5SIL | pdb_00005sil

CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 10 IN COMPLEX WITH C(Nc2ccc1[nH]c(nc1c2)c3cc(cc(c3)C)C)(=O)c4c(cnn4C)Cl, micromolar IC50=0.245656

• PDB DOI: https://doi.org/10.2210/pdb5SIL/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., Peters, J., Rudolph, M.G.
• Funding Organization(s): F. Hoffmann-La Roche

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.231 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: other

Literature

Crystal Structure of a human phosphodiesterase 10 complex

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 39.88 kDa 
• Atom Count: 2,657 
• Modeled Residue Count: 314 
• Deposited Residue Count: 343 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A	A	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JQC (Subject of Investigation/LOI)	D [auth A]	4-chloro-N-[2-(3,5-dimethylphenyl)-1H-benzimidazol-5-yl]-1-methyl-1H-pyrazole-5-carboxamide C20 H18 Cl N5 O RNLFENJAPRXOBL-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.231 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.534	α = 90
b = 141.534	β = 90
c = 141.534	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-12 
Deposition Author(s): Joseph, C., Benz, J., Flohr, A., Peters, J., Rudolph, M.G.

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Funding Organization	Location	Grant Number
F. Hoffmann-La Roche	Switzerland	--

Revision History  

• Version 1.0: 2022-10-12
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-16
  Changes: Data collection, Structure summary