Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T86014 | Target Info | |||
| Target Name | Sphingosine kinase 1 (SPHK1) | ||||
| Synonyms | SPK 1; SPK; SPHK1; SK 1; Acetyltransferase SPHK1 | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | SPHK1 | ||||
| Biochemical Class | Kinase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Sphingosine | Ligand Info | |||||
| Structure Description | Crystal structure of Sphingosine Kinase 1 | PDB:3VZB | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [1] |
| PDB Sequence |
AMGSGVLPRP
14 CRVLVLLNPR24 GGKGKALQLF34 RSHVQPLLAE44 AEISFTLMLT54 ERRNHARELV 64 RSEELGRWDA74 LVVMSGDGLM84 HEVVNGLMER94 PDWETAIQKP104 LCSLPAGSGN 114 ALAASLNHYA124 GYEQVTNEDL134 LTNCTLLLCR144 RLLSPMNLLS154 LHTASGLRLF 164 SVLSLAWGFI174 ADVDLESEKY184 RRLGEMRFTL194 GTFLRLAALR204 TYRGRLAYLP 214 VGRVGSKTPA224 SPVVVQQGPV234 DAHLVPLEEP244 VPSHWTVVPD254 EDFVLVLALL 264 HSHLGSEMFA274 APMGRCAAGV284 MHLFYVRAGV294 SRAMLLRLFL304 AMEKGRHMEY 314 ECPYLVYVPV324 VAFRLEPKDG334 KGVFAVDGEL344 MVSEAVQGQV354 HPNYFWMVSG 364
|
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ASP81
4.275
GLY113
4.236
ALA115
4.824
LEU167
3.411
SER168
3.140
ALA170
4.371
PHE173
3.959
ILE174
3.811
VAL177
3.734
ASP178
2.997
PHE192
3.447
THR196
3.723
LEU259
4.232
LEU261
3.926
|
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| Ligand Name: PF-543 | Ligand Info | |||||
| Structure Description | Sphingosine kinase 1 in complex with PF-543 | PDB:4V24 | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [2] |
| PDB Sequence |
PRGVLPRPCR
102 VLVLLNPRGG112 KGKALQLFRS122 HVQPLLAEAE132 ISFTLMLTER142 RNHARELVRS 152 EELGRWDALV162 VMSGDGLMHE172 VVNGLMERPD182 WETAIQKPLC192 SLPAGSGNAL 202 AASLNHYAGY212 EQVTNEDLLT222 NCTLLLCRRL232 LSPMNLLSLH242 TASGLRLFSV 252 LSLAWGFIAD262 VDLESEKYRR272 LGEMRFTLGT282 FLRLAALRTY292 RGRLAYLPVG 302 RVGSKTPASG318 PVDAHLVPLE328 EPVPSHWTVV338 PDEDFVLVLA348 LLHSHLGSEM 358 FAAPMGRCAA368 GVMHLFYVRA378 GVSRAMLLRL388 FLAMEKGRHM398 EYECPYLVYV 408 PVVAFRLEPK418 DGKGVFAVDG428 ELMVSEAVQG438 QVHPNYFWMV448 S |
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ASP167
4.072
ALA201
4.769
LEU253
4.003
SER254
3.893
ALA256
4.088
PHE259
3.600
ILE260
3.483
VAL263
3.465
ASP264
2.505
PHE278
3.702
THR282
3.536
LEU286
4.436
LEU345
3.997
LEU347
3.714
LEU354
3.812
|
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| Ligand Name: VPC-94075 | Ligand Info | |||||
| Structure Description | Crystal structure of Sphingosine Kinase 1 with inhibitor | PDB:3VZC | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [1] |
| PDB Sequence |
MGSGVLPRPC
