5SKD | pdb_00005skd

CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 10 IN COMPLEX WITH C1=CN(N=C(C1=O)c2ccnn2c3cc(ccc3F)F)c4cc(ccc4)OC(F)(F)F, micromolar IC50=0.047063

PDB DOI: https://doi.org/10.2210/pdb5SKD/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., Rogers-Evans, M., Rudolph, M.G.
Funding Organization(s): F. Hoffmann-La Roche

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.177 (Depositor), 0.181 (DCC)
R-Value Work:
0.163 (Depositor), 0.168 (DCC)
R-Value Observed:
0.163 (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: 160.97 kDa
Atom Count: 10,858
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KER (Subject of Investigation/LOI) Query on KER Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth B] SDF format, chain V [auth C] SDF format, chain Y [auth D] MOL2 format, chain G [auth A] MOL2 format, chain P [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain G [auth A] mmCIF format, chain P [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D]	G [auth A], P [auth B], V [auth C], Y [auth D]	3-[1-(2,5-difluorophenyl)-1H-pyrazol-5-yl]-1-[3-(trifluoromethoxy)phenyl]pyridazin-4(1H)-one C₂₀ H₁₁ F₅ N₄ O₂ SXGHQUMVHHJJIH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain P [auth B] Focus chain V [auth C] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain P [auth B] Focus chain V [auth C] Focus chain Y [auth D]
PR Query on PR Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C]	J [auth B] K [auth B] L [auth B] M [auth B] N [auth B] J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], S [auth C], T [auth C], U [auth C]	PRASEODYMIUM ION Pr WCWKKSOQLQEJTE-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain Q [auth C] SDF format, chain W [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain W [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain W [auth D]	E [auth A], H [auth B], Q [auth C], W [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain Q [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain Q [auth C] Focus chain W [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain R [auth C] SDF format, chain X [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain R [auth C] MOL2 format, chain X [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain R [auth C] mmCIF format, chain X [auth D]	F [auth A], I [auth B], R [auth C], X [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain R [auth C] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain R [auth C] Focus chain X [auth D]