SMTL ID : 9g14.1

Human LTC4 synthase in complex with compound 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-trimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: R.111, L.112 Chain C: P.44 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.111, A:R.111 GOL.24: 3 residues within 4Å: Chain A: P.44 Chain B: R.111, L.112 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.111, B:R.111 GOL.47: 3 residues within 4Å: Chain B: P.44 Chain C: R.111, L.112 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.111, C:R.111

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

SO4.2: 2 residues within 4Å: Chain A: H.136 Chain C: D.10 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.136 SO4.25: 2 residues within 4Å: Chain A: D.10 Chain B: H.136 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.136 SO4.48: 2 residues within 4Å: Chain B: D.10 Chain C: H.136 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:H.136

3 x GSH: GLUTATHIONE(Non-covalent)

GSH.3: 15 residues within 4Å: Chain A: R.58, N.62, 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: 01.23 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:Y.66 Hydrogen bonds: A:N.62, A:Y.66, A:Y.66, A:R.111, C:S.30 Salt bridges: A:R.58, C:R.37 Water bridges: C:R.37, C:S.64 GSH.26: 15 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, Y.66, Y.100, Y.104, R.111, L.115 Ligands: 01.46 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:S.30, B:N.62, B:Y.66, B:Y.66, B:Y.100, B:R.111 Water bridges: A:R.37, A:S.64 Salt bridges: A:R.37, B:R.58 Hydrophobic interactions: B:Y.66 GSH.49: 15 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, Y.66, Y.100, Y.104, R.111, L.115 Ligands: 01.69 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain C Hydrogen bonds: B:S.30, C:N.62, C:Y.66, C:Y.66, C:Y.100, C:R.111 Water bridges: B:R.37, B:S.64 Salt bridges: B:R.37, C:R.58 Hydrophobic interactions: C:Y.66

