BMRB Entry 34831

Name: Molecular Docking of SPF30 Tudor domain with synthetic inhibitor 4-(pyridin-2-yl)thiazol-2-amine
Published: 2023-11-11

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PDB ID: 8poi
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34831
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Molecular Docking of SPF30 Tudor domain with synthetic inhibitor 4-(pyridin-2-yl)thiazol-2-amine

Deposition date:

2023-07-04

Original release date:

2023-11-11

Authors:

Borggraefe, J.; Gaussmann, S.; Sattler, M.

Citation:

Citation: Enders, L.; Siklos, M.; Borggrafe, J.; Gaussmann, S.; Koren, A.; Malik, M.; Tomek, T.; Schuster, M.; Reinis, J.; Hahn, E.; Rukavina, A.; Reicher, A.; Casteels, T.; Bock, C.; Winter, G.; Hannich, J.; Sattler, M.; Kubicek, S.. "Pharmacological perturbation of the phase-separating protein SMNDC1." Nat. Commun. 14, 4504-4504 (2023).
PubMed: 37587144

Assembly members:

Assembly members:
entity_1, polymer, 64 residues, 6935.511 Da.
entity_2, non-polymer, 177.226 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: ASTQPTHSWKVGDKCMAVWS EDGQCYEAEIEEIDEENGTA AITFAGYGNAEVTPLLNLKP VEEG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	198
1H chemical shifts	322

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2

Entities:

Entity 1, unit_1 64 residues - 6935.511 Da.

1

ALA

SER

THR

GLN

PRO

THR

HIS

SER

TRP

LYS

2

VAL

GLY

ASP

LYS

CYS

MET

ALA

VAL

TRP

SER

3

GLU

ASP

GLY

GLN

CYS

TYR

GLU

ALA

GLU

ILE

4

GLU

ILE

ASP

GLU

ASN

GLY

THR

ALA

5

ALA

ILE

THR

PHE

ALA

GLY

TYR

GLY

ASN

ALA

6

GLU

VAL

THR

PRO

LEU

ASN

LEU

LYS

PRO

7

VAL

GLU

GLY

Entity 2, unit_2 - C8 H7 N3 S - 177.226 Da.

1

ZTI

Samples:

sample_1: SPF30(65-128), [U-13C; U-15N], 1 mM; cmp13, NA-, 20 mM; sodium phosphate, NA-, 20 mM; NaCl, NA-, 50 mM; DTT, NA-, 5 mM

sample_conditions_1: ionic strength: 70 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
2D NOESY w1-13C-filtered	sample_1	isotropic	sample_conditions_1
3D NOESY w2-w1-13C filtered	sample_1	isotropic	sample_conditions_1
2D NOESY w2-13C-filtered	sample_1	isotropic	sample_conditions_1

Software:

CARA v1.9.1.7, Keller and Wuthrich - chemical shift assignment, peak picking

HADDOCK, Bonvin - structure calculation

NMR spectrometers:

Bruker AVANCE III 800 MHz