7A8Q

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-654

PDB DOI: https://doi.org/10.2210/pdb7A8Q/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-08-30 Released: 2021-10-06
Deposition Author(s): Singh, A.K., Blaazer, A.R., Zara, L., de Esch, I.J.P., Leurs, R., Brown, D.G.
Funding Organization(s): European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.229
R-Value Work: 0.187
R-Value Observed: 0.189

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

hPDE4D2 structure with inhibitor NPD-654

Singh, A.K., Brown, D.G.

To be published.

Macromolecule Content

Total Structure Weight: 172.36 kDa
Atom Count: 11,327
Modelled Residue Count: 1,302
Deposited Residue Count: 1,456
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-specific 3',5'-cyclic phosphodiesterase 4D	A, B, C, D	364	Homo sapiens	Mutation(s): 0 Gene Names: PDE4D, DPDE3 EC: 3.1.4.53
UniProt & NIH Common Fund Data Resources
Find proteins for Q08499 (Homo sapiens) Explore Q08499 Go to UniProtKB: Q08499
PHAROS: Q08499 GTEx: ENSG00000113448
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08499
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
R4H (Subject of Investigation/LOI) Query on R4H Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain UA [auth D] SDF format, chain X [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain UA [auth D] MOL2 format, chain X [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain UA [auth D] mmCIF format, chain X [auth B]	GA [auth C], UA [auth D], X [auth B]	2-cycloheptyl-5-[4-methoxy-3-[[4-(1~{H}-1,2,3,4-tetrazol-5-yl)phenyl]methoxy]phenyl]-4,4-dimethyl-pyrazolidin-3-one C₂₇ H₃₄ N₆ O₃ QTPLHRMVDWVYKA-XMMPIXPASA-N		Interactions Focus chain GA [auth C] Focus chain UA [auth D] Focus chain X [auth B] Interactions & Density Focus chain GA [auth C] Focus chain UA [auth D] Focus chain X [auth B]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain N [auth A] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Z [auth B]	FA [auth C], N [auth A], Y [auth B], YA [auth D], Z [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain N [auth A] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Interactions & Density Focus chain FA [auth C] Focus chain N [auth A] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain VA [auth D] SDF format, chain WA [auth D] SDF format, chain XA [auth D] MOL2 format, chain HA [auth C] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain XA [auth D] mmCIF format, chain HA [auth C] mmCIF format, chain VA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain XA [auth D]	HA [auth C], VA [auth D], WA [auth D], XA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain HA [auth C] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Interactions & Density Focus chain HA [auth C] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain E [auth A] SDF format, chain JA [auth D] SDF format, chain Q [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain Q [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain Q [auth B]	AA [auth C], E [auth A], JA [auth D], Q [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain E [auth A] Focus chain JA [auth D] Focus chain Q [auth B] Interactions & Density Focus chain AA [auth C] Focus chain E [auth A] Focus chain JA [auth D] Focus chain Q [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain S [auth B] SDF format, chain SA [auth D] SDF format, chain T [auth B] SDF format, chain TA [auth D] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	CA [auth C] DA [auth C] EA [auth C] G [auth A] H [auth A] CA [auth C], DA [auth C], EA [auth C], G [auth A], H [auth A], I [auth A], IA [auth C], J [auth A], K [auth A], L [auth A], LA [auth D], M [auth A], MA [auth D], NA [auth D], O [auth A], OA [auth D], P [auth A], PA [auth D], QA [auth D], RA [auth D], S [auth B], SA [auth D], T [auth B], TA [auth D], U [auth B], V [auth B], W [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain F [auth A] SDF format, chain KA [auth D] SDF format, chain R [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain R [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain R [auth B]	BA [auth C], F [auth A], KA [auth D], R [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain F [auth A] Focus chain KA [auth D] Focus chain R [auth B] Interactions & Density Focus chain BA [auth C] Focus chain F [auth A] Focus chain KA [auth D] Focus chain R [auth B]