Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T86528 | Target Info | |||
| Target Name | Geranyltranstransferase (FDPS) | ||||
| Synonyms | KIAA1293; Geranylgeranyl pyrophosphate synthase; Geranylgeranyl diphosphate synthase; GGPS1; GGPPSase; GGPP synthase; Farnesyltranstransferase; Farnesyl pyrophosphate synthase; Farnesyl diphosphate synthase; FPS protein; FPP synthase; Dimethylallyltranstransferase; (2E,6E)-farnesyl diphosphate synthase | ||||
| Target Type | Successful Target | ||||
| Gene Name | FDPS | ||||
| Biochemical Class | Alkyl aryl transferase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Isopentenyl pyrophosphate | Ligand Info | |||
| Canonical SMILES | CC(=C)CCOP(=O)(O)OP(=O)(O)O | ||||
| InChI | 1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8) | ||||
| InChIKey | NUHSROFQTUXZQQ-UHFFFAOYSA-N | ||||
| PubChem Compound ID | 1195 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 4NKE The effects of Lysine 200 and Phenylalanine 239 Farnesyl Pyrophosphate Synthase (FPPS) mutations on the catalytic activity, crystal structure and inhibition by nitrogen containing bisphosphonates | ||||||
| Method | X-ray diffraction | Resolution | 1.46 Å | Mutation | Yes | [1] |
| PDB Sequence |
VYAQEKQDFV
18 QHFSQIVRVL28 TEHPEIGDAI42 ARLKEVLEYN52 TIGGKYNRGL62 TVVVAFRELV 72 EPRKQDADSL82 QRAWTVGWCV92 ELLQAFFLVA102 DDIMDSSLTR112 RGQICWYQKP 122 GVGLDAINDA132 NLLEACIYRL142 LKLYCREQPY152 YLNLIELFLQ162 SSYQTEIGQT 172 LDLLTAPQGN182 VDLVRFTEKR192 YKSIVKYKTA202 FYSFYLPIAA212 AMYMAGIDGE 222 KEHANAKKIL232 LEMGEFAQIQ242 DDYLDLFGDP252 SVTGKIGTDI262 QDNKCSWLVV 272 QCLQRATPEQ282 YQILKENYGQ292 KEAEKVARVK302 ALYEELDLPA312 VFLQYEEDSY 322 SHIMALIEQY332 AAPLPPAVFL342 GLARKIYK
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| PDB ID: 4KPD Crystal Structure of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate | ||||||
| Method | X-ray diffraction | Resolution | 1.96 Å | Mutation | Yes | [2] |
| PDB Sequence |
VYAQEKQDFV
18 QHFSQIVRVL28 TEHPEIGDAI42 ARLKEVLEYN52 AIGGKYNRGL62 TVVVAFRELV 72 EPRKQDADSL82 QRAWTVGWCV92 ELLQAFFLVA102 DDIMDSSLTR112 RGQICWYQKP 122 GVGLDAINDA132 NLLEACIYRL142 LKLYCREQPY152 YLNLIELFLQ162 SSYQTEIGQT 172 LDLLTAPQGN182 VDLVRFTEKR192 YKSIVKYKTA202 FFSFYLPIAA212 AMYMAGIDGE 222 KEHANAKKIL232 LEMGEFFQIQ242 DDYLDLFGDP252 SVTGKIGTDI262 QDNKCSWLVV 272 QCLQRATPEQ282 YQILKENYGQ292 KEAEKVARVK302 ALYEELDLPA312 VFLQYEEDSY 322 SHIMALIEQY332 AAPLPPAVFL342 GLARKIYKRR352 K
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| PDB ID: 4KQS Crystal Structure of Farnesyl Pyrophosphate Synthase Mutant (Y204A) Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate | ||||||
| Method | X-ray diffraction | Resolution | 1.97 Å | Mutation | Yes | [3] |
| PDB Sequence |
VYAQEKQDFV
18 QHFSQIVRVL28 TEPEIGDAIA43 RLKEVLEYNA53 IGGKYNRGLT63 VVVAFRELVE 73 PRKQDADSLQ83 RAWTVGWCVE93 LLQAFFLVAD103 DIMDSSLTRR113 GQICWYQKPG 123 VGLDAINDAN133 LLEACIYRLL143 KLYCREQPYY153 LNLIELFLQS163 SYQTEIGQTL 173 DLLTAPQGNV183 DLVRFTEKRY193 KSIVKYKTAF203 ASFYLPIAAA213 MYMAGIDGEK 223 EHANAKKILL233 EMGEFFQIQD243 DYLDLFGDPS253 VTGKIGTDIQ263 DNKCSWLVVQ 273 CLQRATPEQY283 QILKENYGQK293 EAEKVARVKA303 LYEELDLPAV313 FLQYEEDSYS 323 HIMALIEQYA333 APLPPAVFLG343 LARKIYKRRK353
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| PDB ID: 4KQU Crystal Structure of Farnesyl Synthase Mutant (Y204A) Complexed with Mg, Alendronate and Isopentenyl Pyrophosphate | ||||||
| Method | X-ray diffraction | Resolution | 2.07 Å | Mutation | Yes | [4] |
| PDB Sequence |
YAQEKQDFVQ
