SMTL ID : 7a8q.4 (3 other biounits)

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-654

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 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.1, H2O.1

1 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.1, H2O.2, H2O.3, H2O.3, H2O.4

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

EDO.3: 2 residues within 4Å: Chain A: P.105, D.317 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.317 EDO.4: 7 residues within 4Å: Chain A: S.134, F.266, Q.269, S.281, P.282, C.284 Ligands: R4H.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.134, A:S.134, A:P.282 EDO.5: 4 residues within 4Å: Chain A: F.164, F.175, R.183, R.187 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.183 EDO.6: 2 residues within 4Å: Chain A: K.188, D.192 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.192 EDO.7: 6 residues within 4Å: Chain A: N.41, A.81, N.87, N.88, I.89, R.261 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.41, A:N.88, A:R.261 Water bridges: A:Y.79 EDO.8: 7 residues within 4Å: Chain A: L.101, T.104, W.310, V.314, D.317, I.321 Ligands: EDO.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.104, A:W.310, A:D.317 EDO.9: 1 residues within 4Å: Chain A: E.108 No protein-ligand interaction detected (PLIP) EDO.10: 5 residues within 4Å: Chain A: N.26, K.27, W.28, V.100 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.26, A:W.28 EDO.11: 3 residues within 4Å: Chain A: T.74, H.78, E.169 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.74, A:E.169, A:E.169

1 x R4H: 2-cycloheptyl-5-[4-methoxy-3-[[4-(1~{H}-1,2,3,4-tetrazol-5-yl)phenyl]methoxy]phenyl]-4,4-dimethyl-pyrazolidin-3-one(Non-covalent)

R4H.12: 15 residues within 4Å: Chain A: Y.85, H.86, M.199, L.245, N.247, W.258, T.259, I.262, F.266, M.283, S.294, Q.295, G.297, F.298 Ligands: EDO.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.245, A:F.298, A:F.298, A:F.298 Hydrogen bonds: A:Q.295 pi-Stacking: A:F.298

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

PEG.13: 2 residues within 4Å: Chain A: V.46, H.49 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.49 PEG.14: 6 residues within 4Å: Chain A: T.112, L.114, E.115, S.185, M.189, Y.229 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.115, A:S.185 Water bridges: A:T.112, A:L.114 PEG.15: 5 residues within 4Å: Chain A: P.251, L.252, T.324, D.327, N.328 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.252, A:D.327

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

EPE.16: 8 residues within 4Å: Chain A: H.31, V.32, F.33, R.34, E.37, Q.253, L.254, Q.257 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.33, A:R.34, A:Q.253, A:Q.257 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-654. 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
D

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

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