Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T40909 | Target Info | |||
| Target Name | Rhinovirus Protease 3C (HRV P3C) | ||||
| Synonyms | Rhinovirus P3C | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | HRV P3C | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Lauric acid | Ligand Info | |||||
| Structure Description | HUMAN RHINOVIRUS SEROTYPE 2 (HRV2) | PDB:1FPN | ||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [1] |
| PDB Sequence |
LVVPNINSSN
24 PTTSNSAPAL34 DAAETGHTSS44 VQPEDVIETR54 YVQTSQTRDE64 MSLESFLGRS 74 GCIHESKLEV84 TLANYNKENF94 TVWAINLQEM104 AQIRRKFELF114 TYTRFDSEIT 124 LVPCISALSQ134 DIGHITMQYM144 YVPPGAPVPN154 SRDDYAWQSG164 TNASVFWQHG 174 QAYPRFSLPF184 LSVASAYYMF194 YDGYDEQDQN204 YGTANTNNMG214 SLCSRIVTEK 224 HIHKVHIMTR234 IYHKAKHVKA244 WCPRPPRALE254 YTRAHRTNFK264 IEDRSIQTAI 274 VTRPIITTA
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ILE77
4.640
TRP97
4.783
ILE99
3.349
ASN100
3.561
LEU101
3.184
GLN102
3.032
PHE119
4.772
SER121
3.804
ILE123
3.686
TYR145
4.104
PHE180
4.648
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Vapendavir | Ligand Info | |||||
| Structure Description | Structure of HRV2 capsid complexed with antiviral compound BTA798 | PDB:3VDD | ||||
| Method | X-ray diffraction | Resolution | 3.20 Å | Mutation | No | [2] |
| PDB Sequence |
ENYIDEVLNE
13 VLVVPNINSS23 NPTTSNSAPA33 LDAAETGHTS43 SVQPEDVIET53 RYVQTSQTRD 63 EMSLESFLGR73 SGCIHESKLE83 VTLANYNKEN93 FTVWAINLQE103 MAQIRRKFEL 113 FTYTRFDSEI123 TLVPCISALS133 QDIGHITMQY143 MYVPPGAPVP153 NSRDDYAWQS 163 GTNASVFWQH173 GQAYPRFSLP183 FLSVASAYYM193 FYDGYDEQDQ203 NYGTANTNNM 213 GSLCSRIVTE223 KHIHKVHIMT233 RIYHKAKHVK243 AWCPRPPRAL253 EYTRAHRTNF 263 KIEDRSIQTA273 IVTRPIITTA283
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ILE99
3.585
ASN100
4.163
LEU101
3.157
GLN102
4.721
PHE119
4.190
SER121
3.520
ILE123
3.598
TYR143
3.356
MET144
3.746
TYR145
3.207
ALA167
3.152
SER168
4.129
VAL169
4.296
PHE180
3.210
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| Ligand Name: ethyl (4R)-4-[[(2S,4S)-1-[(2S)-3-methyl-2-[(5-methyl-1,2-oxazole-3-carbonyl)amino]butanoyl]-4-phenylpyrrolidine-2-carbonyl]amino]-5-[(3S)-2-oxopyrrolidin-3-yl]pentanoate | Ligand Info | |||||
| Structure Description | Novel inhibitors of human rhinovirus 3C protease | PDB:5FX6 | ||||
| Method | X-ray diffraction | Resolution | 1.45 Å | Mutation | No | [3] |
| PDB Sequence |
GPEEEFGMSL
10 IKHNSCVITT20 ENGKFTGLGV30 YDRFVVVPTH40 ADPGKEIQVD50 GITTKVIDSY 60 DLYNKNGIKL70 EITVLKLDRN80 EKFRDIRRYI90 PNNEDDYPNC100 NLALLANQPE 110 PTIINVGDVV120 SYGNILLSGN130 QTARMLKYSY140 PTKSGYCGGV150 LYKIGQVLGI 160 HVGGNGRDGF170 SAMLLRSYFT180
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6OY or .6OY2 or .6OY3 or :36OY;style chemicals stick;color identity;select .A:22 or .A:25 or .A:40 or .A:125 or .A:126 or .A:127 or .A:128 or .A:142 or .A:143 or .A:144 or .A:145 or .A:146 or .A:147 or .A:161 or .A:162 or .A:163 or .A:164 or .A:165 or .A:166 or .A:170; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: ethyl (4R)-4-[[(2S,3R)-1-[(2S)-3-methyl-2-[(5-methyl-1,2-oxazole-3-carbonyl)amino]butanoyl]-3-phenylpyrrolidine-2-carbonyl]amino]-5-[(3S)-2-oxopyrrolidin-3-yl]pentanoate | Ligand Info | |||||
| Structure Description | Novel inhibitors of human rhinovirus 3C protease | PDB:5FX5 | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [3] |
| PDB Sequence |
GPEEEFGMSL
10 IKHNSCVITT20 ENGKFTGLGV30 YDRFVVVPTH40 ADPGKEIQVD50 GITTKVIDSY 60 DLYNKNGIKL70 EITVLKLDRN80 EKFRDIRRYI90 PNNEDDYPNC100 NLALLANQPE 110 PTIINVGDVV120 SYGNILLSGN130 QTARMLKYSY140 PTKSGYCGGV150 LYKIGQVLGI 160 HVGGNGRDGF170 SAMLLRSYFT180
