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- PDB-4cc5: Fragment-Based Discovery of 6 Azaindazoles As Inhibitors of Bacte... -

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Basic information

Entry
Database: PDB / ID: 4cc5
TitleFragment-Based Discovery of 6 Azaindazoles As Inhibitors of Bacterial DNA Ligase
ComponentsDNA LIGASE
KeywordsLIGASE / ANTIBIOTIC DESIGN
Function / homology
Function and homology information


DNA ligase (NAD+) / DNA ligase (NAD+) activity / DNA replication / DNA repair / DNA binding / metal ion binding / cytosol
Similarity search - Function
Dna Ligase; domain 1 - #70 / Zinc-finger, NAD-dependent DNA ligase C4-type / NAD-dependent DNA ligase C4 zinc finger domain / NAD-dependent DNA ligase, active site / NAD-dependent DNA ligase, conserved site / NAD-dependent DNA ligase signature 1. / NAD-dependent DNA ligase signature 2. / NAD-dependent DNA ligase / NAD-dependent DNA ligase, OB-fold / NAD-dependent DNA ligase, adenylation ...Dna Ligase; domain 1 - #70 / Zinc-finger, NAD-dependent DNA ligase C4-type / NAD-dependent DNA ligase C4 zinc finger domain / NAD-dependent DNA ligase, active site / NAD-dependent DNA ligase, conserved site / NAD-dependent DNA ligase signature 1. / NAD-dependent DNA ligase signature 2. / NAD-dependent DNA ligase / NAD-dependent DNA ligase, OB-fold / NAD-dependent DNA ligase, adenylation / NAD-dependent DNA ligase, N-terminal / NAD-dependent DNA ligase adenylation domain / NAD-dependent DNA ligase OB-fold domain / Ligase N family / DisA/LigA, helix-hairpin-helix motif / Helix-hairpin-helix motif / DNA ligase/mRNA capping enzyme / Helix hairpin bin / RuvA domain 2-like / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / D-amino Acid Aminotransferase; Chain A, domain 1 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Dna Ligase; domain 1 / Helix Hairpins / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-chloranyl-6-(1H-1,2,4-triazol-3-yl)pyrazine / DNA ligase
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsHoward, S. / Amin, N. / Benowitz, A.B. / Chiarparin, E. / Cui, H. / Deng, X. / Heightman, T.D. / Holmes, D.J. / Hopkins, A. / Huang, J. ...Howard, S. / Amin, N. / Benowitz, A.B. / Chiarparin, E. / Cui, H. / Deng, X. / Heightman, T.D. / Holmes, D.J. / Hopkins, A. / Huang, J. / Jin, Q. / Kreatsoulas, C. / Martin, A.C.L. / Massey, F. / McCloskey, L. / Mortenson, P.N. / Pathuri, P. / Tisi, D. / Williams, P.A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2013
Title: Fragment-Based Discovery of 6-Azaindazoles as Inhibitors of Bacterial DNA Ligase.
Authors: Howard, S. / Amin, N. / Benowitz, A.B. / Chiarparin, E. / Cui, H. / Deng, X. / Heightman, T.D. / Holmes, D.J. / Hopkins, A. / Huang, J. / Jin, Q. / Kreatsoulas, C. / Martin, A.C.L. / Massey, ...Authors: Howard, S. / Amin, N. / Benowitz, A.B. / Chiarparin, E. / Cui, H. / Deng, X. / Heightman, T.D. / Holmes, D.J. / Hopkins, A. / Huang, J. / Jin, Q. / Kreatsoulas, C. / Martin, A.C.L. / Massey, F. / Mccloskey, L. / Mortenson, P.N. / Pathuri, P. / Tisi, D. / Williams, P.A.
History
DepositionOct 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0023
Polymers36,7251
Non-polymers2782
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)170.363, 39.523, 48.587
Angle α, β, γ (deg.)90.00, 90.13, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA LIGASE / POLYDEOXYRIBONUCLEOTIDE SYNTHASE [NAD(+)]


Mass: 36724.789 Da / Num. of mol.: 1 / Fragment: ADENYLATION DOMAIN, RESIDUES 1-312
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9AIU7, DNA ligase (NAD+)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-L5V / 2-chloranyl-6-(1H-1,2,4-triazol-3-yl)pyrazine


Mass: 181.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4ClN5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.23 Å3/Da / Density % sol: 44.77 % / Description: NONE
Crystal growpH: 7.5 / Details: 1.6M (NH4)2SO4, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.88→85 Å / Num. obs: 26855 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 7
Reflection shellResolution: 1.88→1.9 Å / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0031refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JSL

3jsl


Resolution: 1.88→85.18 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.896 / SU B: 8.565 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1390 5.3 %RANDOM
Rwork0.18932 ---
obs0.1932 24676 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.023 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å20.65 Å2
2--2.18 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.88→85.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 17 298 2803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192550
X-RAY DIFFRACTIONr_bond_other_d0.0010.022375
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9633446
X-RAY DIFFRACTIONr_angle_other_deg0.7742.9985471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8745307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.3425.071140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01515454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6021518
X-RAY DIFFRACTIONr_chiral_restr0.0850.2371
X-RAY DIFFRACTIONr_gen_planes_refined00.022928
X-RAY DIFFRACTIONr_gen_planes_other00.02586
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_it1.6252.7811231
X-RAY DIFFRACTIONr_mcbond_other1.6162.7781230
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7223.6151319
X-RAY DIFFRACTIONr_scbond_other2.7113.5991316
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.0687.108919
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.876→1.925 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 115 -
Rwork0.264 1662 -
obs--90.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.98370.5491-0.40041.6534-0.3141.9139-0.0543-0.2240.13930.012-0.0168-0.13210.03540.16080.07110.08310.0083-0.02560.0215-0.00340.0269.6317.683438.2923
21.98820.6237-0.72271.019-0.12081.60250.0029-0.07-0.0409-0.0397-0.0167-0.11670.03680.15560.01380.05660.0177-0.03520.0188-0.00860.045125.94118.125315.2419
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 60
2X-RAY DIFFRACTION2A61 - 309

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