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- PDB-5fx6: Novel inhibitors of human rhinovirus 3C protease -

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Basic information

Entry
Database: PDB / ID: 5fx6
TitleNovel inhibitors of human rhinovirus 3C protease
ComponentsRHINOVIRUS 3C PROTEASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Trypsin-like serine proteases / Thrombin, subunit H / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chem-6OY / Genome polyprotein
Similarity search - Component
Biological speciesHUMAN RHINOVIRUS 2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsKawatkar, S. / Ek, M. / Hoesch, V. / Gagnon, M. / Nilsson, E. / Lister, T. / Olsson, L. / Patel, J. / Yu, Q.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2016
Title: Design and Structure-Activity Relationships of Novel Inhibitors of Human Rhinovirus 3C Protease.
Authors: Kawatkar, S.P. / Gagnon, M. / Hoesch, V. / Tiong-Yip, C. / Johnson, K. / Ek, M. / Nilsson, E. / Lister, T. / Olsson, L. / Patel, J. / Yu, Q.
History
DepositionFeb 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / 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_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RHINOVIRUS 3C PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7362
Polymers20,1261
Non-polymers6101
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.046, 77.641, 34.112
Angle α, β, γ (deg.)90.00, 104.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RHINOVIRUS 3C PROTEASE


Mass: 20125.793 Da / Num. of mol.: 1 / Fragment: 3C PROTEASE, RESIDUES 1508-1687
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN RHINOVIRUS 2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04936, EC: 2.4.22.28
#2: Chemical ChemComp-6OY / ethyl (4R)-4-[[(2S,4S)-1-[(2S)-3-methyl-2-[(5-methyl-1,2-oxazol-3-yl)carbonylamino]butanoyl]-4-phenyl-pyrrolidin-2-yl]carbonylamino]-5-[(3S)-2-oxidanylidenepyrrolidin-3-yl]pentanoate


Mass: 609.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H43N5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsETHYL (4R)-4-[[(2S, 4S)-1-[(2S)-3-METHYL-2-[(5-METHYLISOXAZOLE-3-CARBONYL)AMINO]BUTANOY

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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: 2.16 Å3/Da / Density % sol: 48.16 % / Description: NONE
Crystal growDetails: 0.2 M CACL2, 0,1 M TRIS PH 8.5, 25% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178
DetectorType: RIGAKU CCD / Detector: CCD / Date: Jul 12, 2013 / Details: OSMIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.34→77.64 Å / Num. obs: 33577 / % possible obs: 86.7 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.2
Reflection shellResolution: 1.34→1.42 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.5 / % possible all: 31.5

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XYA

2xya


Resolution: 1.45→32.89 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.069 / SU Rfree Cruickshank DPI: 0.066
RfactorNum. reflection% reflectionSelection details
Rfree0.186 1475 4.93 %RANDOM
Rwork0.154 ---
obs0.156 29911 98.5 %-
Displacement parametersBiso mean: 14.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.5022 Å20 Å2-3.0899 Å2
2---1.5651 Å20 Å2
3---2.0673 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.45→32.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1405 0 44 272 1721
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092922HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.125249HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d682SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes41HARMONIC2
X-RAY DIFFRACTIONt_gen_planes436HARMONIC5
X-RAY DIFFRACTIONt_it2922HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.97
X-RAY DIFFRACTIONt_other_torsion14.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion198SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3401SEMIHARMONIC4
Refinement TLS params.Method: refined / Origin x: 4.861 Å / Origin y: 0.5217 Å / Origin z: 15.5119 Å
111213212223313233
T-0.0635 Å20.0023 Å2-0.033 Å2--0.0922 Å20.0007 Å2--0.0241 Å2
L0.5608 °2-0.1123 °2-0.1325 °2-1.1107 °20.107 °2--0.6807 °2
S-0.0047 Å °0.0221 Å °-0.0023 Å °0.017 Å °-0.0008 Å °-0.0105 Å °-0.0271 Å °-0.0459 Å °0.0055 Å °

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