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HOV or .HOV2 or .HOV3 or :3HOV;style chemicals stick;color identity;select .A:22 or .A:23 or .A:24 or .A:25 or .A:40 or .A:71 or .A:107 or .A:125 or .A:126 or .A:127 or .A:128 or .A:130 or .A:132 or .A:142 or .A:143 or .A:144 or .A:145 or .A:146 or .A:147 or .A:161 or .A:162 or .A:163 or .A:164 or .A:165 or .A:166 or .A:170; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ASN22
3.349
GLY23
3.809
LYS24
3.269
PHE25
3.356
HIS40
3.185
GLU71
3.436
ASN107
4.069
ILE125
4.202
LEU126
3.022
LEU127
3.598
SER128
3.040
ASN130
4.364
THR132
4.949
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| Ligand Name: Unk-Dap(1)-Phe(4-F)-Glu(2)-ol.D-N(2)Pro-(1) | Ligand Info | |||||
| Structure Description | Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease inhibitors | PDB:6FFN | ||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [4] |
| PDB Sequence |
GSGPEEEFGM
8 SLIKHNSCVI18 TTENGKFTGL28 GVYDRFVVVP38 THADPGKEIQ48 VDGITTKVID 58 SYDLYNKNGI68 KLEITVLKLD78 RNEKFRDIRR88 YIPNNEDDYP98 NCNLALLANQ 108 PEPTIINVGD118 VVSYGNILLS128 GNQTARMLKY138 SYPTKSGYCG148 GVLYKIGQVL 158 GIHVGGNGRD168 GFSAMLLRSY178 FT
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .D8K or .D8K2 or .D8K3 or :3D8K;style chemicals stick;color identity;select .A:25 or .A:40 or .A:71 or .A:125 or .A:126 or .A:127 or .A:128 or .A:129 or .A:130 or .A:132 or .A:142 or .A:143 or .A:144 or .A:146 or .A:147 or .A:161 or .A:162 or .A:163 or .A:164 or .A:165 or .A:166 or .A:170; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PHE25
3.935
HIS40
2.795
GLU71
3.481
ILE125
4.421
LEU126
2.978
LEU127
3.522
SER128
2.894
GLY129
4.945
ASN130
3.330
THR132
4.267
THR142
2.775
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| Ligand Name: N-[(2S,5S,14S)-2-[(4-fluorophenyl)methyl]-5-(hydroxymethyl)-9-methyl-3,8,15-trioxo-1,4,9-triazacyclopentadec-14-yl]-5-methyl-1,2-oxazole-3-carboxamide | Ligand Info | |||||
| Structure Description | Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease inhibitors | PDB:6FFS | ||||
| Method | X-ray diffraction | Resolution | 1.86 Å | Mutation | No | [4] |
| PDB Sequence |
GSGPEEEFGM
8 SLIKHNSCVI18 TTENGKFTGL28 GVYDRFVVVP38 THADPGKEIQ48 VDGITTKVID 58 SYDLYNKNGI68 KLEITVLKLD78 RNEKFRDIRR88 YIPNNEDDYP98 NCNLALLANQ 108 PEPTIINVGD118 VVSYGNILLS128 GNQTARMLKY138 SYPTKSGYCG148 GVLYKIGQVL 158 GIHVGGNGRD168 GFSAMLLRSY178 FT
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .D8E or .D8E2 or .D8E3 or :3D8E;style chemicals stick;color identity;select .A:25 or .A:40 or .A:71 or .A:125 or .A:126 or .A:127 or .A:128 or .A:129 or .A:130 or .A:132 or .A:142 or .A:143 or .A:144 or .A:147 or .A:161 or .A:162 or .A:163 or .A:164 or .A:165 or .A:166 or .A:170; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PHE25
3.864
HIS40
2.895
GLU71
3.641
ILE125
4.357
LEU126
3.006
LEU127
3.421
SER128
2.915
GLY129
4.978
ASN130
3.103
THR132
4.391
THR142
2.831
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| Ligand Name: 2-Phenylquinolin-4-ol | Ligand Info | |||||
| Structure Description | Non-covalent inhibtors of rhinovirus 3C protease. | PDB:2XYA | ||||
| Method | X-ray diffraction | Resolution | 2.40 Å | Mutation | No | [5] |
| PDB Sequence |
GSGPEEEFGM
8 SLIKHNSCVI18 TTENGKFTGL28 GVYDRFVVVP38 THADPGKEIQ48 VDGITTKVID 58 SYDLYNKNGI68 KLEITVLKLD78 RNEKFRDIRR88 YIPNNEDDYP98 NCNLALLANQ 108 PEPTIINVGD118 VVSYGNILLS128 GNQTARMLKY138 SYPTKSGYCG148 GVLYKIGQVL 158 GIHVGGNGRD168 GFSAMLLRSY178 FT
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7L4 or .7L42 or .7L43 or :37L4;style chemicals stick;color identity;select .A:142 or .A:143 or .A:144 or .A:147 or .A:161 or .A:162 or .A:163 or .A:164 or .A:165 or .A:166; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-{2-(4-Fluoro-benzyl)-6-methyl-5-[(5-methyl-isoxazole-3-carbonyl)-amino]-4-oxo-heptanoylamino}-5-(2-oxo-pyrrolidin-3-YL)-pentanoic acid ethyl ester | Ligand Info | |||||
| Structure Description | TYPE 2 RHINOVIRUS 3C PROTEASE WITH AG7088 INHIBITOR | PDB:1CQQ | ||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [6] |
| PDB Sequence |
GPEEEFGMSL
10 IKHNSCVITT20 ENGKFTGLGV30 YDRFVVVPTH40 ADPGKEIQVD50 GITTKVIDSY 60 DLYNKNGIKL70 EITVLKLDRN80 EKFRDIRRYI90 PNNEDDYPNC100 NLALLANQPE 110 PTIINVGDVV120 SYGNILLSGN130 QTARMLKYSY140 PTKSGYCGGV150 LYKIGQVLGI 160 HVGGNGRDGF170 SAMLLRSYFT180
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AG7 or .AG72 or .AG73 or :3AG7;style chemicals stick;color identity;select .A:22 or .A:23 or .A:24 or .A:25 or .A:40 or .A:71 or .A:107 or .A:122 or .A:125 or .A:126 or .A:127 or .A:128 or .A:129 or .A:130 or .A:132 or .A:142 or .A:143 or .A:144 or .A:145 or .A:146 or .A:147 or .A:161 or .A:162 or .A:163 or .A:164 or .A:165 or .A:166 or .A:168 or .A:170; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ASN22
2.690
GLY23
3.304
LYS24
2.533
PHE25
2.688
HIS40
1.603
GLU71
2.775
ASN107
2.980
TYR122
4.878
ILE125
2.962
LEU126
2.248
LEU127
2.919
SER128
1.889
GLY129
4.563
ASN130
2.283
THR132
4.414
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| Ligand Name: Z-VAM-FMK;zVAM.fmk | Ligand Info | |||||
| Structure Description | Rhinovirus A2 2A protease in complex with zVAM.fmk | PDB:7ARA | ||||
| Method | X-ray diffraction | Resolution | 2.24 Å | Mutation | No | [7] |
| PDB Sequence |
GPSDMYVHVG
10 NLIYRNLHLF20 NSEMHESILV30 SYSSDLIIYR40 TNTVGDDYIP50 SCDCTQATYY 60 CKHKNRYFPI70 TVTSHDWYEI80 QESEYYPKHI90 QYNLLIGEGP100 CEPGDCGGKL 110 LCKHGVIGIV120 TAGGDNHVAF130 IDLRHFHCA
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .S7N or .S7N2 or .S7N3 or :3S7N;style chemicals stick;color identity;select .A:16 or .A:18 or .A:19 or .A:78 or .A:80 or .A:81 or .A:82 or .A:83 or .A:85 or .A:96 or .A:102 or .A:103 or .A:104 or .A:105 or .A:106 or .A:120 or .A:121 or .A:122 or .A:123 or .A:124 or .A:125 or .A:127 or .A:128 or .A:129; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ASN16
4.969
HIS18
3.323
LEU19
4.578
TYR78
3.302
ILE80
3.840
GLN81
3.240
GLU82
3.885
SER83
3.519
TYR85
3.154
ILE96
3.526
GLU102
4.896
PRO103
3.977
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structure of human rhinovirus serotype 2 (HRV2). J Mol Biol. 2000 Jul 28;300(5):1179-94. | ||||
| REF 2 | An Orally Available 3-Ethoxybenzisoxazole Capsid Binder with Clinical Activity against Human Rhinovirus. ACS Med Chem Lett. 2012 Feb 13;3(4):303-7. | ||||
| REF 3 | Design and structure-activity relationships of novel inhibitors of human rhinovirus 3C protease. Bioorg Med Chem Lett. 2016 Jul 15;26(14):3248-3252. | ||||
| REF 4 | Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease inhibitors. Bioorg Med Chem Lett. 2018 Mar 1;28(5):906-909. | ||||
| REF 5 | Non-covalent inhibitors of rhinovirus 3C protease. Bioorg Med Chem Lett. 2011 Jan 15;21(2):777-80. | ||||
| REF 6 | Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes. Proc Natl Acad Sci U S A. 1999 Sep 28;96(20):11000-7. | ||||
| REF 7 | Defining substrate selection by rhinoviral 2A proteinase through its crystal structure with the inhibitor zVAM.fmk. Virology. 2021 Oct;562:128-141. | ||||
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