[English] 日本語
Yorodumi- PDB-6vkc: Crystal Structure of Inhibitor JNJ-36811054 in Complex with Prefu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vkc | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of Inhibitor JNJ-36811054 in Complex with Prefusion RSV F Glycoprotein | |||||||||
Components | Prefusion RSV F (DS-Cav1),Envelope glycoprotein | |||||||||
Keywords | VIRAL PROTEIN / Inhibitor / complex | |||||||||
Function / homology | Function and homology information positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane ...positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Human respiratory syncytial virus Human immunodeficiency virus 1 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | McLellan, J.S. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Discovery of 3-({5-Chloro-1-[3-(methylsulfonyl)propyl]-1H-indol-2-yl}methyl)-1-(2,2,2-trifluoroethyl)-1,3-dihydro-2H-imidazo[4,5-c]pyridin-2-one (JNJ-53718678), a Potent and Orally ...Title: Discovery of 3-({5-Chloro-1-[3-(methylsulfonyl)propyl]-1H-indol-2-yl}methyl)-1-(2,2,2-trifluoroethyl)-1,3-dihydro-2H-imidazo[4,5-c]pyridin-2-one (JNJ-53718678), a Potent and Orally Bioavailable Fusion Inhibitor of Respiratory Syncytial Virus. Authors: Vendeville, S. / Tahri, A. / Hu, L. / Demin, S. / Cooymans, L. / Vos, A. / Kwanten, L. / Van den Berg, J. / Battles, M.B. / McLellan, J.S. / Koul, A. / Raboisson, P. / Roymans, D. / Jonckers, T.H.M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6vkc.cif.gz | 196.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6vkc.ent.gz | 152.8 KB | Display | PDB format |
PDBx/mmJSON format | 6vkc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/6vkc ftp://data.pdbj.org/pub/pdb/validation_reports/vk/6vkc | HTTPS FTP |
---|
-Related structure data
Related structure data | 6vkdC 6vkeC 5ea4S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
-Protein / Sugars , 2 types, 2 molecules F
#1: Protein | Mass: 63218.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human respiratory syncytial virus, (gene. exp.) Human immunodeficiency virus 1 Production host: Homo sapiens (human) References: UniProt: Q84850, UniProt: M1E1E4, UniProt: P03420*PLUS |
---|---|
#2: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 5 types, 100 molecules
#3: Chemical | ChemComp-CL / | ||||||
---|---|---|---|---|---|---|---|
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-R0J / | #6: Chemical | ChemComp-TAR / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.67 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 1.52M K/Na tartrate, 0.2M LiSO4, 0.1M CHES pH 9.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→46.61 Å / Num. obs: 25576 / % possible obs: 100 % / Redundancy: 20.1 % / Biso Wilson estimate: 54.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.04 / Rrim(I) all: 0.182 / Net I/σ(I): 14.9 / Num. measured all: 514782 / Scaling rejects: 60 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EA4 Resolution: 2.6→46.606 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.99
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 146.77 Å2 / Biso mean: 61.1089 Å2 / Biso min: 26.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→46.606 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|