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

PLM.4: 6 residues within 4Å: Chain A: H.82, E.83, G.84, A.85, L.88 Ligands: LMT.20 Ligand excluded by PLIP PLM.6: 3 residues within 4Å: Chain A: F.95, L.98 Ligands: PLM.7 Ligand excluded by PLIP PLM.7: 6 residues within 4Å: Chain A: L.21, L.91, V.92, F.95 Ligands: PLM.6, PLM.16 Ligand excluded by PLIP PLM.8: 4 residues within 4Å: Chain A: L.138, L.142, A.145 Ligands: PAM.13 Ligand excluded by PLIP PLM.9: 3 residues within 4Å: Chain A: F.137 Chain C: L.14 Ligands: PAM.5 Ligand excluded by PLIP PLM.10: 6 residues within 4Å: Chain A: A.72, I.79 Chain C: L.71, W.75 Ligands: PLM.33, PLM.56 Ligand excluded by PLIP PLM.16: 3 residues within 4Å: Chain A: L.91 Ligands: PLM.7, PAM.44 Ligand excluded by PLIP PLM.17: 6 residues within 4Å: Chain A: R.99, Q.102, G.103, A.113, P.114, A.117 Ligand excluded by PLIP PLM.18: 1 residues within 4Å: Ligands: PAM.15 Ligand excluded by PLIP PLM.22: 2 residues within 4Å: Chain A: Y.28, Q.102 Ligand excluded by PLIP PLM.27: 6 residues within 4Å: Chain B: H.82, E.83, G.84, A.85, L.88 Ligands: LMT.43 Ligand excluded by PLIP PLM.29: 3 residues within 4Å: Chain B: F.95, L.98 Ligands: PLM.30 Ligand excluded by PLIP PLM.30: 6 residues within 4Å: Chain B: L.21, L.91, V.92, F.95 Ligands: PLM.29, PLM.39 Ligand excluded by PLIP PLM.31: 4 residues within 4Å: Chain B: L.138, L.142, A.145 Ligands: PAM.36 Ligand excluded by PLIP PLM.32: 3 residues within 4Å: Chain A: L.14 Chain B: F.137 Ligands: PAM.28 Ligand excluded by PLIP PLM.33: 6 residues within 4Å: Chain A: L.71, W.75 Chain B: A.72, I.79 Ligands: PLM.10, PLM.56 Ligand excluded by PLIP PLM.39: 3 residues within 4Å: Chain B: L.91 Ligands: PLM.30, PAM.67 Ligand excluded by PLIP PLM.40: 6 residues within 4Å: Chain B: R.99, Q.102, G.103, A.113, P.114, A.117 Ligand excluded by PLIP PLM.41: 1 residues within 4Å: Ligands: PAM.38 Ligand excluded by PLIP PLM.45: 2 residues within 4Å: Chain B: Y.28, Q.102 Ligand excluded by PLIP PLM.50: 6 residues within 4Å: Chain C: H.82, E.83, G.84, A.85, L.88 Ligands: LMT.66 Ligand excluded by PLIP PLM.52: 3 residues within 4Å: Chain C: F.95, L.98 Ligands: PLM.53 Ligand excluded by PLIP PLM.53: 6 residues within 4Å: Chain C: L.21, L.91, V.92, F.95 Ligands: PLM.52, PLM.62 Ligand excluded by PLIP PLM.54: 4 residues within 4Å: Chain C: L.138, L.142, A.145 Ligands: PAM.59 Ligand excluded by PLIP PLM.55: 3 residues within 4Å: Chain B: L.14 Chain C: F.137 Ligands: PAM.51 Ligand excluded by PLIP PLM.56: 6 residues within 4Å: Chain B: L.71, W.75 Chain C: A.72, I.79 Ligands: PLM.10, PLM.33 Ligand excluded by PLIP PLM.62: 3 residues within 4Å: Chain C: L.91 Ligands: PAM.21, PLM.53 Ligand excluded by PLIP PLM.63: 6 residues within 4Å: Chain C: R.99, Q.102, G.103, A.113, P.114, A.117 Ligand excluded by PLIP PLM.64: 1 residues within 4Å: Ligands: PAM.61 Ligand excluded by PLIP PLM.68: 2 residues within 4Å: Chain C: Y.28, Q.102 Ligand excluded by PLIP

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

PAM.5: 9 residues within 4Å: Chain A: A.130, L.133, L.134, F.137 Chain C: D.10, A.13, L.14, E.83 Ligands: PLM.9 Ligand excluded by PLIP PAM.11: 5 residues within 4Å: Chain A: A.127, L.131, L.134 Ligands: PAM.12, LMT.20 Ligand excluded by PLIP PAM.12: 7 residues within 4Å: Chain A: W.123, V.126, A.127, A.130 Chain C: L.24 Ligands: PAM.11, LMT.19 Ligand excluded by PLIP PAM.13: 8 residues within 4Å: Chain A: L.142, A.145, G.148, R.149, L.150, R.151 Ligands: PLM.8, PAM.14 Ligand excluded by PLIP PAM.14: 1 residues within 4Å: Ligands: PAM.13 Ligand excluded by PLIP PAM.15: 1 residues within 4Å: Ligands: PLM.18 Ligand excluded by PLIP PAM.21: 4 residues within 4Å: Chain C: L.14, A.17, L.91 Ligands: PLM.62 Ligand excluded by PLIP PAM.28: 9 residues within 4Å: Chain A: D.10, A.13, L.14, E.83 Chain B: A.130, L.133, L.134, F.137 Ligands: PLM.32 Ligand excluded by PLIP PAM.34: 5 residues within 4Å: Chain B: A.127, L.131, L.134 Ligands: PAM.35, LMT.43 Ligand excluded by PLIP PAM.35: 7 residues within 4Å: Chain A: L.24 Chain B: W.123, V.126, A.127, A.130 Ligands: PAM.34, LMT.42 Ligand excluded by PLIP PAM.36: 8 residues within 4Å: Chain B: L.142, A.145, G.148, R.149, L.150, R.151 Ligands: PLM.31, PAM.37 Ligand excluded by PLIP PAM.37: 1 residues within 4Å: Ligands: PAM.36 Ligand excluded by PLIP PAM.38: 1 residues within 4Å: Ligands: PLM.41 Ligand excluded by PLIP PAM.44: 4 residues within 4Å: Chain A: L.14, A.17, L.91 Ligands: PLM.16 Ligand excluded by PLIP PAM.51: 9 residues within 4Å: Chain B: D.10, A.13, L.14, E.83 Chain C: A.130, L.133, L.134, F.137 Ligands: PLM.55 Ligand excluded by PLIP PAM.57: 5 residues within 4Å: Chain C: A.127, L.131, L.134 Ligands: PAM.58, LMT.66 Ligand excluded by PLIP PAM.58: 7 residues within 4Å: Chain B: L.24 Chain C: W.123, V.126, A.127, A.130 Ligands: PAM.57, LMT.65 Ligand excluded by PLIP PAM.59: 8 residues within 4Å: Chain C: L.142, A.145, G.148, R.149, L.150, R.151 Ligands: PLM.54, PAM.60 Ligand excluded by PLIP PAM.60: 1 residues within 4Å: Ligands: PAM.59 Ligand excluded by PLIP PAM.61: 1 residues within 4Å: Ligands: PLM.64 Ligand excluded by PLIP PAM.67: 4 residues within 4Å: Chain B: L.14, A.17, L.91 Ligands: PLM.39 Ligand excluded by PLIP

