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- PDB-9o7r: Crystal structure of human adenosine kinase (ADK) in complex with... -

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Basic information

Entry
Database: PDB / ID: 9o7r
TitleCrystal structure of human adenosine kinase (ADK) in complex with inhibitor BKI-1553
ComponentsIsoform 2 of Adenosine kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / adenosine kinase (ADK) / inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


dATP biosynthetic process / adenosine kinase / adenosine kinase activity / dAMP salvage / ribonucleoside monophosphate biosynthetic process / deoxyadenosine kinase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / Ribavirin ADME / GMP salvage / Purine salvage ...dATP biosynthetic process / adenosine kinase / adenosine kinase activity / dAMP salvage / ribonucleoside monophosphate biosynthetic process / deoxyadenosine kinase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / Ribavirin ADME / GMP salvage / Purine salvage / AMP salvage / purine ribonucleoside salvage / purine nucleobase metabolic process / RNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Adenosine kinase / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like
Similarity search - Domain/homology
Chem-UW5 / Adenosine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of human adenosine kinase (ADK) in complex with inhibitor BKI-1553
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionApr 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,28421
Polymers52,3721
Non-polymers1,91220
Water18010
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)112.867, 112.867, 114.473
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Isoform 2 of Adenosine kinase / AK / Adenosine 5'-phosphotransferase


Mass: 52372.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADK / Plasmid: HosaA.19365.a.VZ21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P55263, adenosine kinase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-UW5 / 1-{4-amino-3-[6-(cyclopropyloxy)naphthalen-2-yl]-1H-pyrazolo[3,4-d]pyrimidin-1-yl}-2-methylpropan-2-ol / UW1553


Mass: 389.450 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23N5O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.48 Å3/Da / Density % sol: 64.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 2.4M ammonium sulfate, 0.1M Citrate pH 4.0. HosaA.19365.a.VZ21.PC00201 at 18 mg/mL. Cocrystallization with 2mM inhibitor. plate 14484 A12 drop 2, Puck: PSL1502, Cryo: 2.5M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 26, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.41→46.51 Å / Num. obs: 29195 / % possible obs: 99.9 % / Redundancy: 26.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.028 / Rrim(I) all: 0.145 / Χ2: 1.12 / Net I/σ(I): 20.4 / Num. measured all: 764558
Reflection shellResolution: 2.41→2.47 Å / % possible obs: 100 % / Redundancy: 24.4 % / Rmerge(I) obs: 2.989 / Num. measured all: 51512 / Num. unique obs: 2114 / CC1/2: 0.577 / Rpim(I) all: 0.617 / Rrim(I) all: 3.053 / Χ2: 0.95 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(dev_5570: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→46.51 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 1342 4.61 %
Rwork0.2225 --
obs0.2243 29106 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.41→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2667 0 104 10 2781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022808
X-RAY DIFFRACTIONf_angle_d0.5073800
X-RAY DIFFRACTIONf_dihedral_angle_d15.4051010
X-RAY DIFFRACTIONf_chiral_restr0.041411
X-RAY DIFFRACTIONf_plane_restr0.004477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.50.47271270.42252714X-RAY DIFFRACTION100
2.5-2.60.37071430.35772699X-RAY DIFFRACTION100
2.6-2.710.3187960.31732771X-RAY DIFFRACTION100
2.71-2.860.29041400.29152728X-RAY DIFFRACTION100
2.86-3.040.29681440.28872733X-RAY DIFFRACTION100
3.04-3.270.32441210.27752761X-RAY DIFFRACTION100
3.27-3.60.25661230.21362787X-RAY DIFFRACTION100
3.6-4.120.22391530.19682769X-RAY DIFFRACTION100
4.12-5.190.22591280.17052846X-RAY DIFFRACTION100
5.19-46.510.24571670.20422956X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.03750.98030.55843.1786-0.46336.60190.1369-0.6631-0.28870.4907-0.045-0.07260.00350.81650.03630.58670.06220.03190.77510.12890.706-29.73211.6796-11.2916
23.42560.46370.18682.14650.26635.5181-0.1350.0434-0.08-0.31140.0299-0.1984-0.45810.95090.05360.5164-0.03890.06070.5378-0.00370.515-30.36117.8375-26.4169
33.62710.50460.31522.69270.10385.8932-0.15280.0397-0.2838-0.280.10830.04650.2323-0.14480.07680.62590.02450.02510.3863-0.0250.4674-43.7976-3.5925-32.9185
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 64 )
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 206 )
3X-RAY DIFFRACTION3chain 'A' and (resid 207 through 344 )

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