6IBF | pdb_00006ibf

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-417

PDB DOI: https://doi.org/10.2210/pdb6IBF/pdb

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

Deposited: 2018-11-29 Released: 2019-12-18
Deposition Author(s): Singh, A.K., Brown, D.G.
Funding Organization(s): European Union

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free:
0.262 (Depositor), 0.262 (DCC)
R-Value Work:
0.203 (Depositor), 0.210 (DCC)
R-Value Observed:
0.206 (Depositor)

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-417

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

To be published.

Macromolecule Content

Total Structure Weight: 173.71 kDa
Atom Count: 11,470
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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4I7 (Subject of Investigation/LOI) Query on 4I7 Download:Ideal Coordinates CCD File SDF format, chain GB [auth D] SDF format, chain LA [auth C] SDF format, chain Q [auth A] SDF format, chain DA [auth B] MOL2 format, chain GB [auth D] MOL2 format, chain LA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain DA [auth B] mmCIF format, chain GB [auth D] mmCIF format, chain LA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain DA [auth B]	DA [auth B], GB [auth D], LA [auth C], Q [auth A]	(4~{a}~{S},8~{a}~{R})-4-[4-methoxy-3-[[2-(trifluoromethyl)phenyl]methoxy]phenyl]-2-(1-thieno[3,2-d]pyrimidin-4-ylpiperidin-4-yl)-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-one C₃₄ H₃₂ F₃ N₅ O₃ S BVADHKPPTNFKBH-LOSJGSFVSA-N		Interactions Focus chain DA [auth B] Focus chain GB [auth D] Focus chain LA [auth C] Focus chain Q [auth A] Interactions & Density Focus chain DA [auth B] Focus chain GB [auth D] Focus chain LA [auth C] Focus chain Q [auth A]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain CB [auth D] SDF format, chain IA [auth C] SDF format, chain N [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain IA [auth C] MOL2 format, chain N [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain CB [auth D] mmCIF format, chain IA [auth C] mmCIF format, chain N [auth A]	AA [auth B], CB [auth D], IA [auth C], N [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain CB [auth D] Focus chain IA [auth C] Focus chain N [auth A] Interactions & Density Focus chain AA [auth B] Focus chain CB [auth D] Focus chain IA [auth C] Focus chain N [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain XA [auth D] SDF format, chain YA [auth D] MOL2 format, chain XA [auth D] MOL2 format, chain YA [auth D] mmCIF format, chain XA [auth D] mmCIF format, chain YA [auth D]	XA [auth D], YA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain XA [auth D] Focus chain YA [auth D] Interactions & Density Focus chain XA [auth D] Focus chain YA [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain EA [auth C] SDF format, chain NA [auth D] SDF format, chain R [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain NA [auth D] MOL2 format, chain R [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain NA [auth D] mmCIF format, chain R [auth B]	E [auth A], EA [auth C], NA [auth D], R [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain EA [auth C] Focus chain NA [auth D] Focus chain R [auth B] Interactions & Density Focus chain E [auth A] Focus chain EA [auth C] Focus chain NA [auth D] Focus chain R [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain BB [auth D] SDF format, chain CA [auth B] SDF format, chain DB [auth D] SDF format, chain EB [auth D] SDF format, chain FB [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain HB [auth D] SDF format, chain I [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain O [auth A] 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 SA [auth D] SDF format, chain T [auth B] SDF format, chain TA [auth D] SDF format, chain U [auth B] SDF format, chain UA [auth D] SDF format, chain V [auth B] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] SDF format, chain J [auth A] SDF format, chain AB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain EB [auth D] MOL2 format, chain FB [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain HB [auth D] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain O [auth A] 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 SA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain AB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain DB [auth D] mmCIF format, chain EB [auth D] mmCIF format, chain FB [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain HB [auth D] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain O [auth A] 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 SA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain AB [auth D]	AB [auth D] BA [auth B] BB [auth D] CA [auth B] DB [auth D] AB [auth D], BA [auth B], BB [auth D], CA [auth B], DB [auth D], EB [auth D], FB [auth D], G [auth A], GA [auth C], H [auth A], HA [auth C], HB [auth D], I [auth A], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], M [auth A], MA [auth C], O [auth A], P [auth A], PA [auth D], QA [auth D], RA [auth D], SA [auth D], T [auth B], TA [auth D], U [auth B], UA [auth D], V [auth B], VA [auth D], W [auth B], WA [auth D], X [auth B], Y [auth B], Z [auth B], ZA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] 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 KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] 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 KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZA [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain OA [auth D] SDF format, chain S [auth B] SDF format, chain FA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain FA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain FA [auth C]	F [auth A], FA [auth C], OA [auth D], S [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain FA [auth C] Focus chain OA [auth D] Focus chain S [auth B] Interactions & Density Focus chain F [auth A] Focus chain FA [auth C] Focus chain OA [auth D] Focus chain S [auth B]