15 RVLVLLNPRG25 GKGKALQLFR35 SHVQPLLAEA45 EISFTLMLTE55 RRNHARELVR 65 SEELGRWDAL75 VVMSGDGLMH85 EVVNGLMERP95 DWETAIQKPL105 CSLPAGSGNA 115 LAASLNHYAG125 YEQVTNEDLL135 TNCTLLLCRR145 LLSPMNLLSL155 HTASGLRLFS 165 VLSLAWGFIA175 DVDLESEKYR185 MRFTLGTFLR199 LAALRTYRGR209 LAYLPVGRVG 219 SKTQGPVDAH237 LVPLEEPVPS247 HWTVVPDEDF257 VLVLALLHSH267 LGSEMFAAPM 277 GRCAAGVMHL287 FYVRAGVSRA297 MLLRLFLAME307 KGRHMEYECP317 YLVYVPVVAF 327 RLEPKDGKGV337 FAVDGELMVS347 EAVQGQVHPN357 YFWMVSG
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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 .UUL or .UUL2 or .UUL3 or :3UUL;style chemicals stick;color identity;select .A:173 or .A:174 or .A:177 or .A:178 or .A:192 or .A:196 or .A:259 or .A:261 or .A:268 or .A:272 or .A:274 or .A:288 or .A:290 or .A:299 or .A:302 or .A:303 or .A:306 or .A:311 or .A:319; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: (2r,4s)-1-[2-(4-{[4-(3,4-Dichlorophenyl)-1,3-Thiazol-2-Yl]amino}phenyl)ethyl]-2-(Hydroxymethyl)piperidin-4-Ol | Ligand Info | |||||
| Structure Description | Crystal Structure of SphK1 with inhibitor | PDB:4L02 | ||||
| Method | X-ray diffraction | Resolution | 2.75 Å | Mutation | No | [3] |
| PDB Sequence |
AMGSGVLPRP
14 CRVLVLLNPR24 GGKGKALQLF34 RSHVQPLLAE44 AEISFTLMLT54 ERRNHARELV 64 RSEELGRWDA74 LVVMSGDGLM84 HEVVNGLMER94 PDWETAIQKP104 LCSLPAGSGN 114 ALAASLNHYA124 GYEQVTNEDL134 LTNCTLLLCR144 RLLSPMNLLS154 LHTASGLRLF 164 SVLSLAWGFI174 ADVDLESEKY184 RRLGEMRFTL194 GTFLRLAALR204 TYRGRLAYLP 214 VGRVGSKTPA224 SPVVVQQGPV234 DAHLVPLEEP244 VPSHWTVVPD254 EDFVLVLALL 264 HSHLGSEMFA274 APMGRCAAGV284 MHLFYVRAGV294 SRAMLLRLFL304 AMEKGRHMEY 314 ECPYLVYVPV324 VAFRLEPKDG334 KGVFAVDGEL344 MVSEAVQGQV354 HPNYFWMVSG 364
|
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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 .1V2 or .1V22 or .1V23 or :31V2;style chemicals stick;color identity;select .A:81 or .A:113 or .A:114 or .A:115 or .A:167 or .A:168 or .A:170 or .A:173 or .A:174 or .A:177 or .A:178 or .A:192 or .A:196 or .A:259 or .A:261 or .A:268 or .A:272 or .A:274 or .A:288 or .A:290 or .A:299 or .A:302 or .A:303 or .A:306 or .A:311 or .A:312 or .A:319 or .A:339 or .A:341 or .A:342; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ASP81
2.696
GLY113
4.019
ASN114
4.886
ALA115
4.419
LEU167
3.909
SER168
3.621
ALA170
3.820
PHE173
3.431
ILE174
3.768
VAL177
3.631
ASP178
2.469
PHE192
3.693
THR196
3.068
LEU259
3.914
LEU261
3.422
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Molecular basis of sphingosine kinase 1 substrate recognition and catalysis. Structure. 2013 May 7;21(5):798-809. | ||||
| REF 2 | Crystal Structure of Sphingosine Kinase 1 with PF-543. ACS Med Chem Lett. 2014 Oct 27;5(12):1329-33. | ||||
| REF 3 | Structure guided design of a series of sphingosine kinase (SphK) inhibitors. Bioorg Med Chem Lett. 2013 Aug 15;23(16):4608-16. | ||||
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