3KKT | pdb_00003kkt

Crystal structure of human PDE4b with 5-[3-[(1S,2S,4R)-Bicyclo[2.2.1]hept-2-yloxy]-4-methoxyp henyl]tetrahydro-2(1H)-pyrimidinone reveals ordering of the C-terminal helix residues 502-509.

PDB DOI: https://doi.org/10.2210/pdb3KKT/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-11-06 Released: 2009-11-24
Deposition Author(s): Cheng, R.K.Y., Crawley, L., Barker, J., Whittaker, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free:
0.295 (Depositor), 0.277 (DCC)
R-Value Work:
0.235 (Depositor)
R-Value Observed:
0.238 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of human PDE4b with 5-[3-[(1S,2S,4R)-Bicyclo[2.2.1]hept-2-yloxy]-4-methoxyp henyl]tetrahydro-2(1H)-pyrimidinone reveals ordering of the C-terminal helix residues 502-509.

Cheng, R.K.Y., Crawley, L., Barker, J., Whittaker, M.

To be published.

Macromolecule Content

Total Structure Weight: 92.4 kDa
Atom Count: 5,684
Modeled Residue Count: 685
Deposited Residue Count: 796
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-specific 3',5'-cyclic phosphodiesterase 4B	A, B	398	Homo sapiens	Mutation(s): 0 Gene Names: DPDE4, PDE4B EC: 3.1.4.17 (PDB Primary Data), 3.1.4.53 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q07343 (Homo sapiens) Explore Q07343 Go to UniProtKB: Q07343
PHAROS: Q07343 GTEx: ENSG00000184588
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q07343
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0CP Query on 0CP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	5-{3-[(1S,2S,4R)-bicyclo[2.2.1]hept-2-yloxy]-4-methoxyphenyl}tetrahydropyrimidin-2(1H)-one C₁₈ H₂₄ N₂ O₃ LITNEAPWQHVPOK-FFSVYQOJSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
B3P Query on B3P Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₁₁ H₂₆ N₂ O₆ HHKZCCWKTZRCCL-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.295 (Depositor), 0.277 (DCC)
R-Value Work: 0.235 (Depositor)
R-Value Observed: 0.238 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.74	α = 90
b = 89.74	β = 90
c = 337.443	γ = 120

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
CrystalClear	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-11-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-11-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Refinement description, Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary