Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T17067 | Target Info | |||
| Target Name | Isopeptidase T (USP5) | ||||
| Synonyms | Ubiquitin-specific-processing protease 5; Ubiquitin thioesterase 5; Ubiquitin carboxyl-terminal hydrolase 5; ISOT; Deubiquitinating enzyme 5 | ||||
| Target Type | Preclinical Target | ||||
| Gene Name | USP5 | ||||
| Biochemical Class | Peptidase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Ethylamine | Ligand Info | |||||
| Structure Description | Covalent Ubiquitin-Usp5 Complex | PDB:3IHP | ||||
| Method | X-ray diffraction | Resolution | 2.80 Å | Mutation | No | [1] |
| PDB Sequence |
MAELSEEALL
10 SVLPTIRVPK20 AGDRVHKDEC30 AFSFDTPESE40 GGLYICMNTF50 LGFGKQYVER 60 HFNKTGQRVY70 LHLRRTDEDV120 KIVILPDYLE130 IARDGLGGLP140 DIVRDRVTSA 150 VEALLSVRQV176 SKHAFSLKQL186 DNPARIPPCG196 WKCSKCDMRE206 NLWLNLTDGS 216 ILCGRRYDGS227 GGNNHAVEHY237 RETGYPLAVK247 LGTITPDGAD257 VYSYDEDDMV 267 LDPSLAEHLS277 HFGIDMPLFG322 PGYTGIRNLG332 NSCYLNSVVQ342 VLFSIPDFQR 352 KYVDKLEKIF362 QNAPTDPTQD372 FSTQVAKLGH382 GLLSGEDGIA413 PRMFKALIGK 423 GHPEFSTNRQ433 QDAQEFFLHL443 INMVERNCRS453 SENPNEVFRF463 LVEEKIKCLA 473 TEKVKYTQRV483 DYIMQLPVPM493 DAALNKEELL503 EYEEKKRQAE513 EEKMALPELV 523 RAQVPFSSCL533 EAYGAPEQVD543 DFWSTALQAK553 SVAVKTTRFA563 SFPDYLVIQI 573 KKFTFGLDWV583 PKKLDVSIEM593 PEELDISQLR603 GTGLQPGEEE613 LPDIESVIIQ 639 LVEMGFPMDA649 CRKAVYYTGN659 SGAEAAMNWV669 MSHMDDPDFA679 NPLILPPPED 702 CVTTIVSMGF712 SRDQALKALR722 ATNNSLERAV732 DWIFSHIDDL742 DAEAAMDPKV 771 RDGPGKYQLF781 AFISHMGTST791 MCGHYVCHIK801 KEGRWVIYND811 QKVCASEKPP 821 KDLGYIYFYQ831 RVA
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| Ligand Name: Usp5-IN-1 | Ligand Info | |||||
| Structure Description | Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with (5-((4-(4-chlorophenyl)piperidin-1-yl)sulfonyl)picolinoyl)glycine | PDB:7MS7 | ||||
| Method | X-ray diffraction | Resolution | 1.45 Å | Mutation | No | [2] |
| PDB Sequence |
VRQVSKHAFS
182 LKQLDNPARI192 PPCGWKCSKC202 DMRENLWLNL212 TDGSILCGRR222 YFDGSGGNNH 232 AVEHYRETGY242 PLAVKLGTIT252 PDGADVYSYD262 EDDMVLDPSL272 AEHLSHFGID 282 MLK
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| Ligand Name: N-[2-fluoro-4-(4-phenylpiperidine-1-sulfonyl)benzoyl]glycine | Ligand Info | |||||
| Structure Description | Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with (2-fluoro-4-((4-phenylpiperidin-1-yl)sulfonyl)benzoyl)glycine | PDB:7MS6 | ||||
| Method | X-ray diffraction | Resolution | 1.55 Å | Mutation | No | [2] |
| PDB Sequence |
VRQVSKHAFS
182 LKQLDNPARI192 PPCGWKCSKC202 DMRENLWLNL212 TDGSILCGRR222 YFDGSGGNNH 232 AVEHYRETGY242 PLAVKLGTIT252 PDGADVYSYD262 EDDMVLDPSL272 AEHLSHFGID 282 M
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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 .ZPV or .ZPV2 or .ZPV3 or :3ZPV;style chemicals stick;color identity;select .A:209 or .A:219 or .A:220 or .A:221 or .A:223 or .A:224 or .A:225 or .A:227 or .A:233 or .A:234 or .A:259 or .A:261 or .A:266; 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-Oxo-4H-quinazolin-3-yl)-acetic acid | Ligand Info | |||||
| Structure Description | Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with (4-oxoquinazolin-3(4H)-yl)acetic acid | PDB:6NFT | ||||
| Method | X-ray diffraction | Resolution | 1.65 Å | Mutation | No | [3] |
| PDB Sequence |
GEVRQVSKHA
180 FSLKQLDNPA190 RIPPCGWKCS200 KCDMRENLWL210 NLTDGSILCG220 RRYFDGSGGN 230 NHAVEHYRET240 GYPLAVKLGT250 ITPDGADVYS260 YDEDDMVLDP270 SLAEHLSHFG 280 IDMLK
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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 .KKG or .KKG2 or .KKG3 or :3KKG;style chemicals stick;color identity;select .A:209 or .A:219 or .A:220 or .A:221 or .A:223 or .A:233 or .A:234 or .A:259 or .A:261 or .A:264 or .A:266; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3-(5-Phenyl-1,3,4-oxadiazol-2-yl)propanoic acid | Ligand Info | |||||
