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- PDB-6gou: Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Com... -

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Basic information

Entry
Database: PDB / ID: 6gou
TitleDevelopment of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I
ComponentsAlkyldihydroxyacetonephosphate synthase, peroxisomalAlkylglycerone phosphate synthase
KeywordsFLAVOPROTEIN / Ether phospholipids / catalytic mechanism / inhibitor / anti-cancer
Function / homology
Function and homology information


alkylglycerone-phosphate synthase / alkylglycerone-phosphate synthase activity / ether lipid biosynthetic process / peroxisomal membrane / FAD binding / peroxisome
Similarity search - Function
Double Stranded RNA Binding Domain - #650 / GMP Synthetase; Chain A, domain 3 - #330 / Alpha-Beta Plaits - #3450 / Alkyldihydroxyacetonephosphate synthase / Vanillyl-alcohol Oxidase; Chain A, domain 4 / Vanillyl-alcohol Oxidase; Chain A, domain 4 / FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal ...Double Stranded RNA Binding Domain - #650 / GMP Synthetase; Chain A, domain 3 - #330 / Alpha-Beta Plaits - #3450 / Alkyldihydroxyacetonephosphate synthase / Vanillyl-alcohol Oxidase; Chain A, domain 4 / Vanillyl-alcohol Oxidase; Chain A, domain 4 / FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / GMP Synthetase; Chain A, domain 3 / Double Stranded RNA Binding Domain / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-F6T / FLAVIN-ADENINE DINUCLEOTIDE / Alkyldihydroxyacetonephosphate synthase, peroxisomal
Similarity search - Component
Biological speciesCavia porcellus (domestic guinea pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.9 Å
AuthorsMattevi, A. / Piano, V.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchFellowship 18022 Italy
CitationJournal: Eur J Med Chem / Year: 2018
Title: Development of alkyl glycerone phosphate synthase inhibitors: Structure-activity relationship and effects on ether lipids and epithelial-mesenchymal transition in cancer cells.
Authors: Stazi, G. / Battistelli, C. / Piano, V. / Mazzone, R. / Marrocco, B. / Marchese, S. / Louie, S.M. / Zwergel, C. / Antonini, L. / Patsilinakos, A. / Ragno, R. / Viviano, M. / Sbardella, G. / ...Authors: Stazi, G. / Battistelli, C. / Piano, V. / Mazzone, R. / Marrocco, B. / Marchese, S. / Louie, S.M. / Zwergel, C. / Antonini, L. / Patsilinakos, A. / Ragno, R. / Viviano, M. / Sbardella, G. / Ciogli, A. / Fabrizi, G. / Cirilli, R. / Strippoli, R. / Marchetti, A. / Tripodi, M. / Nomura, D.K. / Mattevi, A. / Mai, A. / Valente, S.
History
DepositionJun 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Alkyldihydroxyacetonephosphate synthase, peroxisomal
A: Alkyldihydroxyacetonephosphate synthase, peroxisomal
B: Alkyldihydroxyacetonephosphate synthase, peroxisomal
C: Alkyldihydroxyacetonephosphate synthase, peroxisomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,93311
Polymers291,7554
Non-polymers4,1787
Water0
1
B: Alkyldihydroxyacetonephosphate synthase, peroxisomal
hetero molecules

D: Alkyldihydroxyacetonephosphate synthase, peroxisomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,1396
Polymers145,8772
Non-polymers2,2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_454-x-1/2,y+1/2,-z-1/21
2
A: Alkyldihydroxyacetonephosphate synthase, peroxisomal
C: Alkyldihydroxyacetonephosphate synthase, peroxisomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,7945
Polymers145,8772
Non-polymers1,9163
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.958, 120.644, 148.160
Angle α, β, γ (deg.)90.00, 95.27, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
31B
41C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111D1 - 999
2111A1 - 999
3111B1 - 999
4111C1 - 999

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.373122, 0.057442, 0.926003), (-0.100822, 0.98966, -0.102016), (-0.922288, -0.131426, -0.363472)-38.87326, -25.82035, -148.23099
3given(0.999939, 0.009042, 0.006405), (-0.010151, 0.979271, 0.202301), (-0.004443, -0.202353, 0.979303)0.10556, -51.98299, 11.49169
4given(0.36945, -0.038358, -0.928459), (0.077943, 0.996906, -0.010171), (0.925976, -0.068609, 0.371297)-28.58513, -3.10157, 77.44884

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Components

#1: Protein
Alkyldihydroxyacetonephosphate synthase, peroxisomal / Alkylglycerone phosphate synthase / Alkyl-DHAP synthase / Alkylglycerone-phosphate synthase


Mass: 72938.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cavia porcellus (domestic guinea pig) / Gene: AGPS / Production host: Escherichia coli (E. coli)
References: UniProt: P97275, alkylglycerone-phosphate synthase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-F6T / (3~{S})-3-[2,6-bis(fluoranyl)phenyl]-~{N}-[(2-oxidanylidene-1,3-dihydrobenzimidazol-5-yl)methyl]butanamide


Mass: 345.343 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H17F2N3O2

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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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: PEG 1500 20%, HEPES, PH 7.5, 100 MM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jun 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.9→48 Å / Num. obs: 57552 / % possible obs: 100 % / Redundancy: 7.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.181 / Net I/σ(I): 11.2
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4493 / CC1/2: 0.826 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5ADZ

5adz


Resolution: 2.9→48 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.881 / SU B: 18.83 / SU ML: 0.349 / Cross valid method: THROUGHOUT / ESU R Free: 0.429 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25817 2934 5.1 %RANDOM
Rwork0.21858 ---
obs0.22057 54617 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å2-1.93 Å2
2--2.42 Å20 Å2
3----1.15 Å2
Refinement stepCycle: 1 / Resolution: 2.9→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17058 0 287 0 17345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01917754
X-RAY DIFFRACTIONr_bond_other_d0.0070.0216104
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.97224073
X-RAY DIFFRACTIONr_angle_other_deg1.2233.00137363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36352157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68324820
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.939152958
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.31515112
X-RAY DIFFRACTIONr_chiral_restr0.080.22594
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02119708
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023682
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3674.7318664
X-RAY DIFFRACTIONr_mcbond_other3.3664.738663
X-RAY DIFFRACTIONr_mcangle_it5.4277.08710809
X-RAY DIFFRACTIONr_mcangle_other5.4277.08710810
X-RAY DIFFRACTIONr_scbond_it3.2895.0689090
X-RAY DIFFRACTIONr_scbond_other3.2895.0689091
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4747.47313265
X-RAY DIFFRACTIONr_long_range_B_refined8.2253.67519684
X-RAY DIFFRACTIONr_long_range_B_other8.2253.67319685
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 8217 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Auth asym-IDRms dev position (Å)
A13.44
B10.53
C6.43
D20.74
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 218 -
Rwork0.328 4022 -
obs--100 %

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