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9o7q

Crystal structure of human adenosine kinase (ADK) in complex with inhibitor BKI-1676

Method: X-RAY DIFFRACTION Dmax: 65.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 2 of Adenosine kinase

Homo sapiens

UniProt P55263

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–345 Not recorded A1B95 1-[(3P)-3-[6-(cyclopropyloxy)naphthalen-2-yl]-4-(methylamino)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]-2-methylpropan-2-ol × 1 SO4 SULFATE ION × 13 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；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/A8 drop 2, Puck: PSL1512, Cryo: 2.5M lithium sulfate Resolution 2.81 Å R-free 0.265

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9O7Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BX4 STRUCTURE OF HUMAN ADENOSINE KINASE AT 1.50 ANGSTROMS Deposited 1998-10-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–345（345 aa）
Not recorded CL CHLORIDE ION × 2 MG MAGNESIUM ION × 3 ADN ADENOSINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；20%PEG 4K, 0.16M MGCL2, 0.1M TRIS, PH 7.5
Resolution 1.50 Å R-free 0.226
4O1L Human Adenosine Kinase in complex with inhibitor Deposited 2013-12-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 17–362（346 aa） Fragment：UNP residues 17-362
Chain B 17–362（346 aa） Fragment：UNP residues 17-362
Not recorded MG MAGNESIUM ION × 4 HO4 5-ethynyl-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.263
4O1L Human Adenosine Kinase in complex with inhibitor Deposited 2013-12-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 17–362（346 aa） Fragment：UNP residues 17-362
Not recorded MG MAGNESIUM ION × 2 HO4 5-ethynyl-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.263
4O1L Human Adenosine Kinase in complex with inhibitor Deposited 2013-12-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 17–362（346 aa） Fragment：UNP residues 17-362
Not recorded MG MAGNESIUM ION × 2 HO4 5-ethynyl-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.263
9O7P Crystal structure of human adenosine kinase (ADK) in complex with inhibitor BKI-1817 Deposited 2025-04-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–345（345 aa）
Not recorded CL CHLORIDE ION × 3 SO4 SULFATE ION × 15 A1B96 (6M)-6-{4-amino-1-[(1-methylpiperidin-4-yl)methyl]-1H-pyrazolo[3,4-d]pyrimidin-3-yl}quinolin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；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: PSL1601, Cryo: 2.5M lithium sulfate
Resolution 2.51 Å R-free 0.246
9O7R Crystal structure of human adenosine kinase (ADK) in complex with inhibitor BKI-1553 Deposited 2025-04-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–345（345 aa）
Not recorded CL CHLORIDE ION × 5 UW5 1-{4-amino-3-[6-(cyclopropyloxy)naphthalen-2-yl]-1H-pyrazolo[3,4-d]pyrimidin-1-yl}-2-methylpropan-2-ol × 1 SO4 SULFATE ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；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
Resolution 2.41 Å R-free 0.258

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ADK_HUMAN
Isoform P55263-2
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 121–465； UniProt 1–345

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9o7q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9o7q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9o7q
Deposition date deposition_date2025-04-15
最后修订 last_revision2026-05-06
Structure title titleCrystal structure of human adenosine kinase (ADK) in complex with inhibitor BKI-1676
Keywords keywords;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, adenosine kinase (ADK), inhibitor, TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR complex ;; TRANSFERASE/TRANSFERASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.69 Å
Radius of gyration Rg (electron density) rg_electron19.77 Å
Forward intensity I(0) i051819200.00
Molecular weight molecular_weight36794.0 kDa
Excluded volume excluded_volume35171 ų
Envelope volume envelope_volume57440 ų
Hydration-shell volume shell_volume23532 ų
Envelope diameter envelope_diameter67.9 Å
Shell Rg shell_rg26.85 Å
Envelope Rg envelope_rg20.07 Å
Shape Rg shape_rg19.71 Å
Total Rg total_rg20.50 Å
Total atoms total_atoms2755
Residues n_residues339
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax65.9 Å
Rg (real space) rg_real20.56 Å
Rg uncertainty (real space) rg_real_error0.47 Å
I(0) (real space) i0_real5.1820e+07
I(0) uncertainty (real space) i0_real_error7.3980e+05
Rg (reciprocal space) rg_reciprocal20.59 Å
I(0) (reciprocal space) i0_reciprocal51820000.0000
Solution quality estimate total_estimate0.8150
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.7 Å
Skewness Skewness skewness0.173
Kurtosis Kurtosis kurtosis-0.423
Angular range angular_range— – 0.3850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15700000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.869; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)