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- PDB-7sly: Vanin-1 complexed with Compound 27 -

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Basic information

Entry
Database: PDB / ID: 7sly
TitleVanin-1 complexed with Compound 27
ComponentsPantetheinase
KeywordsHYDROLASE / Pantetheine / SBDD / pyrimdine carboxamide
Function / homology
Function and homology information


pantetheine hydrolase / pantetheine hydrolase activity / pantothenate metabolic process / chronic inflammatory response / coenzyme A catabolic process / Vitamin B5 (pantothenate) metabolism / Post-translational modification: synthesis of GPI-anchored proteins / positive regulation of T cell differentiation in thymus / acute inflammatory response / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway ...pantetheine hydrolase / pantetheine hydrolase activity / pantothenate metabolic process / chronic inflammatory response / coenzyme A catabolic process / Vitamin B5 (pantothenate) metabolism / Post-translational modification: synthesis of GPI-anchored proteins / positive regulation of T cell differentiation in thymus / acute inflammatory response / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / azurophil granule membrane / side of membrane / cell-cell adhesion / response to oxidative stress / inflammatory response / innate immune response / Neutrophil degranulation / extracellular region / membrane / plasma membrane
Similarity search - Function
Biotinidase-like, eukaryotic / Biotinidase/VNN family / Vanin, C-terminal / Vanin C-terminal domain / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase
Similarity search - Domain/homology
Chem-9S5 / Pantetheinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsVajdos, F.F.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery of a Series of Pyrimidine Carboxamides as Inhibitors of Vanin-1.
Authors: Casimiro-Garcia, A. / Allais, C. / Brennan, A. / Choi, C. / Dower, G. / Farley, K.A. / Fleming, M. / Flick, A. / Frisbie, R.K. / Hall, J. / Hepworth, D. / Jones, H. / Knafels, J.D. / Kortum, ...Authors: Casimiro-Garcia, A. / Allais, C. / Brennan, A. / Choi, C. / Dower, G. / Farley, K.A. / Fleming, M. / Flick, A. / Frisbie, R.K. / Hall, J. / Hepworth, D. / Jones, H. / Knafels, J.D. / Kortum, S. / Lovering, F.E. / Mathias, J.P. / Mohan, S. / Morgan, P.M. / Parng, C. / Parris, K. / Pullen, N. / Schlerman, F. / Stansfield, J. / Strohbach, J.W. / Vajdos, F.F. / Vincent, F. / Wang, H. / Wang, X. / Webster, R. / Wright, S.W.
History
DepositionOct 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pantetheinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2726
Polymers53,8021
Non-polymers2,4705
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.980, 110.973, 147.885
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pantetheinase / Pantetheine hydrolase / Tiff66 / Vascular non-inflammatory molecule 1 / Vanin-1


Mass: 53801.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VNN1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O95497, pantetheine hydrolase

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Sugars , 3 types, 4 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D- ...beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DManpb1-6[DManpb1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 119 molecules

#5: Chemical ChemComp-9S5 / (8-oxa-2-azaspiro[4.5]decan-2-yl)(2-{[(1S)-1-(pyrazin-2-yl)ethyl]amino}pyrimidin-5-yl)methanone


Mass: 368.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24N6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES pH 6.1-6.7, 22-33% PEG-MME-2000, 10 mM TCEP
PH range: 6.1-6.7

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 28458 / % possible obs: 98.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 55.5 Å2 / Rmerge(I) obs: 0.078 / Χ2: 1.041 / Net I/σ(I): 12 / Num. measured all: 173822
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.17-2.255.50.7826381.03193.4
2.25-2.3460.57927721.003197.3
2.34-2.446.20.47928271.042199.8
2.44-2.576.30.34728471.0921100
2.57-2.736.30.21128461.061100
2.73-2.956.30.1428591.0281100
2.95-3.246.20.10628671.031100
3.24-3.716.20.06728881.01199.9
3.71-4.676.20.07729141.038199.8
4.67-5060.05230001.068198.9

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALEPACKdata scaling
BUSTER2.11.6refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: internal model

Resolution: 2.17→44.38 Å / Cor.coef. Fo:Fc: 0.9331 / Cor.coef. Fo:Fc free: 0.9248 / SU R Cruickshank DPI: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.229 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.179
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 1436 5.05 %RANDOM
Rwork0.19 ---
obs0.1917 28418 98.98 %-
Displacement parametersBiso max: 147.2 Å2 / Biso mean: 65.13 Å2 / Biso min: 39.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.8254 Å20 Å20 Å2
2---22.8278 Å20 Å2
3---22.0025 Å2
Refine analyzeLuzzati coordinate error obs: 0.306 Å
Refinement stepCycle: final / Resolution: 2.17→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3622 0 166 118 3906
Biso mean--78.96 68.04 -
Num. residues----461
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1331SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes95HARMONIC2
X-RAY DIFFRACTIONt_gen_planes580HARMONIC5
X-RAY DIFFRACTIONt_it3927HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion544SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4458SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3927HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5394HARMONIC21.25
X-RAY DIFFRACTIONt_omega_torsion3.98
X-RAY DIFFRACTIONt_other_torsion18.98
LS refinement shellResolution: 2.17→2.25 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2822 139 5.01 %
Rwork0.2434 2635 -
all0.2454 2774 -
obs--93.82 %

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