| Structure Description | Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoate | PDB:6DXT | ||||
| Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | No | [3] |
| PDB Sequence |
VRQVSKHAFS
182 LKQLDNPARI192 PPCGWKCSKC202 DMRENLWLNL212 TDGSILCGRR222 YFDGSGGNNH 232 AVEHYRETGY242 PLAVKLGTIT252 PDGADVYSYD262 EDDMVLDPSL272 AEHLSHFGID 282 ML
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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 .HHY or .HHY2 or .HHY3 or :3HHY;style chemicals stick;color identity;select .A:209 or .A:219 or .A:220 or .A:221 or .A:223 or .A:233 or .A:234 or .A:259 or .A:261 or .A:264 or .A:265 or .A:266; 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-{4-[4-(3,4-Difluorophenyl)piperidine-1-sulfonyl]phenyl}-4-oxobutanoic acid | Ligand Info | |||||
| Structure Description | Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 4-(4-(4-(3,4-difluoro-phenyl)-piperidin-1-ylsulfonyl)-phenyl)-4-oxo-butanoic acid | PDB:7MS5 | ||||
| Method | X-ray diffraction | Resolution | 1.98 Å | Mutation | No | [2] |
| PDB Sequence |
GEVRQVSKHA
180 FSLKQLDNPA190 RIPPCGWKCS200 KCDMRENLWL210 NLTDGSILCG220 RRYFDGSGGN 230 NHAVEHYRET240 GYPLAVKLGT250 ITPDGADVYS260 YDEDDMVLDP270 SLAEHLSHFG 280 IDMLK
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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 .ZOG or .ZOG2 or .ZOG3 or :3ZOG;style chemicals stick;color identity;select .A:209 or .A:219 or .A:220 or .A:221 or .A:223 or .A:225 or .A:227 or .A:233 or .A:234 or .A:259 or .A:261 or .A:266; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-(4-Tert-butylphenyl)-4-oxobutanoic acid | Ligand Info | |||||
| Structure Description | Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 4-(4-tert-butylphenyl)-4-oxobutanoate | PDB:6DXH | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [3] |
| PDB Sequence |
VRQVSKHAFS
182 LKQLDNPARI192 PPCGWKCSKC202 DMRENLWLNL212 TDGSILCGRR222 YFDGSGGNNH 232 AVEHYRETGY242 PLAVKLGTIT252 PDGADVYSYD262 EDDMVLDPSL272 AEHLSHFGID 282 MLKMQKT
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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 .HH4 or .HH42 or .HH43 or :3HH4;style chemicals stick;color identity;select .A:209 or .A:219 or .A:220 or .A:221 or .A:233 or .A:234 or .A:259 or .A:261 or .A:264 or .A:265 or .A:266; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (2R)-2-(4-oxoquinazolin-3(4H)-yl)propanoic acid | Ligand Info | |||||
| Structure Description | Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 2-(4-oxoquinazolin-3(4H)-yl)propanoic acid | PDB:6P9G | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [3] |
| PDB Sequence |
VRQVSKHAFS
182 LKQLDNPARI192 PPCGWKCSKC202 DMRENLWLNL212 TDGSILCGRR222 YFDGSGGNNH 232 AVEHYRETGY242 PLAVKLGTIT252 PDGADVYSYD262 EDDMVLDPSL272 AEHLSHFGID 282 MLKMQKT
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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 .O4Y or .O4Y2 or .O4Y3 or :3O4Y;style chemicals stick;color identity;select .A:209 or .A:219 or .A:220 or .A:221 or .A:233 or .A:234 or .A:259 or .A:261 or .A:264 or .A:266; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Covalent Ubiquitin-Usp5 Complex | ||||
| REF 2 | Structure-Activity Relationship of USP5 Inhibitors. J Med Chem. 2021 Oct 28;64(20):15017-15036. | ||||
| REF 3 | Discovery of Small Molecule Antagonists of the USP5 Zinc Finger Ubiquitin-Binding Domain. J Med Chem. 2019 Nov 27;62(22):10144-10155. | ||||
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