7ABJ | pdb_00007abj

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1361

PDB DOI: https://doi.org/10.2210/pdb7ABJ/pdb

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

Deposited: 2020-09-07 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: 2.11 Å
R-Value Free:
0.218 (Depositor), 0.230 (DCC)
R-Value Work:
0.181 (Depositor), 0.190 (DCC)
R-Value Observed:
0.183 (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-1361

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

To be published.

Macromolecule Content

Total Structure Weight: 173.21 kDa
Atom Count: 11,436
Modeled Residue Count: 1,301
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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
863 (Subject of Investigation/LOI) Query on 863 Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain MB [auth D] SDF format, chain T [auth A] SDF format, chain UA [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain MB [auth D] MOL2 format, chain T [auth A] MOL2 format, chain UA [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain MB [auth D] mmCIF format, chain T [auth A] mmCIF format, chain UA [auth C]	HA [auth B], MB [auth D], T [auth A], UA [auth C]	5-(3-(cyclopentyloxy)-4-methoxyphenyl)-2-isopropyl-4,4-dimethyl-2,4-dihydro-3H-pyrazol-3-one C₂₀ H₂₈ N₂ O₃ XDNJVOAEUWIGML-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain MB [auth D] Focus chain T [auth A] Focus chain UA [auth C] Interactions & Density Focus chain HA [auth B] Focus chain MB [auth D] Focus chain T [auth A] Focus chain UA [auth C]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain V [auth A] SDF format, chain SA [auth C] SDF format, chain NB [auth D] SDF format, chain IA [auth B] SDF format, chain GA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain NB [auth D] MOL2 format, chain IA [auth B] MOL2 format, chain GA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain NB [auth D] mmCIF format, chain IA [auth B] mmCIF format, chain GA [auth B]	GA [auth B], IA [auth B], NB [auth D], SA [auth C], V [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain IA [auth B] Focus chain NB [auth D] Focus chain SA [auth C] Focus chain V [auth A] Interactions & Density Focus chain GA [auth B] Focus chain IA [auth B] Focus chain NB [auth D] Focus chain SA [auth C] Focus chain V [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain KA [auth C] SDF format, chain KB [auth D] SDF format, chain JB [auth D] SDF format, chain IB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain KB [auth D] MOL2 format, chain JB [auth D] MOL2 format, chain IB [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain KA [auth C] mmCIF format, chain KB [auth D] mmCIF format, chain JB [auth D] mmCIF format, chain IB [auth D]	EA [auth B], IB [auth D], JB [auth D], KA [auth C], KB [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain IB [auth D] Focus chain JB [auth D] Focus chain KA [auth C] Focus chain KB [auth D] Interactions & Density Focus chain EA [auth B] Focus chain IB [auth D] Focus chain JB [auth D] Focus chain KA [auth C] Focus chain KB [auth D]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain R [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain R [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain R [auth A]	FA [auth B], R [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain R [auth A] Interactions & Density Focus chain FA [auth B] Focus chain R [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain WA [auth D] SDF format, chain LA [auth C] SDF format, chain E [auth A] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain LA [auth C] MOL2 format, chain E [auth A] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain LA [auth C] mmCIF format, chain E [auth A]	E [auth A], LA [auth C], W [auth B], WA [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain LA [auth C] Focus chain W [auth B] Focus chain WA [auth D] Interactions & Density Focus chain E [auth A] Focus chain LA [auth C] Focus chain W [auth B] Focus chain WA [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain K [auth A] SDF format, chain ZA [auth D] SDF format, chain Z [auth B] SDF format, chain YA [auth D] SDF format, chain Y [auth B] SDF format, chain VA [auth C] SDF format, chain U [auth A] SDF format, chain TA [auth C] SDF format, chain S [auth A] SDF format, chain RA [auth C] SDF format, chain QA [auth C] SDF format, chain Q [auth A] SDF format, chain PA [auth C] SDF format, chain P [auth A] SDF format, chain OA [auth C] SDF format, chain O [auth A] SDF format, chain NA [auth C] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain LB [auth D] SDF format, chain L [auth A] SDF format, chain JA [auth C] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain HB [auth D] SDF format, chain H [auth A] SDF format, chain GB [auth D] SDF format, chain G [auth A] SDF format, chain FB [auth D] SDF format, chain EB [auth D] SDF format, chain DB [auth D] SDF format, chain DA [auth B] SDF format, chain CB [auth D] SDF format, chain CA [auth B] SDF format, chain BB [auth D] SDF format, chain BA [auth B] SDF format, chain AB [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain ZA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain VA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain LB [auth D] MOL2 format, chain L [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain HB [auth D] MOL2 format, chain H [auth A] MOL2 format, chain GB [auth D] MOL2 format, chain G [auth A] MOL2 format, chain FB [auth D] MOL2 format, chain EB [auth D] MOL2 format, chain DB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain AB [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain ZA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain VA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain LB [auth D] mmCIF format, chain L [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain HB [auth D] mmCIF format, chain H [auth A] mmCIF format, chain GB [auth D] mmCIF format, chain G [auth A] mmCIF format, chain FB [auth D] mmCIF format, chain EB [auth D] mmCIF format, chain DB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain CB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain BB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain AB [auth D]	AA [auth B] AB [auth D] BA [auth B] BB [auth D] CA [auth B] AA [auth B], AB [auth D], BA [auth B], BB [auth D], CA [auth B], CB [auth D], DA [auth B], DB [auth D], EB [auth D], FB [auth D], G [auth A], GB [auth D], H [auth A], HB [auth D], I [auth A], J [auth A], JA [auth C], K [auth A], L [auth A], LB [auth D], M [auth A], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], RA [auth C], S [auth A], TA [auth C], U [auth A], VA [auth C], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain G [auth A] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HB [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain LB [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain S [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain VA [auth C] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain G [auth A] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HB [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain LB [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain S [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain VA [auth C] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain XA [auth D] SDF format, chain X [auth B] SDF format, chain MA [auth C] SDF format, chain F [auth A] MOL2 format, chain XA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain F [auth A] mmCIF format, chain XA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain MA [auth C] mmCIF format, chain F [auth A]	F [auth A], MA [auth C], X [auth B], XA [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain MA [auth C] Focus chain X [auth B] Focus chain XA [auth D] Interactions & Density Focus chain F [auth A] Focus chain MA [auth C] Focus chain X [auth B] Focus chain XA [auth D]