Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T93325 | Target Info | |||
| Target Name | Spliceosome-associated protein 155 (SF3B1) | ||||
| Synonyms | Splicing factor 3B subunit 1; SF3b155; SAP155; SAP 155; Pre-mRNA-splicing factor SF3b 155 kDa subunit | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | SF3B1 | ||||
| Biochemical Class | SF3B1 family | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: 1-Piperazinecarboxylic acid, 4-cycloheptyl-, (2S,3S,4E,6S,7R,10R)-7,10-dihydroxy-2-((1E,3E,5R)-5-hydroxy-6-((2R,3R)-3-((1R,2S)-2-hydroxy-1-methylbutyl)oxiranyl)-1,5-dimethyl-1,3-hexadienyl)-3,7-dimethyl-12-oxooxacyclododec-4-en-6-yl ester | Ligand Info | |||||
| Structure Description | SF3b spliceosomal complex bound to E7107 | PDB:5ZYA | ||||
| Method | Electron microscopy | Resolution | 3.95 Å | Mutation | No | [1] |
| PDB Sequence |
EEQKERKIMK
499 LLLKIKNGTP509 PMRKAALRQI519 TDKAREFGAG529 PLFNQILPLL539 MSPTLEDQER 549 HLLVKVIDRI559 LYKLDDLVRP569 YVHKILVVIE579 PLLIDEDYYA589 RVEGREIISN 599 LAKAAGLATM609 ISTMRPDIDN619 MDEYVRNTTA629 RAFAVVASAL639 GIPSLLPFLK 649 AVCKSKKSWQ659 ARHTGIKIVQ669 QIAILMGCAI679 LPHLRSLVEI689 IEHGLVDEQQ 699 KVRTISALAI709 AALAEAATPY719 GIESFDSVLK729 PLWKGIRQHR739 GKGLAAFLKA 749 IGYLIPLMDA759 EYANYYTREV769 MLILIREFQS779 PDEEMKKIVL789 KVVKQCCGTD 799 GVEANYIKTE809 ILPPFFKHFW819 QHRMALDRRN829 YRQLVDTTVE839 LANKVGAAEI 849 ISRIVDDLKD859 EAEQYRKMVM869 ETIEKIMGNL879 GAADIDHKLE889 EQLIDGILYA 899 FQEQTTEDSV909 MLNGFGTVVN919 ALGKRVKPYL929 PQICGTVLWR939 LNNKSAKVRQ 949 QAADLISRTA959 VVMKTCQEEK969 LMGHLGVVLY979 EYLGEEYPEV989 LGSILGALKA 999 IVNVIGMHKM1009 TPPIKDLLPR1019 LTPILKNRHE1029 KVQENCIDLV1039 GRIADRGAEY 1049 VSAREWMRIC1059 FELLELLKAH1069 KKAIRRATVN1079 TFGYIAKAIG1089 PHDVLATLLE 1105 RQNRVCTTVA1115 IAIVAETCSP1125 FTVLPALMNE1135 YRVPELNVQN1145 GVLKSLSFLF 1155 EYIGEMGKDY1165 IYAVTPLLED1175 ALMDRDLVHR1185 QTASAVVQHM1195 SLGVYGFGCE 1205 DSLNHLLNYV1215 WPNVFETSPH1225 VIQAVMGALE1235 GLRVAIGPCR1245 MLQYCLQGLF 1255 HPARKVRDVY1265 WKIYNSIYIG1275 SQDALIAHYP1285 RIYNDDKNTY1295 IRYELDYIL |
|||||
|
|
||||||
| Ligand Name: [(Z,2S)-5-[[(2R,3R,5S,6S)-6-[(2E,4E)-5-[(2R,3R,4S,6S)-3,4-dihydroxy-6-methoxy-4,6-dimethyloxan-2-yl]-3-methylpenta-2,4-dienyl]-2,5-dimethyloxan-3-yl]amino]-5-oxopent-3-en-2-yl] acetate | Ligand Info | |||||
| Structure Description | Structure of a minimal SF3B core in complex with spliceostatin A (form I) | PDB:7B9C | ||||
