SMTL ID : 9g0u.1

Human LTC4 synthase in complex with AZD9898

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: H.136 Chain B: D.10 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:H.136 Hydrogen bonds: B:D.10, B:D.10 SO4.22: 2 residues within 4Å: Chain B: H.136 Chain C: D.10 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.10, C:D.10 Salt bridges: B:H.136 SO4.43: 2 residues within 4Å: Chain A: D.10 Chain C: H.136 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Salt bridges: C:H.136 Hydrogen bonds: A:D.10

30 x PLM: PALMITIC ACID(Non-covalent)(Non-functional Binders)

PLM.2: 5 residues within 4Å: Chain A: H.82, E.83, G.84, A.85 Ligands: LMT.17 Ligand excluded by PLIP PLM.4: 3 residues within 4Å: Chain A: F.95, L.98 Ligands: PLM.5 Ligand excluded by PLIP PLM.5: 7 residues within 4Å: Chain A: L.25, L.88, L.91, F.95 Ligands: PLM.4, PLM.14, PLM.20 Ligand excluded by PLIP PLM.6: 4 residues within 4Å: Chain A: L.138, A.145, L.150 Ligands: PAM.11 Ligand excluded by PLIP PLM.7: 5 residues within 4Å: Chain A: F.137, W.156 Chain B: L.14 Ligands: PAM.3, PAM.18 Ligand excluded by PLIP PLM.8: 6 residues within 4Å: Chain A: A.72, W.75, I.79 Chain B: W.75 Ligands: PLM.29, PLM.50 Ligand excluded by PLIP PLM.14: 3 residues within 4Å: Chain A: L.91 Ligands: PLM.5, PAM.60 Ligand excluded by PLIP PLM.15: 5 residues within 4Å: Chain A: R.99, G.103, A.113, P.114, A.117 Ligand excluded by PLIP PLM.16: 1 residues within 4Å: Ligands: PAM.13 Ligand excluded by PLIP PLM.20: 5 residues within 4Å: Chain A: L.21, L.24, Y.28, Q.102 Ligands: PLM.5 Ligand excluded by PLIP PLM.23: 5 residues within 4Å: Chain B: H.82, E.83, G.84, A.85 Ligands: LMT.38 Ligand excluded by PLIP PLM.25: 3 residues within 4Å: Chain B: F.95, L.98 Ligands: PLM.26 Ligand excluded by PLIP PLM.26: 7 residues within 4Å: Chain B: L.25, L.88, L.91, F.95 Ligands: PLM.25, PLM.35, PLM.41 Ligand excluded by PLIP PLM.27: 4 residues within 4Å: Chain B: L.138, A.145, L.150 Ligands: PAM.32 Ligand excluded by PLIP PLM.28: 5 residues within 4Å: Chain B: F.137, W.156 Chain C: L.14 Ligands: PAM.24, PAM.39 Ligand excluded by PLIP PLM.29: 6 residues within 4Å: Chain B: A.72, W.75, I.79 Chain C: W.75 Ligands: PLM.8, PLM.50 Ligand excluded by PLIP PLM.35: 3 residues within 4Å: Chain B: L.91 Ligands: PAM.18, PLM.26 Ligand excluded by PLIP PLM.36: 5 residues within 4Å: Chain B: R.99, G.103, A.113, P.114, A.117 Ligand excluded by PLIP PLM.37: 1 residues within 4Å: Ligands: PAM.34 Ligand excluded by PLIP PLM.41: 5 residues within 4Å: Chain B: L.21, L.24, Y.28, Q.102 Ligands: PLM.26 Ligand excluded by PLIP PLM.44: 5 residues within 4Å: Chain C: H.82, E.83, G.84, A.85 Ligands: LMT.59 Ligand excluded by PLIP PLM.46: 3 residues within 4Å: Chain C: F.95, L.98 Ligands: PLM.47 Ligand excluded by PLIP PLM.47: 7 residues within 4Å: Chain C: L.25, L.88, L.91, F.95 Ligands: PLM.46, PLM.56, PLM.62 Ligand excluded by PLIP PLM.48: 4 residues within 4Å: Chain C: L.138, A.145, L.150 Ligands: PAM.53 Ligand excluded by PLIP PLM.49: 5 residues within 4Å: Chain A: L.14 Chain C: F.137, W.156 Ligands: PAM.45, PAM.60 Ligand excluded by PLIP PLM.50: 6 residues within 4Å: Chain A: W.75 Chain C: A.72, W.75, I.79 Ligands: PLM.8, PLM.29 Ligand excluded by PLIP PLM.56: 3 residues within 4Å: Chain C: L.91 Ligands: PAM.39, PLM.47 Ligand excluded by PLIP PLM.57: 5 residues within 4Å: Chain C: R.99, G.103, A.113, P.114, A.117 Ligand excluded by PLIP PLM.58: 1 residues within 4Å: Ligands: PAM.55 Ligand excluded by PLIP PLM.62: 5 residues within 4Å: Chain C: L.21, L.24, Y.28, Q.102 Ligands: PLM.47 Ligand excluded by PLIP

