- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.79 Å
- Oligo State
- monomer
- Ligands
- 3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.2: 2 residues within 4Å:- Chain A: E.144
- Ligands: EDO.12
No protein-ligand interaction detected (PLIP)EDO.6: 2 residues within 4Å:- Chain A: P.105, D.317
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:D.317
EDO.7: 5 residues within 4Å:- Chain A: S.134, F.266, S.281, P.282, C.284
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:S.134, A:S.134, A:P.282
- Water bridges: A:Q.269, A:Q.269
EDO.8: 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.9: 3 residues within 4Å:- Chain A: K.188, I.191, D.192
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:D.192
EDO.10: 5 residues within 4Å:- Chain A: N.41, A.81, N.87, N.88, R.261
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:N.41, A:N.88, A:N.88, A:R.261
- Water bridges: A:R.261
EDO.11: 8 residues within 4Å:- Chain A: V.100, L.101, T.104, W.310, V.314, D.317, A.318, I.321
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:T.104, A:W.310
EDO.12: 2 residues within 4Å:- Chain A: E.144
- Ligands: EDO.2
1 PLIP interactions:1 interactions with chain A- Water bridges: A:E.144
EDO.13: 2 residues within 4Å:- Chain A: H.49, I.69
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:H.49
EDO.14: 6 residues within 4Å:- Chain A: Q.176, N.177, L.178, T.179, K.180, R.183
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.180, A:R.183, A:R.183
EDO.15: 4 residues within 4Å:- Chain A: M.199, M.203, I.302
- Ligands: QWT.5
No protein-ligand interaction detected (PLIP)EDO.16: 1 residues within 4Å:- Chain A: E.108
No protein-ligand interaction detected (PLIP)EDO.21: 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
EDO.23: 4 residues within 4Å:- Chain A: P.64, D.66, T.67, N.171
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.66
- Water bridges: A:Q.176
EDO.24: 2 residues within 4Å:- Chain A: R.329, Q.333
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.329, A:R.329
- Water bridges: A:Q.333
- 1 x ZN: ZINC ION(Non-covalent)
- 1 x MG: MAGNESIUM ION(Non-covalent)
- 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)
- 2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)
- 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
D
SMTL ID : 7aag.4 (3 other biounits)
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-617
cAMP-specific 3',5'-cyclic phosphodiesterase 4D
Related Entries With Identical Sequence
5lbo.1 | 5lbo.2 | 5lbo.3 | 5lbo.4 | 6akr.1 | 6akr.2 | 6akr.3 | 6akr.4 | 6fdi.1 | 6fdi.2 | 6fdi.3 | 6fdi.4 | 6fe7.1 | 6fe7.2 | 6fe7.3 | 6fe7.4 | 6feb.1 | 6feb.2 | 6fet.1 | 6fet.2 | 6fet.3 | 6fet.4 | 6ft0.1 | 6ft0.2 | 6ft0.3 | 6ft0.4 | 6fta.1 | 6fta.2 | 6fta.3 | 6fta.4 more...less...6ftw.1 | 6ftw.2 | 6ftw.3 | 6ftw.4 | 6fw3.1 | 6fw3.2 | 6fw3.3 | 6fw3.4 | 6hwo.1 | 6hwo.2 | 6hwo.3 | 6hwo.4 | 6iag.1 | 6iag.2 | 6iag.3 | 6iag.4 | 6ibf.1 | 6ibf.2 | 6ibf.3 | 6ibf.4 | 6rcw.1 | 6rcw.2 | 6rcw.3 | 6rcw.4 | 7a8q.1 | 7a8q.2 | 7a8q.3 | 7a8q.4 | 7a9v.1 | 7a9v.2 | 7a9v.3 | 7a9v.4 | 7aag.1 | 7aag.2 | 7aag.3 | 7ab9.1 | 7ab9.2 | 7ab9.3 | 7ab9.4 | 7abd.1 | 7abd.2 | 7abd.3 | 7abd.4 | 7abe.1 | 7abe.2 | 7abe.3 | 7abe.4 | 7abj.1 | 7abj.2 | 7abj.3 | 7abj.4