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

LMT.19: 5 residues within 4Å: Chain A: Y.116, R.120, W.123 Ligands: PAM.12, 01.23 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.123, A:W.123, A:W.123 Hydrogen bonds: A:R.120 LMT.20: 6 residues within 4Å: Chain A: F.81, H.82, A.85, L.131 Ligands: PLM.4, PAM.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.82 LMT.42: 5 residues within 4Å: Chain B: Y.116, R.120, W.123 Ligands: PAM.35, 01.46 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.123, B:W.123, B:W.123 Hydrogen bonds: B:R.120 LMT.43: 6 residues within 4Å: Chain B: F.81, H.82, A.85, L.131 Ligands: PLM.27, PAM.34 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.82 LMT.65: 5 residues within 4Å: Chain C: Y.116, R.120, W.123 Ligands: PAM.58, 01.69 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.123, C:W.123, C:W.123 Hydrogen bonds: C:R.120 LMT.66: 6 residues within 4Å: Chain C: F.81, H.82, A.85, L.131 Ligands: PLM.50, PAM.57 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.82

3 x 01: 1-(phenylmethyl)-9-quinoxalin-2-yl-1,9-diazaspiro[5.5]undecan-2-one

01.23: 11 residues within 4Å: Chain A: Y.66, L.69, A.119, L.122, W.123 Chain C: V.23, A.27, S.30, L.31 Ligands: GSH.3, LMT.19 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:V.23, C:A.27, C:L.31, A:Y.66, A:L.69, A:A.119, A:L.122, A:W.123 pi-Stacking: A:W.123, A:W.123 01.46: 11 residues within 4Å: Chain A: V.23, A.27, S.30, L.31 Chain B: Y.66, L.69, A.119, L.122, W.123 Ligands: GSH.26, LMT.42 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.66, B:L.69, B:A.119, B:L.122, B:W.123, A:V.23, A:A.27, A:L.31 pi-Stacking: B:W.123, B:W.123 01.69: 11 residues within 4Å: Chain B: V.23, A.27, S.30, L.31 Chain C: Y.66, L.69, A.119, L.122, W.123 Ligands: GSH.49, LMT.65 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:Y.66, C:L.69, C:A.119, C:L.122, C:W.123, B:V.23, B:A.27, B:L.31 pi-Stacking: C:W.123, 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.
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Leukotriene C4 synthase

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