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PDE4 crystal structure in complex with small molecule inhibitor

X-ray diffraction
2.61Å resolution
PDB entry 5k1i coloured by chain, front view.
PDB entry 5k1i coloured by chain, side view.
PDB entry 5k1i coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
monomeric (preferred)
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: 3',5'-cyclic-AMP phosphodiesterase 4D
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Multimeric state: monomeric
Accessible surface area: 14910.8 Å2
Buried surface area: 245.41 Å2
Dissociation area: 76 Å2
Dissociation energy (ΔGdiss): 16.45 kcal/mol
Dissociation entropy (TΔSdiss): -1.46 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-170654
Assembly 2
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Assembly Name: 3',5'-cyclic-AMP phosphodiesterase 4D
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Multimeric state: monomeric
Accessible surface area: 15021.08 Å2
Buried surface area: 243.95 Å2
Dissociation area: 73.52 Å2
Dissociation energy (ΔGdiss): 15.85 kcal/mol
Dissociation entropy (TΔSdiss): -1.46 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-170654
Assembly 3
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Assembly Name: 3',5'-cyclic-AMP phosphodiesterase 4D
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Multimeric state: monomeric
Accessible surface area: 14741.03 Å2
Buried surface area: 243.12 Å2
Dissociation area: 76.29 Å2
Dissociation energy (ΔGdiss): 17.39 kcal/mol
Dissociation entropy (TΔSdiss): -1.46 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-170654
Assembly 4
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Assembly Name: 3',5'-cyclic-AMP phosphodiesterase 4D
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Multimeric state: monomeric
Accessible surface area: 15011.13 Å2
Buried surface area: 248.33 Å2
Dissociation area: 77.43 Å2
Dissociation energy (ΔGdiss): 17.07 kcal/mol
Dissociation entropy (TΔSdiss): -1.46 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-170654
Assembly 5
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Assembly Name: 3',5'-cyclic-AMP phosphodiesterase 4D
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Multimeric state: monomeric
Accessible surface area: 14816.39 Å2
Buried surface area: 246.5 Å2
Dissociation area: 78.22 Å2
Dissociation energy (ΔGdiss): 16.68 kcal/mol
Dissociation entropy (TΔSdiss): -1.46 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-170654
Assembly 6
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Assembly Name: 3',5'-cyclic-AMP phosphodiesterase 4D
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Multimeric state: monomeric
Accessible surface area: 14952.08 Å2
Buried surface area: 245.08 Å2
Dissociation area: 76.13 Å2
Dissociation energy (ΔGdiss): 17.2 kcal/mol
Dissociation entropy (TΔSdiss): -1.46 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-170654
Assembly 7
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Assembly Name: 3',5'-cyclic-AMP phosphodiesterase 4D
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Multimeric state: monomeric
Accessible surface area: 14764.92 Å2
Buried surface area: 244.52 Å2
Dissociation area: 75.74 Å2
Dissociation energy (ΔGdiss): 16.06 kcal/mol
Dissociation entropy (TΔSdiss): -1.46 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-170654
Assembly 8
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Assembly Name: 3',5'-cyclic-AMP phosphodiesterase 4D
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Multimeric state: monomeric
Accessible surface area: 15088.13 Å2
Buried surface area: 246.82 Å2
Dissociation area: 76.2 Å2
Dissociation energy (ΔGdiss): 16.68 kcal/mol
Dissociation entropy (TΔSdiss): -1.46 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-170654

Macromolecules

3',5'-cyclic-AMP phosphodiesterase 4D
Chains: A, B, C, D, E, F, G, H
Length: 326 amino acids
Theoretical weight: 37.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q08499 (Residues: 388-713; Coverage: 40%)
Gene names: DPDE3, PDE4D
Pfam: 3'5'-cyclic nucleotide phosphodiesterase
InterPro:
CATH: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain
3',5'-cyclic-AMP phosphodiesterase 4D in PDB entry 5k1i, assembly 1, front view.
3',5'-cyclic-AMP phosphodiesterase 4D in PDB entry 5k1i, assembly 1, side view.
3',5'-cyclic-AMP phosphodiesterase 4D in PDB entry 5k1i, assembly 1, top view.
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