5SKF | pdb_00005skf

CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 10 IN COMPLEX WITH C1(=NN(C=CC1=O)c2cccc3c2OC(O3)(F)F)c4ccnn4c5cccc(c5)C#N, micromolar IC50=0.080428

PDB DOI: https://doi.org/10.2210/pdb5SKF/pdb
Deposition Group: G_1002229 ExploreG_1002229

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

Deposited: 2022-02-01 Released: 2022-10-12
Deposition Author(s): Joseph, C., Benz, J., Flohr, A., Rodriguez-Sarmiento, R.M., Rudolph, M.G.
Funding Organization(s): F. Hoffmann-La Roche

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.187 (Depositor), 0.189 (DCC)
R-Value Work:
0.171 (Depositor), 0.177 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of a human phosphodiesterase 10 complex

Flohr, A., Schlatter, D., Kuhn, B., Rudolph, M.G.

To be published.

Macromolecule Content

Total Structure Weight: 160.94 kDa
Atom Count: 10,893
Modeled Residue Count: 1,254
Deposited Residue Count: 1,372
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 and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A	A, B, C, D	343	Homo sapiens	Mutation(s): 0 Gene Names: PDE10A EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y233 (Homo sapiens) Explore Q9Y233 Go to UniProtKB: Q9Y233
PHAROS: Q9Y233 GTEx: ENSG00000112541
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y233
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KF9 (Subject of Investigation/LOI) Query on KF9 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Q [auth B] SDF format, chain W [auth C] SDF format, chain Z [auth D] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain W [auth C] mmCIF format, chain Z [auth D]	I [auth A], Q [auth B], W [auth C], Z [auth D]	3-{5-[1-(2,2-difluoro-2H-1,3-benzodioxol-4-yl)-4-oxo-1,4-dihydropyridazin-3-yl]-1H-pyrazol-1-yl}benzonitrile C₂₁ H₁₁ F₂ N₅ O₃ KRTQYDGONIWUTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain Q [auth B] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain I [auth A] Focus chain Q [auth B] Focus chain W [auth C] Focus chain Z [auth D]
PR Query on PR Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C]	L [auth B] M [auth B] N [auth B] O [auth B] P [auth B] L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], T [auth C], U [auth C], V [auth C]	PRASEODYMIUM ION Pr WCWKKSOQLQEJTE-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain R [auth C] SDF format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain R [auth C] MOL2 format, chain X [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain R [auth C] mmCIF format, chain X [auth D]	E [auth A], J [auth B], R [auth C], X [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain R [auth C] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain R [auth C] Focus chain X [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain S [auth C] SDF format, chain Y [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Y [auth D]	F [auth A], K [auth B], S [auth C], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain S [auth C] Focus chain Y [auth D]