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- PDB-26xc: Identification of AMPD2 Allosteric Inhibitors with Novel Mechanis... -

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Basic information

Entry
Database: PDB / ID: 26xc
TitleIdentification of AMPD2 Allosteric Inhibitors with Novel Mechanism of Action by Fragment Merging Approach
ComponentsAMP deaminase 2
KeywordsMETAL BINDING PROTEIN / AMP deaminase / hydrolase / purine metabolism / zinc / allosteric regulation
Function / homology
Function and homology information


cyclic purine nucleotide metabolic process / AMP deaminase / AMP deaminase activity / IMP biosynthetic process / AMP metabolic process / podocyte development / GMP salvage / Purine salvage / IMP salvage / GTP metabolic process ...cyclic purine nucleotide metabolic process / AMP deaminase / AMP deaminase activity / IMP biosynthetic process / AMP metabolic process / podocyte development / GMP salvage / Purine salvage / IMP salvage / GTP metabolic process / energy homeostasis / ATP metabolic process / cholesterol homeostasis / metal ion binding / identical protein binding / cytosol
Similarity search - Function
AMP deaminase / AMP deaminase / Adenosine/AMP deaminase active site / Adenosine and AMP deaminase signature. / Metal-dependent hydrolase
Similarity search - Domain/homology
5-chloro-1H-benzimidazole / PHOSPHATE ION / AMP deaminase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNomura, A. / Adachi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Not funded Japan
CitationJournal: Slas Discov / Year: 2026
Title: Identification of AMPD2 allosteric inhibitors with novel mechanism of action by fragment merging approach.
Authors: Yamanaka, K. / Uhara, T. / Nomura, A. / Akaki, T. / Adachi, T. / Kitao, Y. / Hantani, Y.
History
DepositionMay 19, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMP deaminase 2
B: AMP deaminase 2
C: AMP deaminase 2
D: AMP deaminase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,21726
Polymers315,0114
Non-polymers2,20622
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16420 Å2
ΔGint-324 kcal/mol
Surface area91390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.440, 162.460, 291.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein
AMP deaminase 2 / AMP deaminase isoform L


Mass: 78752.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMPD2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q01433, AMP deaminase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-ES9 / 5-chloro-1H-benzimidazole


Mass: 152.581 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H5ClN2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 85 mM MES pH 5.9, 20% PEG 8000, 170 mM ammonium sulfate, 15% glycerol, 10 mM ATP, soaked with AMPD2 inhibitor.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→98.79 Å / Num. obs: 96249 / % possible obs: 94.35 % / Redundancy: 4.1 % / Biso Wilson estimate: 44.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.9
Reflection shellResolution: 2.5→2.57 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.04 / Num. unique obs: 5528 / % possible all: 74.18

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8HU6

8hu6


Resolution: 2.5→78.25 Å / SU ML: 0.2733 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.7175
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2223 4801 4.99 %
Rwork0.2148 91402 -
obs0.2152 96203 94.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.68 Å2
Refinement stepCycle: LAST / Resolution: 2.5→78.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19606 0 114 0 19720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012820194
X-RAY DIFFRACTIONf_angle_d1.817727348
X-RAY DIFFRACTIONf_chiral_restr0.0962957
X-RAY DIFFRACTIONf_plane_restr0.01543513
X-RAY DIFFRACTIONf_dihedral_angle_d14.03837528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.31091460.29552293X-RAY DIFFRACTION73.8
2.53-2.560.32921230.28032420X-RAY DIFFRACTION74.33
2.56-2.590.3181190.27862329X-RAY DIFFRACTION73.78
2.59-2.620.28651090.26352430X-RAY DIFFRACTION74.26
2.62-2.660.30011340.27032308X-RAY DIFFRACTION73.18
2.66-2.690.29521180.2622376X-RAY DIFFRACTION73.35
2.69-2.730.30631370.26493028X-RAY DIFFRACTION94.96
2.73-2.770.3081660.26453223X-RAY DIFFRACTION99.85
2.77-2.820.29011810.27863166X-RAY DIFFRACTION99.91
2.82-2.860.28631740.27673205X-RAY DIFFRACTION99.88
2.86-2.910.34941540.27493244X-RAY DIFFRACTION99.88
2.91-2.960.30031700.25763188X-RAY DIFFRACTION99.91
2.96-3.020.25851900.24933180X-RAY DIFFRACTION99.91
3.02-3.080.25521670.25023210X-RAY DIFFRACTION99.94
3.08-3.150.24481320.24843239X-RAY DIFFRACTION99.88
3.15-3.220.26381960.25093173X-RAY DIFFRACTION99.73
3.22-3.30.24211860.23843240X-RAY DIFFRACTION99.85
3.3-3.390.24811670.24223211X-RAY DIFFRACTION99.88
3.39-3.490.24411610.2423199X-RAY DIFFRACTION99.82
3.49-3.610.22771740.21483203X-RAY DIFFRACTION99.91
3.61-3.730.21731590.20133240X-RAY DIFFRACTION99.85
3.73-3.880.22121650.19593250X-RAY DIFFRACTION99.82
3.88-4.060.18641790.18873245X-RAY DIFFRACTION99.85
4.06-4.270.18851680.18683241X-RAY DIFFRACTION99.68
4.27-4.540.15091690.16943207X-RAY DIFFRACTION99.68
4.54-4.890.19811650.17543260X-RAY DIFFRACTION99.68
4.89-5.390.16051690.18563276X-RAY DIFFRACTION99.57
5.39-6.160.22441740.21283228X-RAY DIFFRACTION99.13
6.17-7.760.23491800.21293284X-RAY DIFFRACTION98.94
7.77-78.250.15131690.17273306X-RAY DIFFRACTION95.97

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