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- PDB-9knh: Structural complex of FTO bound with Dac590 -

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Basic information

Entry
Database: PDB / ID: 9knh
TitleStructural complex of FTO bound with Dac590
ComponentsAlpha-ketoglutarate-dependent dioxygenase FTO
KeywordsOXIDOREDUCTASE / N6-methyladenosine(m6A) demethylase / 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 / broad specificity oxidative DNA demethylase activity / oxidative RNA 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 / broad specificity oxidative DNA demethylase activity / oxidative RNA 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 / 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
: / : / N-OXALYLGLYCINE / Alpha-ketoglutarate-dependent dioxygenase FTO
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsYang, C.G. / Yang, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21725801 China
CitationJournal: J.Med.Chem. / Year: 2025
Title: Development of Orally Bioavailable FTO Inhibitors with Potent Antileukemia Efficacy.
Authors: Yang, T. / Dong, Z. / Du, R. / Wang, Y. / Liu, L. / Xue, Y. / Zhang, X. / Liao, Y. / Gan, J. / Yu, X. / Huang, Y. / Yang, C.G.
History
DepositionNov 18, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 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)55,5284
Polymers54,9341
Non-polymers5943
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.316, 140.316, 83.819
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-A1EF4 / 2-[[2-chloranyl-4-(3,5-dimethyl-1,2-oxazol-4-yl)-6-fluoranyl-phenyl]amino]-5-methoxy-benzoic acid


Mass: 390.793 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16ClFN2O4
#3: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
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: 2.89 Å3/Da / Density % sol: 61.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate(pH5.8), 15% PEG3350, 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: Jan 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9735 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 13366 / % possible obs: 87.64 % / Redundancy: 2.09 % / Biso Wilson estimate: 49.06 Å2 / Rrim(I) all: 0.43 / Net I/σ(I): 32.7
Reflection shellResolution: 2.9→3 Å / Num. unique obs: 11923 / Rrim(I) all: 0.2437

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
HKL-3000data reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→28.56 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 2.09 / Phase error: 26.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2639 553 4.64 %
Rwork0.2188 --
obs0.2208 11923 87.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→28.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 38 0 3192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023266
X-RAY DIFFRACTIONf_angle_d0.484467
X-RAY DIFFRACTIONf_dihedral_angle_d4.42473
X-RAY DIFFRACTIONf_chiral_restr0.037506
X-RAY DIFFRACTIONf_plane_restr0.004604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.190.32940.27991949X-RAY DIFFRACTION60
3.19-3.650.28651430.24482939X-RAY DIFFRACTION91
3.66-4.60.24131540.20533236X-RAY DIFFRACTION100
4.6-8.560.25671620.20233246X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -20.7541 Å / Origin y: 12.2487 Å / Origin z: -26.5026 Å
111213212223313233
T0.2437 Å2-0.0054 Å20.042 Å2-0.2725 Å20.0579 Å2--0.2348 Å2
L1.3697 °20.6948 °2-0.2682 °2-7.0468 °2-1.4628 °2--1.2321 °2
S-0.0738 Å °0.0034 Å °0.2479 Å °-0.0825 Å °0.3875 Å °1.0551 Å °0.1287 Å °-0.3007 Å °-0.1578 Å °
Refinement TLS groupSelection details: all

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