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- PDB-4by0: Crystal structure of Trypanosoma cruzi CYP51 bound to the inhibit... -

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Basic information

Entry
Database: PDB / ID: 4by0
TitleCrystal structure of Trypanosoma cruzi CYP51 bound to the inhibitor (R)-N-(3-(1H-indol-3-yl)-1-oxo-1-(pyridin-4-ylamino)propan-2-yl)-3,3'- difluoro-(1,1'-biphenyl)-4-carboxamide
ComponentsSTEROL 14-ALPHA DEMETHYLASE
KeywordsOXIDOREDUCTASE / STEROL 14-DEMETHYLASE / STEROL BIOSYNTHESIS / CHAGAS DISEASE
Function / homology
Function and homology information


sterol 14alpha-demethylase / sterol 14-demethylase activity / sterol biosynthetic process / iron ion binding / heme binding / membrane
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
Chem-5PS / PROTOPORPHYRIN IX CONTAINING FE / Sterol 14-alpha demethylase / Sterol 14-alpha demethylase
Similarity search - Component
Biological speciesTRYPANOSOMA CRUZI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsChoi, J.Y. / Calvet, C.M. / Vierira, D.F. / Gunatilleke, S.S. / Cameron, M.D. / McKerrow, J.H. / Podust, L.M. / Roush, W.R.
CitationJournal: Acs Med.Chem.Lett. / Year: 2014
Title: R-Configuration of 4-Aminopyridyl-Based Inhibitors of Cyp51 Confers Superior Efficacy Against Trypanosoma Cruzi
Authors: Choi, J.Y. / Calvet, C.M. / Vieira, D.F. / Gunatilleke, S.S. / Cameron, M.D. / Mckerrow, J.H. / Podust, L.M. / Roush, W.R.
History
DepositionJul 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Dec 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: STEROL 14-ALPHA DEMETHYLASE
B: STEROL 14-ALPHA DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8006
Polymers106,5742
Non-polymers2,2264
Water23413
1
A: STEROL 14-ALPHA DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4003
Polymers53,2871
Non-polymers1,1132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: STEROL 14-ALPHA DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4003
Polymers53,2871
Non-polymers1,1132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.167, 124.167, 119.839
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein STEROL 14-ALPHA DEMETHYLASE / TC14DM / CYTOCHROME P450 51 / LANOSTEROL 14-ALPHA DEMETHYLASE


Mass: 53286.820 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-481
Source method: isolated from a genetically manipulated source
Details: 32 N-TERMINUS RESIDUES ARE REPLACED WITH THE SEQUENCE MAKKTSSKGKL, 6XHIS TAG ENGINEERED AT THE C- TERMINUS
Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Plasmid: PCW / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: Q5I4E1, UniProt: Q7Z1V1*PLUS, sterol 14alpha-demethylase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-5PS / (R)-N-(3-(1H-indol-3-yl)-1-oxo-1-(pyridin-4-ylamino)propan-2-yl)-3,3'-difluoro-(1,1'-biphenyl)-4-carboxamide


Mass: 496.507 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H22F2N4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPROTOPORPHYRIN IX CONTAINING FE (HEM): THIOLATE BOND TO CYS 422
Sequence detailsFIRST 32 RESIDUES AT THE N-TERMINUS ARE REPLACED WITH THE MAKKTSSKGKL SEQUENCE, 6XHIS TAG ...FIRST 32 RESIDUES AT THE N-TERMINUS ARE REPLACED WITH THE MAKKTSSKGKL SEQUENCE, 6XHIS TAG ENGINEERED 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: 2.47 Å3/Da / Density % sol: 50.3 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2 M AMMONIUM SULFATE; 0.1 M BIS-TRIS, PH 6.5; 25% PEG 3550

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 18, 2012 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 3.1→119.84 Å / Num. obs: 19806 / % possible obs: 100 % / Observed criterion σ(I): 0.5 / Redundancy: 8.2 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 9.6
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 8.4 % / Rmerge(I) obs: 1.34 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WX2

2wx2


Resolution: 3.1→80.16 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.879 / SU B: 29.614 / SU ML: 0.528 / Cross valid method: THROUGHOUT / ESU R Free: 0.567 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29748 1013 5.1 %RANDOM
Rwork0.23195 ---
obs0.23545 18756 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.23 Å20 Å2
2---0.23 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 3.1→80.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6661 0 160 13 6834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197003
X-RAY DIFFRACTIONr_bond_other_d0.0030.026469
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.9919553
X-RAY DIFFRACTIONr_angle_other_deg0.873314821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2695879
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.48823.636286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.334151059
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6291543
X-RAY DIFFRACTIONr_chiral_restr0.080.21044
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218022
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021617
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_it4.1048.0363528
X-RAY DIFFRACTIONr_mcbond_other4.1048.0353527
X-RAY DIFFRACTIONr_mcangle_it6.52612.0484403
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4858.1323475
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 72 -
Rwork0.296 1359 -
obs--99.58 %

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