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- PDB-8hub: AMP deaminase 2 in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 8hub
TitleAMP deaminase 2 in complex with an inhibitor
ComponentsAMP deaminase 2
KeywordsHYDROLASE / Complex / Deaminase / AMP / IMP / Energy metabolism / inhibitor / allosteric inhibitor
Function / homology
Function and homology information


cyclic purine nucleotide metabolic process / AMP deaminase / AMP deaminase activity / IMP biosynthetic process / AMP metabolic process / podocyte development / Purine salvage / IMP salvage / GTP metabolic process / ATP metabolic process ...cyclic purine nucleotide metabolic process / AMP deaminase / AMP deaminase activity / IMP biosynthetic process / AMP metabolic process / podocyte development / Purine salvage / IMP salvage / GTP metabolic process / ATP metabolic process / energy homeostasis / 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 hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-N4X / AMP deaminase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsAdachi, T. / Doi, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2023
Title: The discovery of 3,3-dimethyl-1,2,3,4-tetrahydroquinoxaline-1-carboxamides as AMPD2 inhibitors with a novel mechanism of action.
Authors: Kitao, Y. / Saito, T. / Watanabe, S. / Ohe, Y. / Takahashi, K. / Akaki, T. / Adachi, T. / Doi, S. / Yamanaka, K. / Murai, Y. / Oba, M. / Suzuki, T.
History
DepositionDec 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)316,15811
Polymers315,0114
Non-polymers1,1487
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9270 Å2
ΔGint-195 kcal/mol
Surface area80180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.516, 162.533, 289.758
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-N4X / 3,3-dimethyl-4-(phenylmethyl)-2~{H}-quinoxaline-1-carboxamide


Mass: 295.379 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H21N3O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 85 mM MES ph 5.9, 20% PEG8000, 170 mM ammonium sulfate, 15% glycerol, 10mM compound

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 31, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.24→98.84 Å / Num. obs: 46752 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 80.18 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.032 / Rrim(I) all: 0.087 / Net I/σ(I): 17.9
Reflection shellResolution: 3.24→3.33 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 3407 / CC1/2: 0.925 / Rpim(I) all: 0.187 / Rrim(I) all: 0.516 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8HU6

8hu6


Resolution: 3.25→98.84 Å / SU ML: 0.3984 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.927
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2758 2325 4.98 %
Rwork0.258 44325 -
obs0.2589 46650 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.52 Å2
Refinement stepCycle: LAST / Resolution: 3.25→98.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16809 0 70 0 16879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001717312
X-RAY DIFFRACTIONf_angle_d0.439423456
X-RAY DIFFRACTIONf_chiral_restr0.03632527
X-RAY DIFFRACTIONf_plane_restr0.00343022
X-RAY DIFFRACTIONf_dihedral_angle_d10.57486454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.310.36641540.31672593X-RAY DIFFRACTION99.96
3.31-3.390.29431310.2972559X-RAY DIFFRACTION100
3.39-3.460.29121410.30322588X-RAY DIFFRACTION100
3.46-3.550.2951140.2882605X-RAY DIFFRACTION100
3.55-3.650.28191250.27492599X-RAY DIFFRACTION100
3.65-3.750.33951430.28212564X-RAY DIFFRACTION99.96
3.75-3.880.26271410.27782597X-RAY DIFFRACTION100
3.88-4.010.26361240.25582585X-RAY DIFFRACTION99.96
4.01-4.170.30771310.26162609X-RAY DIFFRACTION100
4.17-4.360.2611280.2312602X-RAY DIFFRACTION100
4.36-4.590.22991460.22892608X-RAY DIFFRACTION99.93
4.59-4.880.24471250.23382626X-RAY DIFFRACTION100
4.88-5.260.26291550.2392595X-RAY DIFFRACTION99.89
5.26-5.790.28331350.25712621X-RAY DIFFRACTION99.89
5.79-6.630.28961230.2842647X-RAY DIFFRACTION99.78
6.63-8.350.2841650.26062627X-RAY DIFFRACTION99.18
8.35-98.840.26121440.2382700X-RAY DIFFRACTION97.1
Refinement TLS params.Method: refined / Origin x: 105.111723507 Å / Origin y: 50.4563482854 Å / Origin z: 35.319982145 Å
111213212223313233
T0.635507980668 Å2-0.230725079197 Å2-0.0291226929453 Å2-0.653333540439 Å20.0858371114195 Å2--0.719490473738 Å2
L1.08629601288 °20.505195584207 °2-0.111932263488 °2-1.20752116565 °2-0.0757902529114 °2--0.734628671476 °2
S-0.124791518428 Å °0.0956938306527 Å °-0.0445148110804 Å °-0.071913947032 Å °0.123378497666 Å °0.101133939365 Å °0.151667752993 Å °0.028362932074 Å °0.705863397651 Å °
Refinement TLS groupSelection details: all

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