6HP0

Complex of Neuraminidase from H1N1 Influenza Virus in Complex with Oseltamivir Triazol Derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Investigation of flexibility of neuraminidase 150-loop using tamiflu derivatives in influenza A viruses H1N1 and H5N1.

Zima, V.Albinana, C.B.Rojikova, K.Pokorna, J.Pachl, P.Rezacova, P.Hudlicky, J.Navratil, V.Majer, P.Konvalinka, J.Kozisek, M.Machara, A.

(2019) Bioorg Med Chem 27: 2935-2947

  • DOI: 10.1016/j.bmc.2019.05.024
  • Primary Citation of Related Structures:  
    6HP0

  • PubMed Abstract: 
  • This study focuses on design, synthesis and in vitro evaluation of inhibitory potency of two series of sialylmimetic that target an exosite ("150-cavity") adjacent to the active site of influenza neuraminidases from A/California/07/2009 (H1N1) pandemic strain and A/chicken/Nakorn-Patom/Thailand/CU-K2-2004 (H5N1) ...

    This study focuses on design, synthesis and in vitro evaluation of inhibitory potency of two series of sialylmimetic that target an exosite ("150-cavity") adjacent to the active site of influenza neuraminidases from A/California/07/2009 (H1N1) pandemic strain and A/chicken/Nakorn-Patom/Thailand/CU-K2-2004 (H5N1). The structure-activity analysis as well as 3-D structure of the complex of parental compound with the pandemic neuraminidase p09N1 revealed high flexibility of the 150-cavity towards various modification of the neuraminidase inhibitors. Furthermore, our comparison of two methods for inhibition constant determination performed at slightly different pH values suggest that the experimental conditions of the measurement could dramatically influence the outcome of the analysis in the compound-dependent manner. Therefore, previously reported K i values determined at non-physiological pH should be carefully scrutinized.


    Organizational Affiliation

    Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 00 Prague 2, Czech Republic; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10 Prague 6, Czech Republic. Electronic address: ales.machara@uochb.cas.cz.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NeuraminidaseA, B, C, D388Influenza A virus (A/Texas/17/2009(H1N1))Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
UniProt
Find proteins for C6KP13 (Influenza A virus)
Explore C6KP13 
Go to UniProtKB:  C6KP13
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseE, G, H3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseF, J2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseI6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G82348BZ
GlyCosmos:  G82348BZ
GlyGen:  G82348BZ
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GJT (Subject of Investigation/LOI)
Query on GJT

Download Ideal Coordinates CCD File 
EA [auth B], M [auth A], PA [auth C], WA [auth D](3~{R},4~{R},5~{S})-4-acetamido-5-[4-(hydroxymethyl)-1,2,3-triazol-1-yl]-3-pentan-3-yloxy-cyclohexene-1-carboxylic acid
C17 H26 N4 O5
IPVDZUUVRPUAMB-ARFHVFGLSA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
FA [auth B], GA [auth B], N [auth A], QA [auth C], XA [auth D], YA [auth D]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
FB [auth D]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth A] , AB [auth D] , BA [auth A] , BB [auth D] , CB [auth D] , DB [auth D] , EB [auth D] , HA [auth B] , 
AA [auth A],  AB [auth D],  BA [auth A],  BB [auth D],  CB [auth D],  DB [auth D],  EB [auth D],  HA [auth B],  IA [auth B],  JA [auth B],  KA [auth B],  LA [auth B],  MA [auth B],  O [auth A],  P [auth A],  Q [auth A],  R [auth A],  RA [auth C],  S [auth A],  SA [auth C],  T [auth A],  TA [auth C],  U [auth A],  V [auth A],  W [auth A],  X [auth A],  Y [auth A],  Z [auth A],  ZA [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
CA [auth B], DA [auth B], K [auth A], L [auth A], NA [auth C], OA [auth C], UA [auth D], VA [auth D]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GJT Binding MOAD:  6HP0 Ki: 470 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.842α = 90
b = 126.861β = 93.93
c = 96.906γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-09-19 
  • Released Date: 2019-09-11 
  • Deposition Author(s): Pachl, P., Pokorna, J.

Funding OrganizationLocationGrant Number
Ministry of Education (Czech Republic)Czech RepublicInterBioMed LO1302

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary