SMTL ID : 9g0v.2 (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-12-mer

Ligands

24 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 Ligand excluded by PLIP PLM.3: 4 residues within 4Å: Chain A: L.21, L.24, Y.28 Ligands: 01.10 Ligand excluded by PLIP 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 Ligand excluded by PLIP PLM.8: 4 residues within 4Å: Chain B: L.21, L.24, Y.28 Ligands: 01.15 Ligand excluded by PLIP 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 Ligand excluded by PLIP PLM.13: 4 residues within 4Å: Chain C: L.21, L.24, Y.28 Ligands: 01.5 Ligand excluded by PLIP PLM.16: 7 residues within 4Å: Chain D: A.72, W.75, I.79 Chain F: L.71, W.75 Ligands: PLM.21, PLM.26 Ligand excluded by PLIP PLM.18: 4 residues within 4Å: Chain D: L.21, L.24, Y.28 Ligands: 01.25 Ligand excluded by PLIP PLM.21: 7 residues within 4Å: Chain D: L.71, W.75 Chain E: A.72, W.75, I.79 Ligands: PLM.16, PLM.26 Ligand excluded by PLIP PLM.23: 4 residues within 4Å: Chain E: L.21, L.24, Y.28 Ligands: 01.30 Ligand excluded by PLIP PLM.26: 7 residues within 4Å: Chain E: L.71, W.75 Chain F: A.72, W.75, I.79 Ligands: PLM.16, PLM.21 Ligand excluded by PLIP PLM.28: 4 residues within 4Å: Chain F: L.21, L.24, Y.28 Ligands: 01.20 Ligand excluded by PLIP PLM.31: 7 residues within 4Å: Chain G: A.72, W.75, I.79 Chain I: L.71, W.75 Ligands: PLM.36, PLM.41 Ligand excluded by PLIP PLM.33: 4 residues within 4Å: Chain G: L.21, L.24, Y.28 Ligands: 01.40 Ligand excluded by PLIP PLM.36: 7 residues within 4Å: Chain G: L.71, W.75 Chain H: A.72, W.75, I.79 Ligands: PLM.31, PLM.41 Ligand excluded by PLIP PLM.38: 4 residues within 4Å: Chain H: L.21, L.24, Y.28 Ligands: 01.45 Ligand excluded by PLIP PLM.41: 7 residues within 4Å: Chain H: L.71, W.75 Chain I: A.72, W.75, I.79 Ligands: PLM.31, PLM.36 Ligand excluded by PLIP PLM.43: 4 residues within 4Å: Chain I: L.21, L.24, Y.28 Ligands: 01.35 Ligand excluded by PLIP PLM.46: 7 residues within 4Å: Chain J: A.72, W.75, I.79 Chain L: L.71, W.75 Ligands: PLM.51, PLM.56 Ligand excluded by PLIP PLM.48: 4 residues within 4Å: Chain J: L.21, L.24, Y.28 Ligands: 01.55 Ligand excluded by PLIP PLM.51: 7 residues within 4Å: Chain J: L.71, W.75 Chain K: A.72, W.75, I.79 Ligands: PLM.46, PLM.56 Ligand excluded by PLIP PLM.53: 4 residues within 4Å: Chain K: L.21, L.24, Y.28 Ligands: 01.60 Ligand excluded by PLIP PLM.56: 7 residues within 4Å: Chain K: L.71, W.75 Chain L: A.72, W.75, I.79 Ligands: PLM.46, PLM.51 Ligand excluded by PLIP PLM.58: 4 residues within 4Å: Chain L: L.21, L.24, Y.28 Ligands: 01.50 Ligand excluded by PLIP

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

LMT.2: 3 residues within 4Å: Chain D: A.145, L.146, L.147 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.147 LMT.7: 3 residues within 4Å: Chain H: A.145, L.146, L.147 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:L.147 LMT.12: 3 residues within 4Å: Chain L: A.145, L.146, L.147 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:L.147 LMT.17: 3 residues within 4Å: Chain A: A.145, L.146, L.147 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.147 LMT.22: 3 residues within 4Å: Chain K: A.145, L.146, L.147 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:L.147 LMT.27: 3 residues within 4Å: Chain I: A.145, L.146, L.147 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:L.147 LMT.32: 3 residues within 4Å: Chain J: A.145, L.146, L.147 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:L.147 LMT.37: 3 residues within 4Å: Chain B: A.145, L.146, L.147 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.147 LMT.42: 3 residues within 4Å: Chain F: A.145, L.146, L.147 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:L.147 LMT.47: 3 residues within 4Å: Chain G: A.145, L.146, L.147 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:L.147 LMT.52: 3 residues within 4Å: Chain E: A.145, L.146, L.147 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:L.147 LMT.57: 3 residues within 4Å: Chain C: A.145, L.146, L.147 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.147

