7N13 | pdb_00007n13

Crystal structure of MTH1 in complex with compound 32

• PDB DOI: https://doi.org/10.2210/pdb7N13/pdb

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


• Deposited: 2021-05-26 Released: 2021-11-03 
• Deposition Author(s): Eron, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.220 (DCC) 

Starting Model: experimental

Literature

Development of an AchillesTAG degradation system and its application to control CAR-T activity

Veits, G.K., Henderson, C.S., Vogelaar, A., Eron, S.J., Lee, L., Hart, A., Deibler, R.W., Baddour, J., Elam, W.A., Agafonov, R.V., Freda, J., Chaturvedi, P., Ladd, B., Carlson, M.W., Vora, H.U., Scott, T.G., Tieu, T., Jain, A., Chen, C.L., Kibbler, E.S., Pop, M.S., He, M., Kern, G., Maple, H.J., Marsh, G.P., Norley, M.C., Oakes, C.S., Henderson, J.A., Sowa, M.E., Phillips, A.J., Proia, D.A., Park, E.S., Patel, J.S., Fisher, S.L., Nasveschuk, C.G., Zeid, R.

(2021) Curr Res Chem Biol 1: 100010

• DOI: https://doi.org/10.1016/j.crchbi.2021.100010

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.84 kDa 
• Atom Count: 2,988 
• Modeled Residue Count: 309 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7,8-dihydro-8-oxoguanine triphosphatase	A, B	158	Homo sapiens	Mutation(s): 0  Gene Names: NUDT1, MTH1 EC: 3.6.1.55 (PDB Primary Data), 3.6.1.56 (PDB Primary Data), 3.6.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P36639 (Homo sapiens) Explore P36639  Go to UniProtKB:  P36639
PHAROS:  P36639 GTEx:  ENSG00000106268

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZRV (Subject of Investigation/LOI)	C [auth A], F [auth B]	4-anilino-6-[4-(butylcarbamoyl)-3-fluorophenyl]-N-cyclopropyl-7-fluoroquinoline-3-carboxamide C30 H28 F2 N4 O2 DBDGLOMDGKMHIN-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.220 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.607	α = 90
b = 67.835	β = 90
c = 79.061	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-11-03 
Deposition Author(s): Eron, S.J.

Revision History  

• Version 1.0: 2021-11-03
  Type: Initial release
  
• Version 1.1: 2022-01-12
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description