7OTH | pdb_00007oth

PARP15 catalytic domain in complex with OUL219

• PDB DOI: https://doi.org/10.2210/pdb7OTH/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-06-10 Released: 2021-12-08 
• Deposition Author(s): Maksimainen, M.M., Lehtio, L.
• Funding Organization(s): Academy of Finland

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.214 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Analogs of TIQ-A as inhibitors of human mono-ADP-ribosylating PARPs.

Maksimainen, M.M., Murthy, S., Sowa, S.T., Galera-Prat, A., Rolina, E., Heiskanen, J.P., Lehtio, L.

(2021) Bioorg Med Chem 52: 116511-116511

• PubMed: 34801828 
• DOI: https://doi.org/10.1016/j.bmc.2021.116511
• Primary Citation Related Structures: 
  7OLJ, 7OM1, 7OMC, 7OQQ, 7OSP, 7OSS, 7OSX, 7OTF, 7OTH, 7OUW, 7OUX


• PubMed Abstract: 
  

  The scaffold of TIQ-A, a previously known inhibitor of human poly-ADP-ribosyltransferase PARP1, was utilized to develop inhibitors against human mono-ADP-ribosyltransferases through structure-guided design and activity profiling. By supplementing the TIQ-A scaffold with small structural changes, based on a PARP10 inhibitor OUL35, selectivity changed from poly-ADP-ribosyltransferases towards mono-ADP-ribosyltransferases. Binding modes of analogs were experimentally verified by determining complex crystal structures with mono-ADP-ribosyltransferase PARP15 and with poly-ADP-ribosyltransferase TNKS2. The best analogs of the study achieved 10-20-fold selectivity towards mono-ADP-ribosyltransferases PARP10 and PARP15 while maintaining micromolar potencies. The work demonstrates a route to differentiate compound selectivity between mono- and poly-ribosyltransferases of the human ARTD family.

---

Organizational Affiliation: 
• Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
Research Unit of Sustainable Chemistry, Faculty of Technology, University of Oulu, Oulu, Finland.
Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 51.22 kDa 
• Atom Count: 3,509 
• Modeled Residue Count: 393 
• Deposited Residue Count: 442 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein mono-ADP-ribosyltransferase PARP15	A, B	221	Homo sapiens	Mutation(s): 0  Gene Names: PARP15, BAL3 EC: 2.4.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q460N3 (Homo sapiens) Explore Q460N3  Go to UniProtKB:  Q460N3
PHAROS:  Q460N3 GTEx:  ENSG00000173200

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VJN (Subject of Investigation/LOI)	C [auth A]	8-propan-2-yloxy-4~{H}-thieno[2,3-c]isoquinolin-5-one C14 H13 N O2 S RRNITWOICYYQGQ-UHFFFAOYSA-N
DMS	D [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
VJN	BindingDB:  7OTH	IC50: min: 1100, max: 1122 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.214 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Diffraction Data: https://doi.org/10.23729/3942aada-8d3a-4391-87ed-2a88cf624d25

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.28	α = 90
b = 68.7	β = 90
c = 160.91	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-12-08 
Deposition Author(s): Maksimainen, M.M., Lehtio, L.

---

Funding Organization	Location	Grant Number
Academy of Finland	Finland	287063
Academy of Finland	Finland	294085

Revision History  

• Version 1.0: 2021-12-08
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description