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- PDB-6d4u: M. thermoresistible GuaB2 delta-CBS in complex with inhibitor Com... -

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Basic information

Entry
Database: PDB / ID: 6d4u
TitleM. thermoresistible GuaB2 delta-CBS in complex with inhibitor Compound 27 (VCC663664)
ComponentsInosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / Complex / Fragment / IMPDH / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain ...Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Aldolase-type TIM barrel
Similarity search - Domain/homology
Chem-FWP / INOSINIC ACID / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesMycobacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAscher, D.B. / Pacitto, A. / Blundell, T.L.
Funding supportEuropean Union, United Kingdom, Australia, 3items
OrganizationGrant numberCountry
European Union (EU)260872European Union
Medical Research Council (MRC, United Kingdom)MR/M026302/1 United Kingdom
National Health and Medical Research Council (NHMRC, Australia)APP1072476 Australia
CitationJournal: Eur.J.Med.Chem. / Year: 2019
Title: Synthesis and Structure-Activity relationship of 1-(5-isoquinolinesulfonyl)piperazine analogues as inhibitors of Mycobacterium tuberculosis IMPDH.
Authors: Singh, V. / Pacitto, A. / Donini, S. / Ferraris, D.M. / Boros, S. / Illyes, E. / Szokol, B. / Rizzi, M. / Blundell, T.L. / Ascher, D.B. / Pato, J. / Mizrahi, V.
History
DepositionApr 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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

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Assembly

Deposited unit
A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6583
Polymers39,8541
Non-polymers8042
Water5,747319
1
A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,63312
Polymers159,4184
Non-polymers3,2158
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
Buried area15950 Å2
ΔGint-101 kcal/mol
Surface area42730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.721, 88.721, 84.552
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-819-

HOH

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Components

#1: Protein Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase / IMPDH


Mass: 39854.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium thermoresistibile (bacteria)
Strain: ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316
Gene: guaB, KEK_23061 / Production host: Escherichia coli (E. coli) / References: UniProt: G7CNL4, IMP dehydrogenase
#2: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical ChemComp-FWP / 2-(2,4-dimethoxyphenyl)-1-{4-[(isoquinolin-5-yl)sulfonyl]piperazin-1-yl}ethan-1-one


Mass: 455.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25N3O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.08 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: sodium acetate, calcium chloride, iso-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.7→61.21 Å / Num. obs: 36025 / % possible obs: 100 % / Redundancy: 2 % / Net I/σ(I): 5.4
Reflection shellResolution: 1.7→1.76 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J5R

5j5r


Resolution: 1.7→61.208 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2022 1783 4.95 %
Rwork0.1748 --
obs0.1761 36018 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→61.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2259 0 55 319 2633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092371
X-RAY DIFFRACTIONf_angle_d1.1523244
X-RAY DIFFRACTIONf_dihedral_angle_d12.912814
X-RAY DIFFRACTIONf_chiral_restr0.051403
X-RAY DIFFRACTIONf_plane_restr0.005414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7460.28621400.25372627X-RAY DIFFRACTION100
1.746-1.79730.23841650.22072607X-RAY DIFFRACTION100
1.7973-1.85540.24651490.20952615X-RAY DIFFRACTION100
1.8554-1.92170.23261620.19352577X-RAY DIFFRACTION100
1.9217-1.99860.27051320.19362619X-RAY DIFFRACTION100
1.9986-2.08960.22491040.18632658X-RAY DIFFRACTION100
2.0896-2.19980.21311420.17392610X-RAY DIFFRACTION100
2.1998-2.33760.19381690.16992608X-RAY DIFFRACTION100
2.3376-2.51810.20311250.16912666X-RAY DIFFRACTION100
2.5181-2.77150.20081230.1712637X-RAY DIFFRACTION100
2.7715-3.17250.19321190.16662651X-RAY DIFFRACTION100
3.1725-3.99690.17061200.15482670X-RAY DIFFRACTION100
3.9969-61.24780.17091330.16492690X-RAY DIFFRACTION100

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