19 HFSQIVRVLT29 EHPEIGDAIA43 RLKEVLEYNA53 IGGKYNRGLT63 VVVAFRELVE 73 PRKQDADSLQ83 RAWTVGWCVE93 LLQAFFLVAD103 DIMDSSLTRR113 GQICWYQKPG 123 VGLDAINDAN133 LLEACIYRLL143 KLYCREQPYY153 LNLIELFLQS163 SYQTEIGQTL 173 DLLTAPQGNV183 DLVRFTEKRY193 KSIVKYKTAF203 ASFYLPIAAA213 MYMAGIDGEK 223 EHANAKKILL233 EMGEFFQIQD243 DYLDLFGDPS253 VTGKIGTDIQ263 DNKCSWLVVQ 273 CLQRATPEQY283 QILKENYGQK293 EAEKVARVKA303 LYEELDLPAV313 FLQYEEDSYS 323 HIMALIEQYA333 APLPPAVFLG343 LARKIYKRRK353
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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 .IPE or .IPE2 or .IPE3 or :3IPE;style chemicals stick;color identity;select .A:56 or .A:57 or .A:58 or .A:59 or .A:60 or .A:93 or .A:96 or .A:100 or .A:112 or .A:113 or .A:201 or .A:205 or .A:239 or .A:240 or .A:243 or .A:257 or .A:353; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4OGU The effects of Lysine 200 and Phenylalanine 239 Farnesyl Pyrophosphate Synthase (FPPS) mutations on the catalytic activity, crystal structure and inhibition by nitrogen containing bisphosphonates | ||||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | Yes | [5] |
| PDB Sequence |
DVYAQEKQDF
17 VQHFSQIVRV27 LTEHPEIGDA41 IARLKEVLEY51 NTIGGKYNRG61 LTVVVAFREL 71 VEPRKQDADS81 LQRAWTVGWC91 VELLQAFFLV101 ADDIMDSSLT111 RRGQICWYQK 121 PGVGLDAIND131 ANLLEACIYR141 LLKLYCREQP151 YYLNLIELFL161 QSSYQTEIGQ 171 TLDLLTAPQG181 NVDLVRFTEK191 RYKSIVKYKT201 AFYSFYLPIA211 AAMYMAGIDG 221 EKEHANAKKI231 LLEMGEFAQI241 QDDYLDLFGD251 PSVTGKIGTD261 IQDNKCSWLV 271 VQCLQRATPE281 QYQILKENYG291 QKEAEKVARV301 KALYEELDLP311 AVFLQYEEDS 321 YSHIMALIEQ331 YAAPLPPAVF341 LGLARKIYK
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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 .IPE or .IPE2 or .IPE3 or :3IPE;style chemicals stick;color identity;select .A:56 or .A:57 or .A:58 or .A:60 or .A:93 or .A:96 or .A:100 or .A:112 or .A:113 or .A:201 or .A:204 or .A:205 or .A:239 or .A:240 or .A:243 or .A:257; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4NG6 The effects of Lysine 200 and Phenylalanine 239 Farnesyl Pyrophosphate Synthase (FPPS) mutations on the catalytic activity, crystal structure and inhibition by nitrogen containing bisphosphonates | ||||||
| Method | X-ray diffraction | Resolution | 2.35 Å | Mutation | Yes | [6] |
| PDB Sequence |
YAQEKQDFVQ
19 HFSQIVRVLT29 EDEMGHPEIG39 DAIARLKEVL49 EYNAIGGKYN59 RGLTVVVAFR 69 ELVEPRKQDA79 DSLQRAWTVG89 WCVELLQAFF99 LVADDIMDSS109 LTRRGQICWY 119 QKPGVGLDAI129 NDANLLEACI139 YRLLKLYCRE149 QPYYLNLIEL159 FLQSSYQTEI 169 GQTLDLLTAP179 QGNVDLVRFT189 EKRYKSIVKY199 LTAFYSFYLP209 IAAAMYMAGI 219 DGEKEHANAK229 KILLEMGEFF239 QIQDDYLDLF249 GDPSVTGKIG259 TDIQDNKCSW 269 LVVQCLQRAT279 PEQYQILKEN289 YGQKEAEKVA299 RVKALYEELD309 LPAVFLQYEE 319 DSYSHIMALI329 EQYAAPLPPA339 VFLGLARKIY349 KRRK
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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 .IPE or .IPE2 or .IPE3 or :3IPE;style chemicals stick;color identity;select .A:56 or .A:57 or .A:58 or .A:59 or .A:60 or .A:93 or .A:96 or .A:100 or .A:112 or .A:113 or .A:201 or .A:204 or .A:205 or .A:239 or .A:240 or .A:243 or .A:257 or .A:353; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 5CG6 Neutron crystal structure of human farnesyl pyrophosphate synthase in complex with risedronate and isopentenyl pyrophosphate | ||||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [7] |
| PDB Sequence |
DVYAQEKQDF