24 x PAM: PALMITOLEIC ACID(Non-covalent)(Non-functional Binders)

PAM.3: 9 residues within 4Å: Chain A: A.130, L.133, L.134, F.137 Chain B: D.10, A.13, L.14, E.83 Ligands: PLM.7 Ligand excluded by PLIP PAM.9: 6 residues within 4Å: Chain A: A.127, A.130, L.131, L.134 Ligands: PAM.10, LMT.17 Ligand excluded by PLIP PAM.10: 5 residues within 4Å: Chain A: W.123, V.126, A.127, A.130 Ligands: PAM.9 Ligand excluded by PLIP PAM.11: 7 residues within 4Å: Chain A: A.145, G.148, R.149, L.150, R.151 Ligands: PLM.6, PAM.12 Ligand excluded by PLIP PAM.12: 2 residues within 4Å: Ligands: PAM.11, PAM.13 Ligand excluded by PLIP PAM.13: 2 residues within 4Å: Ligands: PAM.12, PLM.16 Ligand excluded by PLIP PAM.18: 5 residues within 4Å: Chain B: L.14, A.17, L.91 Ligands: PLM.7, PLM.35 Ligand excluded by PLIP PAM.19: 7 residues within 4Å: Chain A: R.111, L.115, Y.116, A.119 Chain B: S.43, P.44 Ligands: 01.21 Ligand excluded by PLIP PAM.24: 9 residues within 4Å: Chain B: A.130, L.133, L.134, F.137 Chain C: D.10, A.13, L.14, E.83 Ligands: PLM.28 Ligand excluded by PLIP PAM.30: 6 residues within 4Å: Chain B: A.127, A.130, L.131, L.134 Ligands: PAM.31, LMT.38 Ligand excluded by PLIP PAM.31: 5 residues within 4Å: Chain B: W.123, V.126, A.127, A.130 Ligands: PAM.30 Ligand excluded by PLIP PAM.32: 7 residues within 4Å: Chain B: A.145, G.148, R.149, L.150, R.151 Ligands: PLM.27, PAM.33 Ligand excluded by PLIP PAM.33: 2 residues within 4Å: Ligands: PAM.32, PAM.34 Ligand excluded by PLIP PAM.34: 2 residues within 4Å: Ligands: PAM.33, PLM.37 Ligand excluded by PLIP PAM.39: 5 residues within 4Å: Chain C: L.14, A.17, L.91 Ligands: PLM.28, PLM.56 Ligand excluded by PLIP PAM.40: 7 residues within 4Å: Chain B: R.111, L.115, Y.116, A.119 Chain C: S.43, P.44 Ligands: 01.42 Ligand excluded by PLIP PAM.45: 9 residues within 4Å: Chain A: D.10, A.13, L.14, E.83 Chain C: A.130, L.133, L.134, F.137 Ligands: PLM.49 Ligand excluded by PLIP PAM.51: 6 residues within 4Å: Chain C: A.127, A.130, L.131, L.134 Ligands: PAM.52, LMT.59 Ligand excluded by PLIP PAM.52: 5 residues within 4Å: Chain C: W.123, V.126, A.127, A.130 Ligands: PAM.51 Ligand excluded by PLIP PAM.53: 7 residues within 4Å: Chain C: A.145, G.148, R.149, L.150, R.151 Ligands: PLM.48, PAM.54 Ligand excluded by PLIP PAM.54: 2 residues within 4Å: Ligands: PAM.53, PAM.55 Ligand excluded by PLIP PAM.55: 2 residues within 4Å: Ligands: PAM.54, PLM.58 Ligand excluded by PLIP PAM.60: 5 residues within 4Å: Chain A: L.14, A.17, L.91 Ligands: PLM.14, PLM.49 Ligand excluded by PLIP PAM.61: 7 residues within 4Å: Chain A: S.43, P.44 Chain C: R.111, L.115, Y.116, A.119 Ligands: 01.63 Ligand excluded by PLIP

