SMTL ID : 7k15.1

Crystal structure of the Human Leukotriene B4 Receptor 1 in Complex with Selective Antagonist MK-D-046

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.88 Å

Oligo State

monomer

Ligands

1 x VRJ: N-(tert-butylsulfonyl)-4-fluoro-2-{(3S,4R)-4-hydroxy-3-[(pyridin-2-yl)methyl]-3,4-dihydro-2H-1-benzopyran-7-yl}benzamide(Non-covalent)

VRJ.1: 18 residues within 4Å: Chain A: V.90, F.97, F.100, L.101, H.117, C.120, M.124, R.179, C.191, F.192, P.193, W.406, Y.409, R.439, N.440, I.443, A.446, F.447 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.90, A:F.97, A:F.97, A:F.97, A:F.100, A:I.443, A:I.443, A:F.447, A:F.447 Hydrogen bonds: A:H.117, A:H.117, A:R.179, A:R.179, A:Y.409 pi-Stacking: A:H.117, A:W.406

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: D.87, S.123, S.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.123, A:S.127

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 19 residues within 4Å: Chain A: G.243, S.244, T.245, T.246, G.247, N.248, T.249, S.292, T.293, W.294, G.295, S.298, C.327, G.328, D.329, W.332, Y.334, F.335, C.336 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:W.294, A:W.294, A:W.332 Hydrogen bonds: A:T.245, A:T.246, A:T.246, A:G.247, A:N.248, A:T.249, A:T.249, A:S.292, A:S.292, A:T.293, A:T.293, A:G.295, A:G.328, A:D.329, A:Y.334, A:C.336 pi-Stacking: A:W.294, A:W.332, A:W.332, A:W.332

1 x OLA: OLEIC ACID(Non-covalent)

OLA.4: 8 residues within 4Å: Chain A: M.156, R.159, V.160, G.163, I.164, L.167 Ligands: OLC.6, 2PE.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.159, A:V.160, A:I.164, A:L.167

2 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.5: 7 residues within 4Å: Chain A: L.136, Y.139, I.219, A.222, S.223, S.225, D.226 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.136, A:Y.139, A:Y.139, A:I.219 Hydrogen bonds: A:S.225, A:D.226 OLC.6: 11 residues within 4Å: Chain A: W.129, L.140, V.147, K.150, L.151, L.167, L.171, T.211, L.215 Ligands: OLA.4, 2PE.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.129, A:W.129, A:L.167, A:L.171, A:T.211, A:L.215 Hydrogen bonds: A:K.150, A:K.150

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.7: 5 residues within 4Å: Chain A: K.321, G.380, A.381, I.382, R.383 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.321

1 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.8: 14 residues within 4Å: Chain A: V.75, M.79, A.133, M.134, L.136, D.137, R.138, A.141, L.151, R.152, V.160, F.489 Ligands: OLA.4, OLC.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.152

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.9: 9 residues within 4Å: Chain A: L.231, R.234, A.236, Y.265, D.285, I.382, R.383, R.384, R.387 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.231, A:R.234, A:R.384, A:R.384, A:R.384

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Michaelian, N. et al., Structural insights on ligand recognition at the human leukotriene B4 receptor 1. Nat Commun (2021)

Release Date

2021-02-17

Peptides

Leukotriene B4 receptor 1,Flavodoxin,Leukotriene B4 receptor 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Leukotriene B4 receptor 1,Flavodoxin,Leukotriene B4 receptor 1