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- PDB-6d4v: M. thermoresistible GuaB2 delta-CBS in complex with inhibitor Com... -

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Basic information

Entry
Database: PDB / ID: 6d4v
TitleM. thermoresistible GuaB2 delta-CBS in complex with inhibitor Compound 22 (VCC061422)
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
IMP dehydrogenase / GMP reductase 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 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain ...IMP dehydrogenase / GMP reductase 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 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Aldolase-type TIM barrel
Similarity search - Domain/homology
Chem-FWM / INOSINIC ACID / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesMycobacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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

Downloads & links

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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)40,6043
Polymers39,8541
Non-polymers7502
Water3,927218
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)162,41712
Polymers159,4184
Non-polymers2,9998
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_865-x+3,-y+1,z1
crystal symmetry operation3_745-y+2,x-1,z1
crystal symmetry operation4_675y+1,-x+2,z1
Buried area15710 Å2
ΔGint-99 kcal/mol
Surface area43040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.800, 89.800, 84.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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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 / Inosinic acid


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


Mass: 401.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N3O3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.15 Å3/Da / Density % sol: 42.75 %
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: 2.02→63.5 Å / Num. obs: 22169 / % possible obs: 100 % / Redundancy: 2 % / Net I/σ(I): 10.6
Reflection shellResolution: 2.02→2.09 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K4X

5k4x


Resolution: 2.02→63.498 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2028 956 4.31 %
Rwork0.1675 --
obs0.1691 22167 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→63.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2265 0 51 218 2534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092373
X-RAY DIFFRACTIONf_angle_d1.1273246
X-RAY DIFFRACTIONf_dihedral_angle_d14.136819
X-RAY DIFFRACTIONf_chiral_restr0.046403
X-RAY DIFFRACTIONf_plane_restr0.006415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.12650.31571230.2693052X-RAY DIFFRACTION100
2.1265-2.25980.26791390.22942998X-RAY DIFFRACTION100
2.2598-2.43430.25331100.2023038X-RAY DIFFRACTION100
2.4343-2.67920.22431010.17413052X-RAY DIFFRACTION100
2.6792-3.06690.19571900.16392966X-RAY DIFFRACTION100
3.0669-3.86390.18231480.153031X-RAY DIFFRACTION100
3.8639-63.52960.17561450.13833074X-RAY DIFFRACTION100

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