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- PDB-9kni: Structural complex of FTO bound with 12j -

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Basic information

Entry
Database: PDB / ID: 9kni
TitleStructural complex of FTO bound with 12j
ComponentsAlpha-ketoglutarate-dependent dioxygenase FTO
KeywordsOXIDOREDUCTASE / m6A eraser / FTO Inhibitor / Complex
Function / homology
Function and homology information


regulation of white fat cell proliferation / tRNA demethylase activity / Reversal of alkylation damage by DNA dioxygenases / mRNA N6-methyladenine demethylase / mRNA N6-methyladenosine dioxygenase activity / regulation of respiratory system process / regulation of lipid storage / regulation of brown fat cell differentiation / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity ...regulation of white fat cell proliferation / tRNA demethylase activity / Reversal of alkylation damage by DNA dioxygenases / mRNA N6-methyladenine demethylase / mRNA N6-methyladenosine dioxygenase activity / regulation of respiratory system process / regulation of lipid storage / regulation of brown fat cell differentiation / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / snRNA processing / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / RNA repair / DNA alkylation repair / temperature homeostasis / mRNA destabilization / regulation of multicellular organism growth / adipose tissue development / ferrous iron binding / transferase activity / nuclear speck / intracellular membrane-bounded organelle / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Alpha-ketoglutarate-dependent dioxygenase FTO, C-terminal / Alpha-ketoglutarate-dependent dioxygenase FTO, catalytic domain / Alpha-ketoglutarate-dependent dioxygenase FTO / FTO, C-terminal domain superfamily / FTO catalytic domain / FTO C-terminal domain / FTO catalytic domain / Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily
Similarity search - Domain/homology
: / 2-OXOGLUTARIC ACID / Alpha-ketoglutarate-dependent dioxygenase FTO
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsYang, C.G. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077133 China
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Development of 3-arylaminothiophenic-2-carboxylic acid derivatives as new FTO inhibitors showing potent antileukemia activities.
Authors: Zhang, D. / Liu, L. / Li, M. / Hu, X. / Zhang, X. / Xia, W. / Wang, Z. / Song, X. / Huang, Y. / Dong, Z. / Yang, C.G.
History
DepositionNov 19, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent dioxygenase FTO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4623
Polymers54,9341
Non-polymers5282
Water23413
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.410, 141.410, 83.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Alpha-ketoglutarate-dependent dioxygenase FTO / Fat mass and obesity-associated protein / U6 small nuclear RNA (2'-O-methyladenosine-N(6)-)- ...Fat mass and obesity-associated protein / U6 small nuclear RNA (2'-O-methyladenosine-N(6)-)-demethylase FTO / U6 small nuclear RNA N(6)-methyladenosine-demethylase FTO / mRNA (2'-O-methyladenosine-N(6)-)-demethylase FTO / m6A(m)-demethylase FTO / mRNA N(6)-methyladenosine demethylase FTO / tRNA N1-methyl adenine demethylase FTO


Mass: 54933.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTO, KIAA1752 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9C0B1, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen ...References: UniProt: Q9C0B1, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor, mRNA N6-methyladenine demethylase
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C5H6O5
#3: Chemical ChemComp-A1EF5 / 3-[[2,6-bis(chloranyl)-4-(3,5-dimethyl-1H-pyrazol-4-yl)phenyl]amino]thiophene-2-carboxylic acid


Mass: 382.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13Cl2N3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate, pH 5.4, 12.0% (w/v) polyethylene glycol (PEG) 3350, 8% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9735 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9735 Å / Relative weight: 1
ReflectionResolution: 2.63→49.45 Å / Num. obs: 18535 / % possible obs: 99.7 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.2
Reflection shellResolution: 2.63→2.7 Å / Num. unique obs: 18522 / Rrim(I) all: 0.07

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
XDSdata scaling
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→31.48 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 935 5.05 %
Rwork0.1985 --
obs0.2 18522 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.63→31.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3460 0 34 13 3507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023582
X-RAY DIFFRACTIONf_angle_d0.5744870
X-RAY DIFFRACTIONf_dihedral_angle_d7.161492
X-RAY DIFFRACTIONf_chiral_restr0.04527
X-RAY DIFFRACTIONf_plane_restr0.004641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.770.36951320.31442522X-RAY DIFFRACTION100
2.77-2.940.32211520.28332516X-RAY DIFFRACTION100
2.94-3.170.31011400.27942490X-RAY DIFFRACTION100
3.17-3.490.3104850.24822577X-RAY DIFFRACTION100
3.49-3.990.22781690.21022470X-RAY DIFFRACTION100
3.99-5.020.25321210.16752505X-RAY DIFFRACTION99
5.03-31.480.15771360.16292507X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 21.1012 Å / Origin y: 12.166 Å / Origin z: 29.6243 Å
111213212223313233
T0.5076 Å2-0.0195 Å2-0.0399 Å2-0.4308 Å2-0.037 Å2--0.4942 Å2
L5.103 °2-1.8015 °2-1.7474 °2-2.0429 °20.9877 °2--2.1155 °2
S0.2476 Å °-0.1446 Å °0.2794 Å °-0.1859 Å °-0.0514 Å °-0.2182 Å °-0.3567 Å °0.1375 Å °-0.2044 Å °
Refinement TLS groupSelection details: all

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