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.

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
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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

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

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P36639
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZRV (Subject of Investigation/LOI) Query on ZRV Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	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		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	D [auth A] E [auth A] G [auth B] H [auth B] I [auth B] 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		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-11-03

Deposition Author(s):

Eron, S.J.

Revision History (Full details and data files)

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

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Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left:-5px; } 7N13 | pdb_00007n13

Crystal structure of MTH1 in complex with compound 32

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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