2024-05-15 REL PDBe PDBe PDBe 2018-07-05 2018-10-24 2019-06-05 2024-05-15 European Union 612308 Finland Identification of a druggable VP1-VP3 interprotomer pocket in the capsid of enteroviruses Geraets JA Flatt JW Inhibitor, complex, virus Abdelnabi R Geraets JA Ma Y Mirabelli C Flatt JW Domanska A Delang L Jochmans D Kumar TA Jayaprakash V Sinha BN Leyssen P Butcher SJ Neyts J A novel druggable interprotomer pocket in the capsid of rhino- and enteroviruses. Plos Biol. US 17 e3000281 e3000281 2019 31185007 doi:10.1371/journal.pbio.3000281 1545-7885 6gzv FULLOVERLAP Coxsackievirus B3 (strain Nancy) Coxsackievirus B3 (strain Nancy) 0 1 2 3 4
Coxsackievirus B3 (strain Nancy) NCBI Taxonomy ID: 103903 Full, non-enveloped virion from natural source Diameter: ~314A Triangulation: 1 (pT3) Benzene sulfonamide derivative Molecular weight: 422Da Binding sites on capsid: 60
Coxsackievirus B3 (strain Nancy) Homo sapiens 314.0 1 VIRION STRAIN false false Capsid protein VP1 Coxsackievirus B3 (strain Nancy) Nancy 0.031639438 1 LEVO GPVEDAITAAIGRVADTVGTGPTNSEAIPALTAAETGHTSQVVPGDTMQTRHVKNYHSRSESTIENFLCRSACVYFTEYK NSGAKRYAEWVLTPRQAAQLRRKLEFFTYVRFDLELTFVITSTQQPSTTQNQDAQILTHQIMYVPPGGPVPDKVDSYVWQ TSTNPSVFWTEGNAPPRMSIPFLSIGNAYSNFYDGWSEFSRNGVYGINTLNNMGTLYARHVNAGSTGPIKSTIRIYFKPK HVKAWIPRPPRLCQYEKAKNVNFQPSGVTTTRQSITTMTNTGAF P03313 3.4.22.29 Capsid protein VP2 Coxsackievirus B3 (strain Nancy) Nancy 0.028836502 1 LEVO SPTVEECGYSDRARSITLGNSTITTQECANVVVGYGVWPDYLKDSEATAEDQPTQPDVATCRFYTLDSVQWQKTSPGWWW KLPDALSNLGLFGQNMQYHYLGRTGYTVHVQCNASKFHQGCLLVVCVPEAEMGCATLDNTPSSAELLGGDTAKEFADKPV ASGSNKLVQRVVYNAGMGVGVGNLTIFPHQWINLRTNNSATIVMPYTNSVPMDNMFRHNNVTLMVIPFVPLDYCPGSTTY VPITVTIAPMCAEYNGLRLAGHQ P03313 3.4.22.29 Capsid protein VP3 Coxsackievirus B3 (strain Nancy) Nancy 0.026195727 1 LEVO GLPTMNTPGSCQFLTSDDFQSPSAMPQYDVTPEMRIPGEVKNLMEIAEVDSVVPVQNVGEKVNSMEAYQIPVRSNEGSGT QVFGFPLQPGYSSVFSRTLLGEILNYYTHWSGSIKLTFMFCGSAMATGKFLLAYSPPGAGAPTKRVDAMLGTHVIWDVGL QSSCVLCIPWISQTHYRFVASDEYTAGGFITCWYQTNIVVPADAQSSCYIMCFVSACNDFSVRLLKDTPFISQQNFFQ P03313 3.4.22.29 Capsid protein VP4 Coxsackievirus B3 (strain Nancy) Nancy 0.007580377 1 LEVO MGAQVSTQKTGAHETRLNASGNSIIHYTNINYYKDAASNSANRQDFTQDPGKFTEPVKDIMIKSLPALN P03313 3.4.22.29 4-[[4-[1,3-bis(oxidanylidene)isoindol-2-yl]phenyl]sulfonylamino]benzoic acid 0.000422411 1 FHK singleParticle particle 7.5 0.1 MgCl2 Magnesium chloride 0.01 C8H18N2O4S HEPES ETHANE HOMEMADE PLUNGER
Inhibitor was added at 2500:1 molar ratio to purified CVB3 and incubated for 1h at 37C
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 FEI TITAN KRIOS AUTOGRID HOLDER GATAN K2 SUMMIT (4k x 4k) COUNTING 47.0 1 1COV
Fourier filtered to 40A
 I 4.0 FSC 0.143 CUT-OFF RELION 2.1.beta 4891 MAXIMUM LIKELIHOOD RELION 2.0.4 MAXIMUM LIKELIHOOD RELION 2.1.beta RELION 2.1.beta emd_0103.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 350 350 350 0 0 0 350 350 350 366.8 366.8 366.8 90.0 90.0 90.0 X Y Z -0.051150657 0.1611951 0.0032831568 0.009124994 1.048 1.048 1.048 0.018 AUTHOR Coxsackievirus B3 Nancy in complex with a small-molecule inhibitor FLEXIBLE FIT REAL emd_0103_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 350 350 350 0 0 0 350 350 350 366.8 366.8 366.8 90.0 90.0 90.0 X Y Z -0.008531959 0.019782504 0.0012989277 0.0031851635 1.048 1.048 1.048 AUTHOR emd_0103_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 350 350 350 0 0 0 350 350 350 366.8 366.8 366.8 90.0 90.0 90.0 X Y Z -0.01216333 0.025003208 0.0013197983 0.0031793518 1.048 1.048 1.048 AUTHOR