SMTL ID : 7aag.3 (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

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

DMS.1: 2 residues within 4Å: Chain A: E.275, R.276 No protein-ligand interaction detected (PLIP) DMS.13: 3 residues within 4Å: Chain A: Q.136, I.139, S.200 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.136

1 x ILE: ISOLEUCINE(Covalent)

ILE.2: 7 residues within 4Å: Chain A: E.292, K.293, Y.332, Q.333, S.334, T.335 Ligands: PRO.3 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:E.292, A:K.293 Hydrogen bonds: A:Q.333

1 x PRO: PROLINE(Non-covalent)

PRO.3: 2 residues within 4Å: Chain A: T.335 Ligands: ILE.2 0 PLIP interactions:

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: H.90, H.126, D.127, D.244 Ligands: MG.5 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.2, H2O.4

1 x MG: MAGNESIUM ION(Non-covalent)

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

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.6: 18 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, Y.301, I.302 Ligands: EDO.7, EDO.15 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.245, A:I.262, A:F.298, A:I.302 Hydrogen bonds: A:Q.295 pi-Stacking: A:F.298, A:Y.301

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

EDO.7: 6 residues within 4Å: Chain A: S.134, F.266, P.282, C.284 Ligands: QWT.6, EDO.15 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.8: 4 residues within 4Å: Chain A: F.164, F.175, R.183, R.187 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.183, A:R.187 EDO.9: 3 residues within 4Å: Chain A: L.114, K.181, S.185 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.181, A:S.185, A:S.185 EDO.10: 6 residues within 4Å: Chain A: L.101, T.104, W.310, V.314, D.317, I.321 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.104, A:W.310 Water bridges: A:D.317 EDO.11: 1 residues within 4Å: Chain A: E.144 No protein-ligand interaction detected (PLIP) EDO.15: 5 residues within 4Å: Chain A: H.86, S.134, F.266 Ligands: QWT.6, EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.130 Water bridges: A:H.86 EDO.16: 5 residues within 4Å: Chain A: N.26, E.54, R.55, H.99, S.103 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.54, A:S.103, A:S.103 EDO.17: 5 residues within 4Å: Chain A: F.61, T.112, D.113, L.114, Q.182 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.112, A:D.113, A:L.114 Water bridges: A:T.112 EDO.18: 5 residues within 4Å: Chain A: R.256, E.292, W.331, Y.332, T.335 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.256, A:E.292, A:E.292 EDO.19: 3 residues within 4Å: Chain A: N.140, M.278, E.279 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.140, A:E.279

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

PEG.12: 4 residues within 4Å: Chain A: T.74, D.77, H.78, E.169 No protein-ligand interaction detected (PLIP)

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

EPE.14: 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-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
C

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

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