| Method | X-ray diffraction | Resolution | 2.40 Å | Mutation | No | [2] |
| PDB Sequence |
NLPFLKPDDI
472 QYFDKLLVDV482 DESTLSPEEQ492 KERKIMKLLL502 KIKNGTPPMR512 KAALRQITDK 522 AREFGAGPLF532 NQILPLLMSP542 TLEDQERHLL552 VKVIDRILYK562 LDDLVRPYVH 572 KILVVIEPLL582 IDEDYYARVE592 GREIISNLAK602 AAGLATMIST612 MRPDIDNMDE 622 YVRNTTARAF632 AVVASALGIP642 SLLPFLKAVC652 KSKKSWQARH662 TGIKIVQQIA 672 ILMGCAILPH682 LRSLVEIIEH692 GLVDEQQKVR702 TISALAIAAL712 AEAATPYGIE 722 SFDSVLKPLW732 KGIRQHRGKG742 LAAFLKAIGY752 LIPLMDAEYA762 NYYTREVMLI 772 LIREFQSPDE782 EMKKIVLKVV792 KQCCGTDGVE802 ANYIKTEILP812 PFFKHFWQHR 822 MALDRRNYRQ832 LVDTTVELAN842 KVGAAEIISR852 IVDDLKDEAE862 QYRKMVMETI 872 EKIMGNLGAA882 DIDHKLEEQL892 IDGILYAFQE902 QTTEDSVMLN912 GFGTVVNALG 922 KRVKPYLPQI932 CGTVLWRLNN942 KSAKVRQQAA952 DLISRTAVVM962 KTCQEEKLMG 972 HLGVVLYEYL982 GEEYPEVLGS992 ILGALKAIVN1002 VIGMHKMTPP1012 IKDLLPRLTP 1022 ILKNRHEKVQ1032 ENCIDLVGRI1042 ADRGAEYVSA1052 REWMRICFEL1062 LELLKAHKKA 1072 IRRATVNTFG1082 YIAKAIGPHD1092 VLATLLNNLK1102 VQERQNRVCT1112 TVAIAIVAET 1122 CSPFTVLPAL1132 MNEYRVPELN1142 VQNGVLKSLS1152 FLFEYIGEMG1162 KDYIYAVTPL 1172 LEDALMDRDL1182 VHRQTASAVV1192 QHMSLGVYGF1202 GCEDSLNHLL1212 NYVWPNVFET 1222 SPHVIQAVMG1232 ALEGLRVAIG1242 PCRMLQYCLQ1252 GLFHPARKVR1262 DVYWKIYNSI 1272 YIGSQDALIA1282 HYPRIYNDDK1292 NTYIRYELDY1302 IL
|
|||||
|
|
||||||
| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: (3R,6R,7S,8E,10S,11S,12E,14E,16R,18R,19R,20R,21S)-7-acetoxy-3,6,16,21-tetrahydroxy-6,10,12,16,20-pentamethyl-18,19-epoxytricosa-8,12,14-triene-11-olide | Ligand Info | |||||
| Structure Description | Structure of a minimal SF3B core in complex with pladienolide D (form I) | PDB:7B91 | ||||
| Method | X-ray diffraction | Resolution | 3.00 Å | Mutation | No | [2] |
| PDB Sequence |
NLPFLKPDDI
472 QYFDKLLVDV482 DESTLSPEEQ492 KERKIMKLLL502 KIKNGTPPMR512 KAALRQITDK 522 AREFGAGPLF532 NQILPLLMSP542 TLEDQERHLL552 VKVIDRILYK562 LDDLVRPYVH 572 KILVVIEPLL582 IDEDYYARVE592 GREIISNLAK602 AAGLATMIST612 MRPDIDNMDE 622 YVRNTTARAF632 AVVASALGIP642 SLLPFLKAVC652 KSKKSWQARH662 TGIKIVQQIA 672 ILMGCAILPH682 LRSLVEIIEH692 GLVDEQQKVR702 TISALAIAAL712 AEAATPYGIE 722 SFDSVLKPLW732 KGIRQHRGKG742 LAAFLKAIGY752 LIPLMDAEYA762 NYYTREVMLI 772 LIREFQSPDE782 EMKKIVLKVV792 KQCCGTDGVE802 ANYIKTEILP812 PFFKHFWQHR 822 MALDRRNYRQ832 LVDTTVELAN842 KVGAAEIISR852 IVDDLKDEAE862 