SMTL ID : 5k6j.1

Human Phospodiesterase 4B in complex with pyridyloxy-benzoxaborole based inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.77, H.113, D.114, D.231 Ligands: MG.2, 6QQ.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.77, A:H.113, A:D.114, A:D.231

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.114 Ligands: ZN.1, 6QQ.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.114, H2O.1, H2O.2, H2O.3

1 x 6QQ: 6-[[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1(6),2,4-trien-3-yl]oxy]-5-chloranyl-2-(4-oxidanylidenepentoxy)pyridine-3-carbonitrile(Non-covalent)

6QQ.3: 21 residues within 4Å: Chain A: Y.72, H.73, H.77, H.113, D.114, H.117, M.186, D.231, L.232, N.234, P.235, Y.242, W.245, T.246, I.249, F.253, M.270, Q.282, F.285 Ligands: ZN.1, MG.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.232, A:N.234, A:Y.242, A:W.245, A:I.249, A:F.253, A:F.285, A:F.285 Hydrogen bonds: A:Q.282 Water bridges: A:T.184, A:N.234

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

EDO.4: 7 residues within 4Å: Chain A: T.47, F.48, N.164, L.165, T.166, Q.169 Ligands: EDO.20 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: T.54, H.158, C.159, D.160, M.163 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain A: H.65 Ligands: EDO.7 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: H.65, K.152, L.153 Ligands: EDO.6 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: S.90, P.92, D.95 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: L.88, T.91, W.297, V.301, D.304, A.305, I.308 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: A.6, L.9, E.10 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: S.268, P.269, M.270, C.271, D.272, A.276 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: R.316, N.317 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: P.92, D.304 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: K.7, E.10 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: L.154, F.162, R.170, R.174 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: N.13, E.41, H.86, S.90 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: S.121, F.253, P.269, C.271 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: L.89, L.94, D.95, A.96, V.97, F.98, I.103 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: R.42, D.43, L.44, T.47, D.100, I.103 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: T.47, F.48, D.100, Q.169 Ligands: EDO.4 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, C. et al., To be published. To Be Published

Release Date

2017-05-31

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

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

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