12 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: 2 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:Q.60, B:N.62, B:N.62, B:N.62, B:N.62, B:R.111 Salt bridges: A:R.37, B:R.58 Hydrophobic interactions: B:Y.66 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: 7 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:Y.66 Hydrogen bonds: C:N.62, C:N.62, C:N.62, C:N.62, C:R.111, B:Q.60 Salt bridges: C:R.58, B:R.37 VDW.19: 16 residues within 4Å: Chain D: R.58, N.62, E.65, Y.66, Y.100, Y.104, R.111, L.115 Chain F: S.30, V.33, I.34, R.37, P.44, P.45, Q.60 Ligands: 01.20 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:Y.66 Hydrogen bonds: D:N.62, D:N.62, D:N.62, D:N.62, D:Y.104, D:R.111, F:Q.60 Salt bridges: D:R.58, F:R.37 VDW.24: 16 residues within 4Å: Chain D: S.30, V.33, I.34, R.37, P.44, P.45, Q.60 Chain E: R.58, N.62, E.65, Y.66, Y.100, Y.104, R.111, L.115 Ligands: 01.25 10 PLIP interactions: 2 interactions with chain D, 8 interactions with chain E Hydrogen bonds: D:Q.60, E:N.62, E:N.62, E:N.62, E:N.62, E:Y.104, E:R.111 Salt bridges: D:R.37, E:R.58 Hydrophobic interactions: E:Y.66 VDW.29: 16 residues within 4Å: Chain E: S.30, V.33, I.34, R.37, P.44, P.45, Q.60 Chain F: R.58, N.62, E.65, Y.66, Y.100, Y.104, R.111, L.115 Ligands: 01.30 10 PLIP interactions: 2 interactions with chain E, 8 interactions with chain F Hydrogen bonds: E:Q.60, F:N.62, F:N.62, F:N.62, F:N.62, F:Y.104, F:R.111 Salt bridges: E:R.37, F:R.58 Hydrophobic interactions: F:Y.66 VDW.34: 16 residues within 4Å: Chain G: R.58, N.62, E.65, Y.66, Y.100, Y.104, R.111, L.115 Chain I: S.30, V.33, I.34, R.37, P.44, P.45, Q.60 Ligands: 01.35 10 PLIP interactions: 8 interactions with chain G, 2 interactions with chain I Hydrophobic interactions: G:Y.66 Hydrogen bonds: G:N.62, G:N.62, G:N.62, G:N.62, G:Y.104, G:R.111, I:Q.60 Salt bridges: G:R.58, I:R.37 VDW.39: 16 residues within 4Å: Chain G: S.30, V.33, I.34, R.37, P.44, P.45, Q.60 Chain H: R.58, N.62, E.65, Y.66, Y.100, Y.104, R.111, L.115 Ligands: 01.40 10 PLIP interactions: 2 interactions with chain G, 8 interactions with chain H Hydrogen bonds: G:Q.60, H:N.62, H:N.62, H:N.62, H:N.62, H:Y.104, H:R.111 Salt bridges: G:R.37, H:R.58 Hydrophobic interactions: H:Y.66 VDW.44: 16 residues within 4Å: Chain H: S.30, V.33, I.34, R.37, P.44, P.45, Q.60 Chain I: R.58, N.62, E.65, Y.66, Y.100, Y.104, R.111, L.115 Ligands: 01.45 10 PLIP interactions: 8 interactions with chain I, 2 interactions with chain H Hydrophobic interactions: I:Y.66 Hydrogen bonds: I:N.62, I:N.62, I:N.62, I:N.62, I:Y.104, I:R.111, H:Q.60 Salt bridges: I:R.58, H:R.37 VDW.49: 16 residues within 4Å: Chain J: R.58, N.62, E.65, Y.66, Y.100, Y.104, R.111, L.115 Chain L: S.30, V.33, I.34, R.37, P.44, P.45, Q.60 Ligands: 01.50 9 PLIP interactions: 2 interactions with chain L, 7 interactions with chain J Hydrogen bonds: L:Q.60, J:N.62, J:N.62, J:N.62, J:N.62, J:R.111 Salt bridges: L:R.37, J:R.58 Hydrophobic interactions: J:Y.66 VDW.54: 16 residues within 4Å: Chain J: S.30, V.33, I.34, R.37, P.44, P.45, Q.60 Chain K: R.58, N.62, E.65, Y.66, Y.100, Y.104, R.111, L.115 Ligands: 01.55 9 PLIP interactions: 7 interactions with chain K, 2 interactions with chain J Hydrophobic interactions: K:Y.66 Hydrogen bonds: K:N.62, K:N.62, K:N.62, K:N.62, K:R.111, J:Q.60 Salt bridges: K:R.58, J:R.37 VDW.59: 16 residues within 4Å: Chain K: S.30, V.33, I.34, R.37, P.44, P.45, Q.60 Chain L: R.58, N.62, E.65, Y.66, Y.100, Y.104, R.111, L.115 Ligands: 01.60 9 PLIP interactions: 7 interactions with chain L, 2 interactions with chain K Hydrophobic interactions: L:Y.66 Hydrogen bonds: L:N.62, L:N.62, L:N.62, L:N.62, L:R.111, K:Q.60 Salt bridges: L:R.58, K:R.37

