SMTL ID : 6zba.1

Crystal structure of PDE4D2 in complex with inhibitor LEO39652

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x QDT: 2-methylpropyl 1-[8-methoxy-5-(1-oxidanylidene-3~{H}-2-benzofuran-5-yl)-[1,2,4]triazolo[1,5-a]pyridin-2-yl]cyclopropane-1-carboxylate(Non-covalent)

QDT.1: 15 residues within 4Å: Chain A: Y.83, T.195, M.197, D.242, L.243, N.245, Y.253, W.256, T.257, I.260, F.264, M.281, S.292, Q.293, F.296 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.83, A:L.243, A:I.260, A:F.264, A:F.264, A:F.296, A:F.296 Hydrogen bonds: A:Q.293 Water bridges: A:E.154 pi-Stacking: A:H.84, A:F.296 QDT.15: 15 residues within 4Å: Chain B: Y.83, T.195, M.197, D.242, L.243, N.245, Y.253, W.256, T.257, I.260, F.264, M.281, S.292, Q.293, F.296 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.83, B:L.243, B:F.264, B:F.264, B:F.296 Hydrogen bonds: B:Q.293 pi-Stacking: B:H.84, B:F.296 QDT.23: 15 residues within 4Å: Chain C: Y.83, T.195, M.197, D.242, L.243, N.245, Y.253, W.256, T.257, I.260, F.264, M.281, S.292, Q.293, F.296 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:Y.83, C:L.243, C:I.260, C:F.264, C:F.264, C:F.296, C:F.296 Hydrogen bonds: C:Q.293 pi-Stacking: C:H.84, C:F.296, C:F.296 QDT.35: 14 residues within 4Å: Chain D: Y.83, T.195, M.197, D.242, L.243, N.245, W.256, T.257, I.260, F.264, M.281, S.292, Q.293, F.296 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:Y.83, D:L.243, D:F.264, D:F.296, D:F.296 Hydrogen bonds: D:Q.293 Water bridges: D:E.154 pi-Stacking: D:H.84, D:F.296

28 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 2 residues within 4Å: Chain A: P.103, D.315 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: T.72, H.76, E.167 Chain D: T.139, S.141, R.270, R.274 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: K.186, I.189, D.190 Chain C: N.148, S.150 Ligands: EDO.25 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: N.39, A.79, N.85, N.86, I.87 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: S.132, F.264, S.279, P.280, C.282 Ligand excluded by PLIP EDO.7: 1 residues within 4Å: Chain A: E.106 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: D.64, T.68 Chain D: E.273, R.274 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: F.162, F.173, R.181, R.185 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: V.98, L.99, T.102, W.308, V.312, D.315, I.319 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: N.138, M.276 Chain C: K.178 Chain D: E.168 Ligand excluded by PLIP EDO.16: 8 residues within 4Å: Chain B: T.72, H.76, E.167 Chain C: F.135, L.136, T.139, R.270, R.274 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: K.186, I.189, D.190 Chain D: N.148, D.149, S.150 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: F.162, L.165, F.173, R.181, R.185 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain B: V.98, L.99, T.102, W.308, V.312, D.315, A.316, I.319 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain A: N.140 Chain C: R.181, Q.182, R.185 Ligands: EDO.29 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain A: Q.182 Chain C: Q.134, I.137 Ligands: EDO.4 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain C: T.58, F.59, K.60, N.175, Q.180 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: F.135, T.139, R.274 Chain C: T.72, H.76, E.167 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain C: L.99, T.102, W.308, V.312, D.315, A.316, I.319 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain C: F.162, F.173, R.181, R.185 Ligands: EDO.24 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain C: S.132, F.264, Q.267, S.279, P.280, C.282 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain A: N.148, D.149, S.150 Chain C: K.186, I.189, D.190 Ligand excluded by PLIP EDO.36: 7 residues within 4Å: Chain A: F.135, L.136, T.139, R.274 Chain D: T.72, H.76, E.167 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain D: N.39, A.79, N.85, N.86, I.87 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain D: S.132, F.264, S.279, P.280, C.282 Ligand excluded by PLIP EDO.39: 6 residues within 4Å: Chain D: L.99, T.102, V.312, D.315, A.316, I.319 Ligand excluded by PLIP EDO.40: 2 residues within 4Å: Chain B: Q.182 Chain D: N.138 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain B: N.148, D.149, S.150 Chain D: K.186, I.189, D.190 Ligand excluded by PLIP

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.12: 7 residues within 4Å: Chain A: H.29, V.30, F.31, R.32, Q.251, L.252, Q.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.31, A:R.32 DMS.20: 6 residues within 4Å: Chain B: H.29, V.30, F.31, R.32, L.252, Q.255 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.31, B:R.32 DMS.32: 7 residues within 4Å: Chain C: H.29, V.30, F.31, R.32, Q.251, L.252, Q.255 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.31, C:R.32 DMS.42: 6 residues within 4Å: Chain D: H.29, V.30, F.31, R.32, Q.251, L.252 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:F.31, D:R.32

4 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 3 residues within 4Å: Chain A: D.125, H.157 Ligands: ZN.14 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.125, H2O.2, H2O.4, H2O.5, H2O.6, H2O.9 MG.21: 1 residues within 4Å: Chain B: D.125 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.125, H2O.16, H2O.17, H2O.19, H2O.20, H2O.23 MG.33: 3 residues within 4Å: Chain C: H.124, D.125, H.157 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.125, H2O.29, H2O.30, H2O.32, H2O.32, H2O.35 MG.43: 2 residues within 4Å: Chain D: D.125, H.157 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:D.125, H2O.41, H2O.41, H2O.42, H2O.44, H2O.47

4 x ZN: ZINC ION(Non-covalent)

ZN.14: 5 residues within 4Å: Chain A: H.88, H.124, D.125, D.242 Ligands: MG.13 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.88, A:H.124, A:D.125, A:D.242, H2O.2, H2O.8 ZN.22: 4 residues within 4Å: Chain B: H.88, H.124, D.125, D.242 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.88, B:H.124, B:D.125, B:D.242, H2O.16, H2O.22 ZN.34: 4 residues within 4Å: Chain C: H.88, H.124, D.125, D.242 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.88, C:H.124, C:D.125, C:D.242, H2O.30, H2O.34 ZN.44: 4 residues within 4Å: Chain D: H.88, H.124, D.125, D.242 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.88, D:H.124, D:D.125, D:D.242, H2O.41, H2O.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Larsen, J. et al., Discovery and Early Clinical Development of Isobutyl 1-[8-Methoxy-5-(1-oxo-3 H -isobenzofuran-5-yl)-[1,2,4]triazolo[1,5- a ]pyridin-2-yl]cyclopropanecarboxylate (LEO 39652), a Novel "Dual-Soft" PDE4 Inhibitor for Topical Treatment of Atopic Dermatitis. J.Med.Chem. (2020)

Release Date

2020-09-23

Peptides

cAMP-specific 3',5'-cyclic phosphodiesterase 4D: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
CCC

D
DDD

cAMP-specific 3',5'-cyclic phosphodiesterase 4D