7AAG | pdb_00007aag

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-617

PDB DOI: https://doi.org/10.2210/pdb7AAG/pdb

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

Deposited: 2020-09-04 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: 1.79 Å
R-Value Free:
0.197 (Depositor), 0.206 (DCC)
R-Value Work:
0.167 (Depositor), 0.180 (DCC)
R-Value Observed:
0.168 (Depositor)

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-617

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

To be published.

Macromolecule Content

Total Structure Weight: 175.81 kDa
Atom Count: 11,980
Modeled Residue Count: 1,300
Deposited Residue Count: 1,456
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 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q08499
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QWT (Subject of Investigation/LOI) Query on QWT Download:Ideal Coordinates CCD File SDF format, chain BB [auth C] SDF format, chain G [auth A] SDF format, chain HA [auth B] SDF format, chain TB [auth D] MOL2 format, chain BB [auth C] MOL2 format, chain G [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain TB [auth D] mmCIF format, chain BB [auth C] mmCIF format, chain G [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain TB [auth D]	BB [auth C], G [auth A], HA [auth B], TB [auth D]	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 C₃₀ H₃₈ N₆ O₄ JPXAIORZGBCHIB-UHFFFAOYSA-N		Interactions Focus chain BB [auth C] Focus chain G [auth A] Focus chain HA [auth B] Focus chain TB [auth D] Interactions & Density Focus chain BB [auth C] Focus chain G [auth A] Focus chain HA [auth B] Focus chain TB [auth D]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain JB [auth C] SDF format, chain KC [auth D] SDF format, chain TA [auth B] SDF format, chain W [auth A] SDF format, chain SA [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain KC [auth D] MOL2 format, chain TA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain SA [auth B] mmCIF format, chain JB [auth C] mmCIF format, chain KC [auth D] mmCIF format, chain TA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain SA [auth B]	JB [auth C], KC [auth D], SA [auth B], TA [auth B], W [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain JB [auth C] Focus chain KC [auth D] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain W [auth A] Interactions & Density Focus chain JB [auth C] Focus chain KC [auth D] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain W [auth A]
ILE Query on ILE Download:Ideal Coordinates CCD File SDF format, chain XA [auth C] MOL2 format, chain XA [auth C] mmCIF format, chain XA [auth C]	XA [auth C]	ISOLEUCINE C₆ H₁₃ N O₂ AGPKZVBTJJNPAG-WHFBIAKZSA-N		Interactions Focus chain XA [auth C] Interactions & Density Focus chain XA [auth C]
PRO Query on PRO Download:Ideal Coordinates CCD File SDF format, chain YA [auth C] MOL2 format, chain YA [auth C] mmCIF format, chain YA [auth C]	YA [auth C]	PROLINE C₅ H₉ N O₂ ONIBWKKTOPOVIA-BYPYZUCNSA-N		Interactions Focus chain YA [auth C] Interactions & Density Focus chain YA [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain FC [auth D] SDF format, chain GC [auth D] SDF format, chain HB [auth C] SDF format, chain P [auth A] SDF format, chain PB [auth D] MOL2 format, chain FC [auth D] MOL2 format, chain GC [auth D] MOL2 format, chain HB [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PB [auth D] mmCIF format, chain FC [auth D] mmCIF format, chain GC [auth D] mmCIF format, chain HB [auth C] mmCIF format, chain P [auth A] mmCIF format, chain PB [auth D]	FC [auth D], GC [auth D], HB [auth C], P [auth A], PB [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain FC [auth D] Focus chain GC [auth D] Focus chain HB [auth C] Focus chain P [auth A] Focus chain PB [auth D] Interactions & Density Focus chain FC [auth D] Focus chain GC [auth D] Focus chain HB [auth C] Focus chain P [auth A] Focus chain PB [auth D]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain HC [auth D] SDF format, chain IB [auth C] SDF format, chain IC [auth D] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain VA [auth B] SDF format, chain WA [auth C] SDF format, chain U [auth A] SDF format, chain RA [auth B] MOL2 format, chain HC [auth D] MOL2 format, chain IB [auth C] MOL2 format, chain IC [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain RA [auth B] mmCIF format, chain HC [auth D] mmCIF format, chain IB [auth C] mmCIF format, chain IC [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain WA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain RA [auth B]	HC [auth D] IB [auth C] IC [auth D] Q [auth A] QA [auth B] HC [auth D], IB [auth C], IC [auth D], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], T [auth A], U [auth A], VA [auth B], WA [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain HC [auth D] Focus chain IB [auth C] Focus chain IC [auth D] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain VA [auth B] Focus chain WA [auth C] Interactions & Density Focus chain HC [auth D] Focus chain IB [auth C] Focus chain IC [auth D] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain VA [auth B] Focus chain WA [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain FA [auth B] SDF format, chain RB [auth D] SDF format, chain ZA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain RB [auth D] MOL2 format, chain ZA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain RB [auth D] mmCIF format, chain ZA [auth C]	E [auth A], FA [auth B], RB [auth D], ZA [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain FA [auth B] Focus chain RB [auth D] Focus chain ZA [auth C] Interactions & Density Focus chain E [auth A] Focus chain FA [auth B] Focus chain RB [auth D] Focus chain ZA [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CB [auth C] SDF format, chain CC [auth D] SDF format, chain DA [auth A] SDF format, chain DB [auth C] SDF format, chain DC [auth D] SDF format, chain EA [auth B] SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain JC [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain KB [auth C] SDF format, chain L [auth A] SDF format, chain LB [auth C] SDF format, chain LC [auth D] SDF format, chain MA [auth B] SDF format, chain