12 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: 6 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Y.66, A:L.69, A:L.115, A:A.119, A:L.122, C:A.27, C:L.31 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: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:A.27, A:L.31, B:Y.66, B:L.69, B:L.115, B:A.119, B:L.122 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: 6 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:Y.66, C:L.69, C:L.115, C:A.119, C:L.122, B:A.27, B:L.31 pi-Stacking: C:W.123 01.20: 14 residues within 4Å: Chain D: Y.66, L.69, L.115, A.119, L.122, W.123 Chain F: V.23, L.24, A.27, Y.28, S.30, L.31 Ligands: VDW.19, PLM.28 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:Y.66, D:L.69, D:L.115, D:A.119, D:L.122, F:A.27, F:L.31 pi-Stacking: D:W.123 01.25: 14 residues within 4Å: Chain D: V.23, L.24, A.27, Y.28, S.30, L.31 Chain E: Y.66, L.69, L.115, A.119, L.122, W.123 Ligands: PLM.18, VDW.24 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:Y.66, E:L.69, E:L.115, E:A.119, E:L.122, D:A.27, D:L.31 pi-Stacking: E:W.123 01.30: 14 residues within 4Å: Chain E: V.23, L.24, A.27, Y.28, S.30, L.31 Chain F: Y.66, L.69, L.115, A.119, L.122, W.123 Ligands: PLM.23, VDW.29 8 PLIP interactions: 6 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:Y.66, F:L.69, F:L.115, F:A.119, F:L.122, E:A.27, E:L.31 pi-Stacking: F:W.123 01.35: 14 residues within 4Å: Chain G: Y.66, L.69, L.115, A.119, L.122, W.123 Chain I: V.23, L.24, A.27, Y.28, S.30, L.31 Ligands: VDW.34, PLM.43 8 PLIP interactions: 2 interactions with chain I, 6 interactions with chain G Hydrophobic interactions: I:A.27, I:L.31, G:Y.66, G:L.69, G:L.115, G:A.119, G:L.122 pi-Stacking: G:W.123 01.40: 14 residues within 4Å: Chain G: V.23, L.24, A.27, Y.28, S.30, L.31 Chain H: Y.66, L.69, L.115, A.119, L.122, W.123 Ligands: PLM.33, VDW.39 8 PLIP interactions: 6 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:Y.66, H:L.69, H:L.115, H:A.119, H:L.122, G:A.27, G:L.31 pi-Stacking: H:W.123 01.45: 14 residues within 4Å: Chain H: V.23, L.24, A.27, Y.28, S.30, L.31 Chain I: Y.66, L.69, L.115, A.119, L.122, W.123 Ligands: PLM.38, VDW.44 8 PLIP interactions: 2 interactions with chain H, 6 interactions with chain I Hydrophobic interactions: H:A.27, H:L.31, I:Y.66, I:L.69, I:L.115, I:A.119, I:L.122 pi-Stacking: I:W.123 01.50: 14 residues within 4Å: Chain J: Y.66, L.69, L.115, A.119, L.122, W.123 Chain L: V.23, L.24, A.27, Y.28, S.30, L.31 Ligands: VDW.49, PLM.58 8 PLIP interactions: 6 interactions with chain J, 2 interactions with chain L Hydrophobic interactions: J:Y.66, J:L.69, J:L.115, J:A.119, J:L.122, L:A.27, L:L.31 pi-Stacking: J:W.123 01.55: 14 residues within 4Å: Chain J: V.23, L.24, A.27, Y.28, S.30, L.31 Chain K: Y.66, L.69, L.115, A.119, L.122, W.123 Ligands: PLM.48, VDW.54 8 PLIP interactions: 6 interactions with chain K, 2 interactions with chain J Hydrophobic interactions: K:Y.66, K:L.69, K:L.115, K:A.119, K:L.122, J:A.27, J:L.31 pi-Stacking: K:W.123 01.60: 14 residues within 4Å: Chain K: V.23, L.24, A.27, Y.28, S.30, L.31 Chain L: Y.66, L.69, L.115, A.119, L.122, W.123 Ligands: PLM.53, VDW.59 8 PLIP interactions: 6 interactions with chain L, 2 interactions with chain K Hydrophobic interactions: L:Y.66, L:L.69, L:L.115, L:A.119, L:L.122, K:A.27, K:L.31 pi-Stacking: L: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: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

Leukotriene C4 synthase

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