QYRKMVMETI 872 EKIMGNLGAA882 DIDHKLEEQL892 IDGILYAFQE902 QTTEDSVMLN912 GFGTVVNALG 922 KRVKPYLPQI932 CGTVLWRLNN942 KSAKVRQQAA952 DLISRTAVVM962 KTCQEEKLMG 972 HLGVVLYEYL982 GEEYPEVLGS992 ILGALKAIVN1002 VIGMHKMTPP1012 IKDLLPRLTP 1022 ILKNRHEKVQ1032 ENCIDLVGRI1042 ADRGAEYVSA1052 REWMRICFEL1062 LELLKAHKKA 1072 IRRATVNTFG1082 YIAKAIGPHD1092 VLATLLNNLK1102 VQERQNRVCT1112 TVAIAIVAET 1122 CSPFTVLPAL1132 MNEYRVPELN1142 VQNGVLKSLS1152 FLFEYIGEMG1162 KDYIYAVTPL 1172 LEDALMDRDL1182 VHRQTASAVV1192 QHMSLGVYGF1202 GCEDSLNHLL1212 NYVWPNVFET 1222 SPHVIQAVMG1232 ALEGLRVAIG1242 PCRMLQYCLQ1252 GLFHPARKVR1262 DVYWKIYNSI 1272 YIGSQDALIA1282 HYPRIYNDDK1292 NTYIRYELDY1302 IL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .T2Z or .T2Z2 or .T2Z3 or :3T2Z;style chemicals stick;color identity;select .C:1066 or .C:1067 or .C:1068 or .C:1071 or .C:1074 or .C:1075 or .C:1078 or .C:1079 or .C:1110 or .C:1113 or .C:1114 or .C:1153 or .C:1157; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: pladienolide B | Ligand Info | |||||
| Structure Description | SF3b core in complex with a splicing modulator | PDB:6EN4 | ||||
| Method | X-ray diffraction | Resolution | 3.08 Å | Mutation | No | [3] |
| PDB Sequence |
NLPFLKPDDI
472 QYFDKLLVDV482 DESTLSPEEQ492 KERKIMKLLL502 KIKNGTPPMR512 KAALRQITDK 522 AREFGAGPLF532 NQILPLLMSP542 TLEDQERHLL552 VKVIDRILYK562 LDDLVRPYVH 572 KILVVIEPLL582 IDEDYYARVE592 GREIISNLAK602 AAGLATMIST612 MRPDIDNMDE 622 YVRNTTARAF632 AVVASALGIP642 SLLPFLKAVC652 KSKKSWQARH662 TGIKIVQQIA 672 ILMGCAILPH682 LRSLVEIIEH692 GLVDEQQKVR702 TISALAIAAL712 AEAATPYGIE 722 SFDSVLKPLW732 KGIRQHRGKG742 LAAFLKAIGY752 LIPLMDAEYA762 NYYTREVMLI 772 LIREFQSPDE782 EMKKIVLKVV792 KQCCGTDGVE802 ANYIKTEILP812 PFFKHFWQHR 822 MALDRRNYRQ832 LVDTTVELAN842 KVGAAEIISR852 IVDDLKDEAE862 QYRKMVMETI 872 EKIMGNLGAA882 DIDHKLEEQL892 IDGILYAFQE902 QTTEDSVMLN912 GFGTVVNALG 922 KRVKPYLPQI932 CGTVLWRLNN942 KSAKVRQQAA952 DLISRTAVVM962 KTCQEEKLMG 972 HLGVVLYEYL982 GEEYPEVLGS992 ILGALKAIVN1002 VIGMHKMTPP1012 IKDLLPRLTP 1022 ILKNRHEKVQ1032 ENCIDLVGRI1042 ADRGAEYVSA1052 REWMRICFEL1062 LELLKAHKKA 1072 IRRATVNTFG1082 YIAKAIGPHD1092 VLATLLNNLK1102 VQERQNRVCT1112 TVAIAIVAET 1122 CSPFTVLPAL1132 MNEYRVPELN1142 VQNGVLKSLS1152 FLFEYIGEMG1162 KDYIYAVTPL 1172 LEDALMDRDL1182 VHRQTASAVV1192 QHMSLGVYGF1202 GCEDSLNHLL1212 NYVWPNVFET 1222 SPHVIQAVMG1232 ALEGLRVAIG1242 PCRMLQYCLQ1252 GLFHPARKVR1262 