Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T47623 | Target Info | |||
| Target Name | Heparanase (HPSE) | ||||
| Synonyms | Hpa1; Heparanase-1; Heparanase 8 kDa subunit; Heparanase 50 kDa subunit; HSE1; HPSE1; HPR1; HPA; HEP protein; Endo-glucoronidase | ||||
| Target Type | Successful Target | ||||
| Gene Name | HPSE | ||||
| Biochemical Class | Glycosylase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: 4-Nitrophenol | Ligand Info | |||||
| Structure Description | Glycoside Hydrolase ligand structure 1 | PDB:5E97 | ||||
| Method | X-ray diffraction | Resolution | 1.63 Å | Mutation | No | [1] |
| PDB Sequence |
> Chain A
KFKNSTYSRS 168 SVDVLYTFAN178 CSGLDLIFGL188 NALLRTADLQ198 WNSSNAQLLL208 DYCSSKGYNI 218 SWELGNEPNS228 FLKKADIFIN238 GSQLGEDFIQ248 LHKLLRKSTF258 KNAKLYGPDV 268 GQPRRKTAKM278 LKSFLKAGGE288 VIDSVTWHHY298 YLNGRTATRE308 DFLNPDVLDI 318 FISSVQKVFQ328 VVESTRPGKK338 VWLGETSSAY348 GGGAPLLSDT358 FAAGFMWLDK 368 LGLSARMGIE378 VVMRQVFFGA388 GNYHLVDENF398 DPLPDYWLSL408 LFKKLVGTKV 418 LMASVQGSKR428 RKLRVYLHCT438 NTDNPRYKEG448 DLTLYAINLH458 NVTKYLRLPY 468 PFSNKQVDKY478 LLRPLGPHGL488 LSKSVQLNGL498 TLKMVDDQTL508 PPLMEKPLRP 518 GSSLGLPAFS528 YSFFVIRNAK538 VAACI> Chain B QDVVDLDFFT 45 QEPLHLVSPS55 FLSVTIDANL65 ATDPRFLILL75 GSPKLRTLAR85 GLSPAYLRFG 95 GTKTDFLIFD105 PKKE
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: (1S,2R,3S,4S,5S,6R)-2-(8-azidooctylamino)-3,4,5,6-tetrahydroxycyclohexane-1-carboxylic acid | Ligand Info | |||||
| Structure Description | Crystal structure of human heparanase, in complex with glucuronic acid configured aziridine probe JJB355 | PDB:5L9Y | ||||
| Method | X-ray diffraction | Resolution | 1.88 Å | Mutation | No | [2] |
| PDB Sequence |
> Chain A
FKNSTYSRSS 169 VDVLYTFANC179 SGLDLIFGLN189 ALLRTADLQW199 NSSNAQLLLD209 YCSSKGYNIS 219 WELGNEPNSF229 LKKADIFING239 SQLGEDFIQL249 HKLLRKSTFK259 NAKLYGPDVG 269 QPRRKTAKML279 KSFLKAGGEV289 IDSVTWHHYY299 LNGRTATRED309 FLNPDVLDIF 319 ISSVQKVFQV329 VESTRPGKKV339 WLGETSSAYG349 GGAPLLSDTF359 AAGFMWLDKL 369 GLSARMGIEV379 VMRQVFFGAG389 NYHLVDENFD399 PLPDYWLSLL409 FKKLVGTKVL 419 MASVQGSKRR429 KLRVYLHCTN439 TDNPRYKEGD449 LTLYAINLHN459 VTKYLRLPYP 469 FSNKQVDKYL479 LRPLGPHGLL489 SKSVQLNGLT499 LKMVDDQTLP509 PLMEKPLRPG 519 SSLGLPAFSY529 SFFVIRNAKV539 AACI> Chain B QDVVDLDFFT 45 QEPLHLVSPS55 FLSVTIDANL65 ATDPRFLILL75 GSPKLRTLAR85 GLSPAYLRFG 95 GTKTDFLIFD105 PKKE
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ASN224[A]
3.004
GLU225[A]
3.548
ARG272[A]
3.193
HIS296[A]
4.799
TYR298[A]
2.908
GLU343[A]
1.440
ALA347[A]
4.510
TYR348[A]
3.430
GLY349[A]
2.805
GLY350[A]
2.925
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: (1~{R},2~{S},3~{R},4~{S},5~{S},6~{R})-7-[8-[(azanylidene-{4}-azanylidene)amino]octyl]-3,4,5-tris(oxidanyl)-7-azabicyclo[4.1.0]heptane-2-carboxylic acid | Ligand Info | |||||
| Structure Description | Crystal structure of human heparanase nucleophile mutant (E343Q), in complex with unreacted glucuronic acid configured aziridine probe JJB355 | PDB:5L9Z | ||||
| Method | X-ray diffraction | Resolution | 1.57 Å | Mutation | Yes | [2] |
| PDB Sequence |
> Chain A
KFKNSTYSRS 168 SVDVLYTFAN178 CSGLDLIFGL188 NALLRTADLQ198 WNSSNAQLLL208 DYCSSKGYNI 218 SWELGNEPNS228 FLKKADIFIN238 GSQLGEDFIQ248 LHKLLRKSTF258 KNAKLYGPDV 268 GQPRRKTAKM278 LKSFLKAGGE288 VIDSVTWHHY298 YLNGRTATRE308 DFLNPDVLDI 318 FISSVQKVFQ328 VVESTRPGKK338 VWLGQTSSAY348 GGGAPLLSDT358 FAAGFMWLDK 368 LGLSARMGIE378 VVMRQVFFGA388 GNYHLVDENF398 DPLPDYWLSL408 LFKKLVGTKV 418 LMASVQGSKR428 RKLRVYLHCT438 NTDNPRYKEG448 DLTLYAINLH458 NVTKYLRLPY 468 PFSNKQVDKY478 LLRPLGPHGL488 LSKSVQLNGL498 TLKMVDDQTL508 PPLMEKPLRP 518 GSSLGLPAFS528 YSFFVIRNAK538 VAACI> Chain B QDVVDLDFFT 45 QEPLHLVSPS55 FLSVTIDANL65 ATDPRFLILL75 GSPKLRTLAR85 GLSPAYLRFG 95 GTKTDFLIFD105 PKKE
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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 .GUX or .GUX2 or .GUX3 or :3GUX;style chemicals stick;color identity;select .A:224 or .A:225 or .A:270 or .A:272 or .A:296 or .A:298 or .A:299 or .A:300 or .A:343 or .A:347 or .A:348 or .A:349 or .A:350 or .A:351 or .A:383 or .A:391 or .B:62 or .B:96 or .B:97; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ASN224[A]
2.993
GLU225[A]
3.184
GLN270[A]
3.151
ARG272[A]
3.716
HIS296[A]
4.513
TYR298[A]
3.460
TYR299[A]
3.781
LEU300[A]
4.266
GLN343[A]
2.923
ALA347[A]
4.603
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural characterization of human heparanase reveals insights into substrate recognition. Nat Struct Mol Biol. 2015 Dec;22(12):1016-22. | ||||
| REF 2 | Activity-based probes for functional interrogation of retaining beta-glucuronidases. Nat Chem Biol. 2017 Aug;13(8):867-873. | ||||
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