SMTL ID : 7aag.1 (3 other biounits)

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-617

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.90, H.126, D.127, D.244 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.90, A:H.126, A:D.127, A:D.244, H2O.3, H2O.5

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.127 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.127, H2O.2, H2O.3, H2O.3, H2O.5, H2O.7 MG.25: 2 residues within 4Å: Chain A: H.80, D.82 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.80, A:D.82, A:D.82, H2O.4

1 x QWT: 1-cycloheptyl-3-(4-methoxy-3-{4-[4-(1H-1,2,3,4-tetrazol-5-yl)phenoxy]butoxy}phenyl)-4,4-dimethyl-4,5-dihydro-1H-pyrazol-5-one(Non-covalent)

QWT.3: 15 residues within 4Å: Chain A: Y.85, H.86, M.199, L.245, N.247, I.262, F.266, M.283, S.294, Q.295, G.297, F.298, Y.301, I.302 Ligands: EDO.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.245, A:I.262, A:Y.301, A:I.302, A:I.302 Hydrogen bonds: A:Q.295 pi-Stacking: A:F.298, A:Y.301

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

EDO.4: 5 residues within 4Å: Chain A: S.134, F.266, P.282, C.284 Ligands: QWT.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.134, A:S.134, A:P.282 Water bridges: A:Q.269 EDO.5: 2 residues within 4Å: Chain A: K.180, Q.184 No protein-ligand interaction detected (PLIP) EDO.6: 6 residues within 4Å: Chain A: N.41, A.81, N.87, N.88, I.89, R.261 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.41, A:A.81, A:N.88, A:N.88, A:R.261, A:R.261 EDO.7: 6 residues within 4Å: Chain A: T.112, L.114, E.115, S.185, M.189 Ligands: DMS.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.112, A:T.112, A:S.185, A:S.185 EDO.8: 3 residues within 4Å: Chain A: S.152, N.157, L.195 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.152, A:N.157 EDO.9: 2 residues within 4Å: Chain A: E.144 Ligands: EDO.10 No protein-ligand interaction detected (PLIP) EDO.10: 2 residues within 4Å: Chain A: E.144 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.144 EDO.11: 4 residues within 4Å: Chain A: D.208, T.211, M.212, Q.234 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.208 EDO.18: 3 residues within 4Å: Chain A: K.188, I.191, D.192 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.192 Water bridges: A:K.188, A:K.188, A:D.192 EDO.20: 5 residues within 4Å: Chain A: D.77, Y.79, H.80, A.81 Ligands: EDO.21 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.81 Water bridges: A:H.78, A:H.80 EDO.21: 7 residues within 4Å: Chain A: N.41, R.42, E.76, D.77, Y.79, N.88 Ligands: EDO.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.41, A:R.42, A:D.77, A:Y.79 EDO.22: 3 residues within 4Å: Chain A: T.74, H.78, E.169 No protein-ligand interaction detected (PLIP) EDO.23: 6 residues within 4Å: Chain A: L.101, T.104, W.310, V.314, D.317, I.321 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.104 EDO.24: 6 residues within 4Å: Chain A: N.135, D.151, S.152, S.153, D.198, S.200 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.135, A:D.151, A:S.153, A:D.198, A:S.200 Water bridges: A:V.154 EDO.26: 1 residues within 4Å: Chain A: Q.184 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.12: 6 residues within 4Å: Chain A: M.212, T.215, K.216, K.217, L.225, D.231 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.215, A:K.217, A:L.225, A:D.231

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

DMS.13: 5 residues within 4Å: Chain A: F.164, L.167, F.175, R.183, R.187 No protein-ligand interaction detected (PLIP) DMS.14: 4 residues within 4Å: Chain A: S.185, K.188, Y.229 Ligands: EDO.7 No protein-ligand interaction detected (PLIP) DMS.15: 7 residues within 4Å: Chain A: A.106, K.216, V.218, G.222, L.313, V.314, H.315 No protein-ligand interaction detected (PLIP) DMS.16: 2 residues within 4Å: Chain A: T.60, K.62 No protein-ligand interaction detected (PLIP) DMS.17: 4 residues within 4Å: Chain A: P.64, D.66, T.67, N.171 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.66

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.19: 7 residues within 4Å: Chain A: H.31, V.32, F.33, R.34, E.37, L.254, Q.257 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:F.33, A:R.34, A:Q.257 Water bridges: A:Q.257, A:R.261 Salt bridges: A:H.31, A:E.37, A:E.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, A.K. et al., hPDE4D2 structure with inhibitor NPD-617. To be published

Release Date

2021-10-06

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

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

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