DVYWKIYNSI 1272 YIGSQDALIA1282 HYPRIYNDDK1292 NTYIRYELDY1302 IL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BGZ or .BGZ2 or .BGZ3 or :3BGZ;style chemicals stick;color identity;select .C:1066 or .C:1067 or .C:1068 or .C:1071 or .C:1074 or .C:1075 or .C:1078 or .C:1079 or .C:1110 or .C:1114 or .C:1153 or .C:1157; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: Spliceostatin E | Ligand Info | |||||
| Structure Description | Structure of a minimal SF3B core in complex with the inactive modulator spliceostatin E (form I) | PDB:7OPI | ||||
| Method | X-ray diffraction | Resolution | 3.10 Å | Mutation | No | [2] |
| PDB Sequence |
NLPFLKPDDI
472 QYFDKLLVDV482 DESTLSPEEQ492 KERKIMKLLL502 KIKNGTPPMR512 KAALRQITDK 522 AREFGAGPLF532 NQILPLLMSP542 TLEDQERHLL552 VKVIDRILYK562 LDDLVRPYVH 572 KILVVIEPLL582 IDEDYYARVE592 GREIISNLAK602 AAGLATMIST612 MRPDIDNMDE 622 YVRNTTARAF632 AVVASALGIP642 SLLPFLKAVC652 KSKKSWQARH662 TGIKIVQQIA 672 ILMGCAILPH682 LRSLVEIIEH692 GLVDEQQKVR702 TISALAIAAL712 AEAATPYGIE 722 SFDSVLKPLW732 KGIRQHRGKG742 LAAFLKAIGY752 LIPLMDAEYA762 NYYTREVMLI 772 LIREFQSPDE782 EMKKIVLKVV792 KQCCGTDGVE802 ANYIKTEILP812 PFFKHFWQHR 822 MALDRRNYRQ832 LVDTTVELAN842 KVGAAEIISR852 IVDDLKDEAE862 QYRKMVMETI 872 EKIMGNLGAA882 DIDHKLEEQL892 IDGILYAFQE902 QTTEDSVMLN912 GFGTVVNALG 922 KRVKPYLPQI932 CGTVLWRLNN942 KSAKVRQQAA952 DLISRTAVVM962 KTCQEEKLMG 972 HLGVVLYEYL982 GEEYPEVLGS992 ILGALKAIVN1002 VIGMHKMTPP1012 IKDLLPRLTP 1022 ILKNRHEKVQ1032 ENCIDLVGRI1042 ADRGAEYVSA1052 REWMRICFEL1062 LELLKAHKKA 1072 IRRATVNTFG1082 YIAKAIGPHD1092 VLATLLNNLK1102 VQERQNRVCT1112 TVAIAIVAET 1122 CSPFTVLPAL1132 MNEYRVPELN1142 VQNGVLKSLS1152 FLFEYIGEMG1162 KDYIYAVTPL 1172 LEDALMDRDL1182 VHRQTASAVV1192 QHMSLGVYGF1202 GCEDSLNHLL1212 NYVWPNVFET 1222 SPHVIQAVMG1232 ALEGLRVAIG1242 PCRMLQYCLQ1252 GLFHPARKVR1262 DVYWKIYNSI 1272 YIGSQDALIA1282 HYPRIYNDDK1292 NTYIRYELDY1302 IL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .07I or .07I2 or .07I3 or :307I;style chemicals stick;color identity;select .C:1066 or .C:1067 or .C:1068 or .C:1069 or .C:1071 or .C:1074 or .C:1075 or .C:1078 or .C:1107 or .C:1110 or .C:1111 or .C:1114 or .C:1153 or .C:1157; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: [(~{Z},2~{S})-5-[[4-[(2~{E},4~{E})-3-methyl-5-[(2~{S},4~{R})-4,6,6-trimethyl-4-oxidanyl-oxan-2-yl]penta-2,4-dienyl]cyclohexyl]amino]-5-oxidanylidene-pent-3-en-2-yl] ~{N}-methylcarbamate | Ligand Info | |||||
