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Basic information

Entry
Database: PDB / ID: 2ci0
TitleHigh throughput screening and x-ray crystallography assisted evaluation of small molecule scaffolds for CYP51 inhibitors
ComponentsCYTOCHROME P450 51
KeywordsOXIDOREDUCTASE / HEME / HEME LIPID SYNTHESIS / METAL-BINDING / MONOOXYGENASE / NADP / PROTEIN-INHIBITOR COMPLEX / STEROID BIOSYNTHESIS / STEROL BIOSYNTHESIS
Function / homology
Function and homology information


sterol 14alpha-demethylase (ferredoxin) / sterol 14-demethylase activity / sterol biosynthetic process / sterol 14alpha-demethylase / sterol metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / oxidoreductase activity / iron ion binding / heme binding ...sterol 14alpha-demethylase (ferredoxin) / sterol 14-demethylase activity / sterol biosynthetic process / sterol 14alpha-demethylase / sterol metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / oxidoreductase activity / iron ion binding / heme binding / cytoplasm / cytosol
Similarity search - Function
: / Cytochrome P450, E-class, group IV / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(2R)-2-PHENYL-N-PYRIDIN-4-YLBUTANAMIDE / PROTOPORPHYRIN IX CONTAINING FE / Lanosterol 14-alpha demethylase / Sterol 14alpha-demethylase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsPodust, L.M. / Kim, Y. / Yermalitskaya, L.V. / Von Kries, J.P. / Waterman, M.R.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2007
Title: Small Molecule Scaffolds for Cyp51 Inhibitors Identified by High Throughput Screening and Defined by X-Ray Crystallography
Authors: Podust, L.M. / Von Kries, J.P. / Eddine, A.N. / Kim, Y. / Yermalitskaya, L.V. / Kuehne, R. / Ouellet, H. / Warrier, T. / Altekoster, M. / Lee, J.-S. / Rademann, J. / Oschkinat, H. / ...Authors: Podust, L.M. / Von Kries, J.P. / Eddine, A.N. / Kim, Y. / Yermalitskaya, L.V. / Kuehne, R. / Ouellet, H. / Warrier, T. / Altekoster, M. / Lee, J.-S. / Rademann, J. / Oschkinat, H. / Kaufmann, S.H.E. / Waterman, M.R.
History
DepositionMar 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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_conn
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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME P450 51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3343
Polymers51,4771
Non-polymers8572
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.997, 85.551, 110.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOCHROME P450 51 / STEROL 14ALPHA-DEMETHYLASE CYP51 / YPLI / P450-LIA1 / STEROL 14-ALPHA DEMETHYLASE / LANOSTEROL 14- ...STEROL 14ALPHA-DEMETHYLASE CYP51 / YPLI / P450-LIA1 / STEROL 14-ALPHA DEMETHYLASE / LANOSTEROL 14-ALPHA DEMETHYLASE / P450-14DM


Mass: 51477.285 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: 4XHIS TAG AT THE C-TERMINUS / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: P0A512, UniProt: P9WPP9*PLUS, sterol 14alpha-demethylase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-1CM / (2R)-2-PHENYL-N-PYRIDIN-4-YLBUTANAMIDE


Mass: 240.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 37 TO LEU ENGINEERED RESIDUE IN CHAIN A, CYS 442 TO ALA
Sequence detailsMUTATIONS C37L, C442A 4XHIS TAG AT THE C-TERMINUS

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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: 40 % / Description: NONE
Crystal growpH: 7.5
Details: 15 % PEG 4000,1% ISOPROPANOL, 0.1 M HEPES, PH=7.5; 2 MM (2R)-2-PHENYL-N-PYRIDIN-4- YLBUTANAMIDE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.00931
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 3, 2006
Details: SAGITTAL FOCUSING CRYSTAL AND VERTICALLY FOCUSING DOUBLE MIRROR
RadiationMonochromator: SI (220) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00931 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 65111 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 47.7
Reflection shellResolution: 1.53→1.58 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 9 / % possible all: 89.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X8V

1x8v


Resolution: 1.53→46.42 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 322653.73 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: DISORDERED REGIONS DISORDERED REGIONS WERE OMMITED FROM THE STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.227 6286 10.1 %RANDOM
Rwork0.203 ---
obs0.203 62309 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.3122 Å2 / ksol: 0.38274 e/Å3
Displacement parametersBiso mean: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1-11.74 Å20 Å20 Å2
2---4.19 Å20 Å2
3----7.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.53→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3305 0 61 364 3730
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_mcangle_it1.692
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.952.5
LS refinement shellResolution: 1.53→1.63 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.261 887 9.8 %
Rwork0.238 8176 -
obs--84.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP

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