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- PDB-4bjk: CYP51 of Trypanosoma brucei bound to (S)-N-(3-(1H-indol-3-yl)-1-o... -

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Basic information

Entry
Database: PDB / ID: 4bjk
TitleCYP51 of Trypanosoma brucei bound to (S)-N-(3-(1H-indol-3-yl)-1-oxo-1- (pyridin-4-ylamino)propan-2-yl)-3,3'-difluoro-(1,1'-biphenyl)-4- carboxamide
ComponentsLANOSTEROL 14-ALPHA-DEMETHYLASE
KeywordsOXIDOREDUCTASE / ERGOSTEROL BIOSYNTHESIS
Function / homology
Function and homology information


membrane biogenesis / sterol 14alpha-demethylase / sterol 14-demethylase activity / nuclear envelope / oxidoreductase activity / iron ion binding / heme binding / endoplasmic reticulum
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-18I / PROTOPORPHYRIN IX CONTAINING FE / Lanosterol 14-alpha-demethylase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsPodust, L.M.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Rational Development of 4-Aminopyridyl-Based Inhibitors Targeting Trypanosoma Cruzi Cyp51 as Anti-Chagas Agents.
Authors: Choi, J.Y. / Calvet, C.M. / Gunatilleke, S.S. / Ruiz, C. / Cameron, M.D. / Mckerrow, J.H. / Podust, L.M. / Roush, W.R.
History
DepositionApr 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Oct 30, 2013Group: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _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: LANOSTEROL 14-ALPHA-DEMETHYLASE
B: LANOSTEROL 14-ALPHA-DEMETHYLASE
C: LANOSTEROL 14-ALPHA-DEMETHYLASE
D: LANOSTEROL 14-ALPHA-DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,45812
Polymers212,0064
Non-polymers4,4528
Water2,450136
1
A: LANOSTEROL 14-ALPHA-DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1153
Polymers53,0021
Non-polymers1,1132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LANOSTEROL 14-ALPHA-DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1153
Polymers53,0021
Non-polymers1,1132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LANOSTEROL 14-ALPHA-DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1153
Polymers53,0021
Non-polymers1,1132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: LANOSTEROL 14-ALPHA-DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1153
Polymers53,0021
Non-polymers1,1132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)199.291, 114.671, 136.221
Angle α, β, γ (deg.)90.00, 132.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
LANOSTEROL 14-ALPHA-DEMETHYLASE / STEROL 14-DEMETHYLASE CYP51


Mass: 53001.582 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Plasmid: PCWORI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: Q385E8, sterol 14alpha-demethylase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-18I / 3,3'-difluoro-N-[(2S)-3-(1H-indol-3-yl)-1-oxo-1-(pyridin-4-ylamino)propan-2-yl]biphenyl-4-carboxamide


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


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.76 Å3/Da / Density % sol: 55.5 % / Description: NONE
Crystal growpH: 7.5
Details: 12% PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH), 50 MM KCL, 50 MM HEPES, PH 7.5, 10% JEFFAMINE 600

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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: Feb 24, 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: 2.67→100.48 Å / Num. obs: 64156 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 4.1 % / Biso Wilson estimate: 81.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.7
Reflection shellResolution: 2.67→2.81 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.4 / % possible all: 99.9

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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 2X2N

2x2n


Resolution: 2.67→87.88 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.915 / SU B: 13.57 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R: 1.204 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27352 3243 5.1 %RANDOM
Rwork0.19442 ---
obs0.19849 60761 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.088 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å21.11 Å2
2---1.61 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.67→87.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14054 0 272 136 14462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01914722
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214132
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.99520006
X-RAY DIFFRACTIONr_angle_other_deg0.843332461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96351795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58523.117632
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.413152480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.40615118
X-RAY DIFFRACTIONr_chiral_restr0.0850.22188
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02116548
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023423
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_it4.0256.497186
X-RAY DIFFRACTIONr_mcbond_other4.0256.497185
X-RAY DIFFRACTIONr_mcangle_it5.9289.7338979
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2236.8267536
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: 2.67→2.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 213 -
Rwork0.326 4504 -
obs--99.45 %

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