SMTL ID : 6r7d.3 (3 other biounits)

Crystal structure of LTC4S in complex with AZ13690257

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-trimer

Ligands

3 x JUQ: (1~{S},2~{S})-2-[5-[cyclopropylmethyl(naphthalen-1-yl)amino]-4-methoxy-pyrimidin-2-yl]carbonylcyclopropane-1-carboxylic acid(Non-covalent)

JUQ.1: 17 residues within 4Å: Chain A: N.62, Y.66, L.69, R.97, Y.100, Y.104, R.111, L.115, S.118, A.119, L.122, W.123 Chain C: V.23, Q.26, A.27, S.30 Ligands: PLM.4 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:N.62, A:Y.66, A:L.69, A:L.115, A:A.119, A:L.122, A:L.122, A:W.123, C:A.27 Hydrogen bonds: A:R.97, A:R.97, A:Y.100 Salt bridges: A:R.111 JUQ.6: 16 residues within 4Å: Chain A: V.23, Q.26, A.27, S.30 Chain B: N.62, Y.66, L.69, Y.93, R.97, Y.100, R.111, L.115, S.118, A.119, L.122, W.123 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.66, B:L.69, B:L.115, B:L.122, B:L.122, B:W.123, A:V.23, A:A.27 Hydrogen bonds: B:R.97, B:R.97 Salt bridges: B:R.111 JUQ.9: 16 residues within 4Å: Chain B: V.23, Q.26, A.27, S.30 Chain C: N.62, Y.66, L.69, R.97, Y.100, Y.104, R.111, L.115, S.118, A.119, L.122, W.123 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:Y.66, C:L.69, C:L.115, C:A.119, C:L.122, C:L.122, C:W.123, B:A.27 Hydrogen bonds: C:N.62, C:R.97, C:R.97 Salt bridges: C:R.111

2 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 6 residues within 4Å: Chain A: H.6, H.8 Chain B: H.6, H.8 Chain C: H.6, H.8 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 2 interactions with chain A Metal complexes: C:H.6, C:H.8, B:H.6, B:H.8, A:H.6, A:H.8 NI.10: 2 residues within 4Å: Chain C: H.3, H.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.3, C:H.5

7 x PLM: PALMITIC ACID(Non-covalent)

PLM.3: 2 residues within 4Å: Chain A: P.139, R.143 No protein-ligand interaction detected (PLIP) PLM.4: 3 residues within 4Å: Chain A: R.120, W.123 Ligands: JUQ.1 No protein-ligand interaction detected (PLIP) PLM.5: 8 residues within 4Å: Chain A: H.7, H.8, K.9, L.71, W.75 Chain B: E.11, I.79 Ligands: PLM.8 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.71, A:W.75, A:W.75, B:I.79 Hydrogen bonds: A:H.8, A:K.9 PLM.7: 5 residues within 4Å: Chain B: R.120, W.123, L.124, A.127, A.130 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.123, B:W.123, B:A.127, B:A.130 PLM.8: 6 residues within 4Å: Chain B: L.71, W.75 Chain C: W.75, I.79 Ligands: PLM.5, PLM.12 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.71, B:W.75, B:W.75, C:I.79 PLM.11: 2 residues within 4Å: Chain B: L.14 Chain C: F.137 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.14, C:F.137 PLM.12: 8 residues within 4Å: Chain A: H.8, E.11, W.75, I.79 Chain C: H.7, L.71, W.75 Ligands: PLM.8 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:H.8, A:W.75, C:L.71, C:W.75, C:W.75, C:W.75 Salt bridges: C:H.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Munck Af Rosenschold, M. et al., Discovery of the Oral Leukotriene C4 Synthase Inhibitor (1S,2S)-2-({5-[(5-Chloro-2,4-difluorophenyl)(2-fluoro-2-methylpropyl)amino]-3-methoxypyrazin-2-yl}carbonyl)cyclopropanecarboxylic Acid (AZD9898) as a New Treatment for Asthma. J.Med.Chem. (2019)

Release Date

2019-08-28

Peptides

Leukotriene C4 synthase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

Membrane

We predict this structure to be a membrane protein.
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Leukotriene C4 synthase

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