, R.111, L.115 Chain C: S.30, V.33, I.34, R.37, P.44, P.45, Q.60 Ligands: 01.5 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Y.66 Hydrogen bonds: A:N.62, A:N.62, A:N.62, A:N.62, A:R.111, C:Q.60 Salt bridges: A:R.58, C:R.37 VDW.9: 16 residues within 4Å: Chain A: S.30, V.33, I.34, R.37, P.44, P.45, Q.60 Chain B: R.58, N.62, E.65, Y.66, Y.100, Y.104, R.111, L.115 Ligands: 01.10 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.66 Hydrogen bonds: B:N.62, B:N.62, B:N.62, B:N.62, B:R.111, A:Q.60 Salt bridges: B:R.58, A:R.37 VDW.14: 16 residues within 4Å: Chain B: S.30, V.33, I.34, R.37, P.44, P.45, Q.60 Chain C: R.58, N.62, E.65, Y.66, Y.100, Y.104, R.111, L.115 Ligands: 01.15 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain C Hydrogen bonds: B:Q.60, C:N.62, C:N.62, C:N.62, C:N.62, C:R.111 Salt bridges: B:R.37, C:R.58 Hydrophobic interactions: C:Y.66

3 x 01: 1-[3,4-bis(fluoranyl)phenyl]-9-[6-[2,2,2-tris(fluoranyl)ethoxy]pyrimidin-4-yl]-1,9-diazaspiro[5.5]undecan-2-one

01.5: 14 residues within 4Å: Chain A: Y.66, L.69, L.115, A.119, L.122, W.123 Chain C: V.23, L.24, A.27, Y.28, S.30, L.31 Ligands: VDW.4, PLM.13 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:A.27, C:L.31, A:Y.66, A:L.69, A:L.115, A:A.119, A:L.122 pi-Stacking: A:W.123 01.10: 14 residues within 4Å: Chain A: V.23, L.24, A.27, Y.28, S.30, L.31 Chain B: Y.66, L.69, L.115, A.119, L.122, W.123 Ligands: PLM.3, VDW.9 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.66, B:L.69, B:L.115, B:A.119, B:L.122, A:A.27, A:L.31 pi-Stacking: B:W.123 01.15: 14 residues within 4Å: Chain B: V.23, L.24, A.27, Y.28, S.30, L.31 Chain C: Y.66, L.69, L.115, A.119, L.122, W.123 Ligands: PLM.8, VDW.14 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:A.27, B:L.31, C:Y.66, C:L.69, C:L.115, C:A.119, C:L.122 pi-Stacking: C:W.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoma, G. et al., Discovery of GJG057, a Potent and Highly Selective Inhibitor of Leukotriene C4 Synthase. J.Med.Chem. (2025)

Release Date

2025-02-26

Peptides

Leukotriene C4 synthase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Leukotriene C4 synthase

Related Entries With Identical Sequence