MC [auth D] SDF format, chain N [auth A] SDF format, chain NB [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain OB [auth C] SDF format, chain PA [auth B] SDF format, chain QB [auth D] SDF format, chain UA [auth B] SDF format, chain UB [auth D] SDF format, chain V [auth A] SDF format, chain VB [auth D] SDF format, chain WB [auth D] SDF format, chain X [auth A] SDF format, chain XB [auth D] SDF format, chain Y [auth A] SDF format, chain YB [auth D] SDF format, chain Z [auth A] SDF format, chain ZB [auth D] SDF format, chain NA [auth B] SDF format, chain MB [auth C] SDF format, chain M [auth A] SDF format, chain LA [auth B] SDF format, chain GB [auth C] SDF format, chain EC [auth D] SDF format, chain BC [auth D] SDF format, chain AC [auth D] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CB [auth C] MOL2 format, chain CC [auth D] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth C] MOL2 format, chain DC [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain JC [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LB [auth C] MOL2 format, chain LC [auth D] MOL2 format, chain MA [auth B] MOL2 format, chain MC [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth C] MOL2 format, chain PA [auth B] MOL2 format, chain QB [auth D] MOL2 format, chain UA [auth B] MOL2 format, chain UB [auth D] MOL2 format, chain V [auth A] MOL2 format, chain VB [auth D] MOL2 format, chain WB [auth D] MOL2 format, chain X [auth A] MOL2 format, chain XB [auth D] MOL2 format, chain Y [auth A] MOL2 format, chain YB [auth D] MOL2 format, chain Z [auth A] MOL2 format, chain ZB [auth D] MOL2 format, chain NA [auth B] MOL2 format, chain MB [auth C] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain GB [auth C] MOL2 format, chain EC [auth D] MOL2 format, chain BC [auth D] MOL2 format, chain AC [auth D] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CB [auth C] mmCIF format, chain CC [auth D] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth C] mmCIF format, chain DC [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain JC [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain KB [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LB [auth C] mmCIF format, chain LC [auth D] mmCIF format, chain MA [auth B] mmCIF format, chain MC [auth D] mmCIF format, chain N [auth A] mmCIF format, chain NB [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain OB [auth C] mmCIF format, chain PA [auth B] mmCIF format, chain QB [auth D] mmCIF format, chain UA [auth B] mmCIF format, chain UB [auth D] mmCIF format, chain V [auth A] mmCIF format, chain VB [auth D] mmCIF format, chain WB [auth D] mmCIF format, chain X [auth A] mmCIF format, chain XB [auth D] mmCIF format, chain Y [auth A] mmCIF format, chain YB [auth D] mmCIF format, chain Z [auth A] mmCIF format, chain ZB [auth D] mmCIF format, chain NA [auth B] mmCIF format, chain MB [auth C] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain GB [auth C] mmCIF format, chain EC [auth D] mmCIF format, chain BC [auth D] mmCIF format, chain AC [auth D]	AA [auth A] AC [auth D] BA [auth A] BC [auth D] CB [auth C] AA [auth A], AC [auth D], BA [auth A], BC [auth D], CB [auth C], CC [auth D], DA [auth A], DB [auth C], DC [auth D], EA [auth B], EB [auth C], EC [auth D], FB [auth C], GB [auth C], H [auth A], I [auth A], IA [auth B], J [auth A], JA [auth B], JC [auth D], K [auth A], KA [auth B], KB [auth C], L [auth A], LA [auth B], LB [auth C], LC [auth D], M [auth A], MA [auth B], MB [auth C], MC [auth D], N [auth A], NA [auth B], NB [auth C], O [auth A], OA [auth B], OB [auth C], PA [auth B], QB [auth D], UA [auth B], UB [auth D], V [auth A], VB [auth D], WB [auth D], X [auth A], XB [auth D], Y [auth A], YB [auth D], Z [auth A], ZB [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AC [auth D] Focus chain BA [auth A] Focus chain BC [auth D] Focus chain CB [auth C] Focus chain CC [auth D] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain DC [auth D] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain EC [auth D] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JC [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain LC [auth D] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain MC [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain PA [auth B] Focus chain QB [auth D] Focus chain UA [auth B] Focus chain UB [auth D] Focus chain V [auth A] Focus chain VB [auth D] Focus chain WB [auth D] Focus chain X [auth A] Focus chain XB [auth D] Focus chain Y [auth A] Focus chain YB [auth D] Focus chain Z [auth A] Focus chain ZB [auth D] Interactions & Density Focus chain AA [auth A] Focus chain AC [auth D] Focus chain BA [auth A] Focus chain BC [auth D] Focus chain CB [auth C] Focus chain CC [auth D] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain DC [auth D] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain EC [auth D] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JC [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain LC [auth D] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain MC [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain PA [auth B] Focus chain QB [auth D] Focus chain UA [auth B] Focus chain UB [auth D] Focus chain V [auth A] Focus chain VB [auth D] Focus chain WB [auth D] Focus chain X [auth A] Focus chain XB [auth D] Focus chain Y [auth A] Focus chain YB [auth D] Focus chain Z [auth A] Focus chain ZB [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain CA [auth A] SDF format, chain F [auth A] SDF format, chain GA [auth B] SDF format, chain SB [auth D] MOL2 format, chain AB [auth C] MOL2 format, chain CA [auth A] MOL2 format, chain F [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain SB [auth D] mmCIF format, chain AB [auth C] mmCIF format, chain CA [auth A] mmCIF format, chain F [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain SB [auth D]	AB [auth C], CA [auth A], F [auth A], GA [auth B], SB [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Focus chain CA [auth A] Focus chain F [auth A] Focus chain GA [auth B] Focus chain SB [auth D] Interactions & Density Focus chain AB [auth C] Focus chain CA [auth A] Focus chain F [auth A] Focus chain GA [auth B] Focus chain SB [auth D]