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

LMT.17: 9 residues within 4Å: Chain A: F.81, H.82, A.85, L.128, L.131, L.134, L.138 Ligands: PLM.2, PAM.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.131, A:L.134, A:L.138 Hydrogen bonds: A:H.82 LMT.38: 9 residues within 4Å: Chain B: F.81, H.82, A.85, L.128, L.131, L.134, L.138 Ligands: PLM.23, PAM.30 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.131, B:L.134, B:L.138 Hydrogen bonds: B:H.82 LMT.59: 9 residues within 4Å: Chain C: F.81, H.82, A.85, L.128, L.131, L.134, L.138 Ligands: PLM.44, PAM.51 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.131, C:L.134, C:L.138 Hydrogen bonds: C:H.82

3 x 01: (1~{S},2~{S})-2-[5-[[5-chloranyl-2,4-bis(fluoranyl)phenyl]-(2-fluoranyl-2-methyl-propyl)amino]-3-methoxy-pyrazin-2-yl]carbonylcyclopropane-1-carboxylic acid

01.21: 18 residues within 4Å: Chain A: N.62, Y.66, R.97, Y.100, Y.104, R.111, L.115, S.118, A.119, L.122, W.123, V.126 Chain B: V.23, A.27, S.30, L.31, I.34 Ligands: PAM.19 15 PLIP interactions: 5 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:A.27, B:L.31, B:I.34, A:N.62, A:Y.66, A:L.115, A:L.122 Hydrogen bonds: B:S.30, A:R.97, A:R.97 Halogen bonds: B:V.23 Salt bridges: A:R.111 pi-Stacking: A:Y.66, A:W.123, A:W.123 01.42: 18 residues within 4Å: Chain B: N.62, Y.66, R.97, Y.100, Y.104, R.111, L.115, S.118, A.119, L.122, W.123, V.126 Chain C: V.23, A.27, S.30, L.31, I.34 Ligands: PAM.40 16 PLIP interactions: 5 interactions with chain C, 11 interactions with chain B Hydrophobic interactions: C:A.27, C:L.31, C:I.34, B:N.62, B:Y.66, B:L.115, B:L.122 Hydrogen bonds: C:S.30, B:R.97, B:R.97, B:Y.100 Halogen bonds: C:V.23 Salt bridges: B:R.111 pi-Stacking: B:Y.66, B:W.123, B:W.123 01.63: 18 residues within 4Å: Chain A: V.23, A.27, S.30, L.31, I.34 Chain C: N.62, Y.66, R.97, Y.100, Y.104, R.111, L.115, S.118, A.119, L.122, W.123, V.126 Ligands: PAM.61 16 PLIP interactions: 11 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:N.62, C:Y.66, C:L.115, C:L.122, A:A.27, A:L.31, A:I.34 Hydrogen bonds: C:R.97, C:R.97, C:Y.100, A:S.30 Salt bridges: C:R.111 pi-Stacking: C:Y.66, C:W.123, C:W.123 Halogen bonds: A:V.23

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.
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Leukotriene C4 synthase

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