| Structure Description | Structure of a minimal SF3B core in complex with sudemycin D6 (form II) | PDB:7B92 | ||||
| Method | X-ray diffraction | Resolution | 3.00 Å | Mutation | No | [2] |
| PDB Sequence |
NLPFLKPDDI
472 QYFDKLLVDV482 DESTLSPEEQ492 KERKIMKLLL502 KIKNGTPPMR512 KAALRQITDK 522 AREFGAGPLF532 NQILPLLMSP542 TLEDQERHLL552 VKVIDRILYK562 LDDLVRPYVH 572 KILVVIEPLL582 IDEDYYARVE592 GREIISNLAK602 AAGLATMIST612 MRPDIDNMDE 622 YVRNTTARAF632 AVVASALGIP642 SLLPFLKAVC652 KSKKSWQARH662 TGIKIVQQIA 672 ILMGCAILPH682 LRSLVEIIEH692 GLVDEQQKVR702 TISALAIAAL712 AEAATPYGIE 722 SFDSVLKPLW732 KGIRQHRGKG742 LAAFLKAIGY752 LIPLMDAEYA762 NYYTREVMLI 772 LIREFQSPDE782 EMKKIVLKVV792 KQCCGTDGVE802 ANYIKTEILP812 PFFKHFWQHR 822 MALDRRNYRQ832 LVDTTVELAN842 KVGAAEIISR852 IVDDLKDEAE862 QYRKMVMETI 872 EKIMGNLGAA882 DIDHKLEEQL892 IDGILYAFQE902 QTTEDSVMLN912 GFGTVVNALG 922 KRVKPYLPQI932 CGTVLWRLNN942 KSAKVRQQAA952 DLISRTAVVM962 KTCQEEKLMG 972 HLGVVLYEYL982 GEEYPEVLGS992 ILGALKAIVN1002 VIGMHKMTPP1012 IKDLLPRLTP 1022 ILKNRHEKVQ1032 ENCIDLVGRI1042 ADRGAEYVSA1052 REWMRICFEL1062 LELLKAHKKA 1072 IRRATVNTFG1082 YIAKAIGPHD1092 VLATLLNNLK1102 VQERQNRVCT1112 TVAIAIVAET 1122 CSPFTVLPAL1132 MNEYRVPELN1142 VQNGVLKSLS1152 FLFEYIGEMG1162 KDYIYAVTPL 1172 LEDALMDRDL1182 VHRQTASAVV1192 QHMSLGVYGF1202 GCEDSLNHLL1212 NYVWPNVFET 1222 SPHVIQAVMG1232 ALEGLRVAIG1242 PCRMLQYCLQ1252 GLFHPARKVR1262 DVYWKIYNSI 1272 YIGSQDALIA1282 HYPRIYNDDK1292 NTYIRYELDY1302 IL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .T2W or .T2W2 or .T2W3 or :3T2W;style chemicals stick;color identity;select .C:1066 or .C:1067 or .C:1068 or .C:1069 or .C:1071 or .C:1074 or .C:1075 or .C:1078 or .C:1107 or .C:1110 or .C:1111 or .C:1114 or .C:1157; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | The cryo-EM structure of the SF3b spliceosome complex bound to a splicing modulator reveals a pre-mRNA substrate competitive mechanism of action. Genes Dev. 2018 Feb 1;32(3-4):309-320. | ||||
| REF 2 | Structural basis of intron selection by U2 snRNP in the presence of covalent inhibitors. Nat Commun. 2021 Jul 23;12(1):4491. | ||||
| REF 3 | Structural Basis of Splicing Modulation by Antitumor Macrolide Compounds. Mol Cell. 2018 Apr 19;70(2):265-273.e8. | ||||
If You Find Any Error in Data or Bug in Web Service, Please Kindly Report It to Dr. Zhou and Dr. Zhang.