17 VQHFSQIVRV27 LTEDEMGHPE37 IGDAIARLKE47 VLEYNAIGGK57 YNRGLTVVVA 67 FRELVEPRKQ77 DADSLQRAWT87 VGWCVELLQA97 FFLVADDIMD107 SSLTRRGQIC 117 WYQKPGVGLD127 AINDANLLEA137 CIYRLLKLYC147 REQPYYLNLI157 ELFLQSSYQT 167 EIGQTLDLLT177 APQGNVDLVR187 FTEKRYKSIV197 KYKTAFYSFY207 LPIAAAMYMA 217 GIDGEKEHAN227 AKKILLEMGE237 FFQIQDDYLD247 LFGDPSVTGK257 IGTDIQDNKC 267 SWLVVQCLQR277 ATPEQYQILK287 ENYGQKEAEK297 VARVKALYEE307 LDLPAVFLQY 317 EEDSYSHIMA327 LIEQYAAPLP337 PAVFLGLARK347 IYK
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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 .IPE or .IPE2 or .IPE3 or :3IPE;style chemicals stick;color identity;select .A:56 or .A:57 or .A:58 or .A:59 or .A:60 or .A:93 or .A:96 or .A:100 or .A:112 or .A:113 or .A:201 or .A:204 or .A:205 or .A:239 or .A:240 or .A:243 or .A:257; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 1ZW5 X-ray structure of Farnesyl diphosphate synthase protein | ||||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [8] |
| PDB Sequence |
EKQDFVQHFS
36 QIVRVLTEDE46 HPEIGDAIAR58 LKEVLEYNAI68 GGKYNRGLTV78 VVAFRELVEP 88 RKQDADSLQR98 AWTVGWCVEL108 LQAFFLVADD118 IMDSSLTRRG128 QICWYQKPGV 138 GLDAINDANL148 LEACIYRLLK158 LYCREQPYYL168 NLIELFLQSS178 YQTEIGQTLD 188 LLTAPQGNVD198 LVRFTEKRYK208 SIVKYKTAFY218 SFYLPIAAAM228 YMAGIDGEKE 238 HANAKKILLE248 MGEFFQIQDD258 YLDLFGDPSV268 TGKIGTDIQD278 NKCSWLVVQC 288 LQRATPEQYQ298 ILKENYGQKE308 AEKVARVKAL318 YEELDLPAVF328 LQYEEDSYSH 338 IMALIEQYAA348 PLPPAVFLGL358 ARKIYKRRK
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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 .IPE or .IPE2 or .IPE3 or :3IPE;style chemicals stick;color identity;select .A:70 or .A:71 or .A:72 or .A:73 or .A:74 or .A:107 or .A:110 or .A:114 or .A:126 or .A:127 or .A:215 or .A:218 or .A:219 or .A:253 or .A:254 or .A:257 or .A:271 or .A:365 or .A:367; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 2F8Z Crystal structure of human FPPS in complex with zoledronate and isopentenyl diphosphate | ||||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [9] |
| PDB Sequence |
DVYAQEKQDF
17 VQHFSQIVRV27 LTEDEMGHPE37 IGDAIARLKE47 VLEYNAIGGK57 YNRGLTVVVA 67 FRELVEPRKQ77 DADSLQRAWT87 VGWCVELLQA97 FFLVADDIMD107 SSLTRRGQIC 117 WYQKPGVGLD127 AINDANLLEA137 CIYRLLKLYC147 REQPYYLNLI157 ELFLQSSYQT 167 EIGQTLDLLT177 APQGNVDLVR187 FTEKRYKSIV197 KYKTAFYSFY207 LPIAAAMYMA 217 GIDGEKEHAN227 AKKILLEMGE237 FFQIQDDYLD247 LFGDPSVTGK257 IGTDIQDNKC 267 SWLVVQCLQR277 ATPEQYQILK287 ENYGQKEAEK297 VARVKALYEE307 LDLPAVFLQY 317 EEDSYSHIMA327 LIEQYAAPLP337 PAVFLGLARK347 IYKRRK
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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 .IPE or .IPE2 or .IPE3 or :3IPE;style chemicals stick;color identity;select .F:56 or .F:57 or .F:58 or .F:60 or .F:93 or .F:96 or .F:100 or .F:112 or .F:113 or .F:201 or .F:204 or .F:205 or .F:239 or .F:240 or .F:243 or .F:257 or .F:351 or .F:353; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | The effects of Lysine 200 and Phenylalanine 239 Farnesyl Pyrophosphate Synthase (FPPS) mutations on the catalytic activity, crystal structure and inhibition by nitrogen containing bisphosphonates | ||||
| REF 2 | Crystal Structure of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate | ||||
| REF 3 | Crystal Structure of Farnesyl Pyrophosphate Synthase Mutant (Y204A) Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate | ||||
| REF 4 | Crystal Structure of Farnesyl Synthase Mutant (Y204A) Complexed with Mg, Alendronate and Isopentenyl Pyrophosphate | ||||
| REF 5 | The effects of Lysine 200 and Phenylalanine 239 Farnesyl Pyrophosphate Synthase (FPPS) mutations on the catalytic activity, crystal structure and inhibition by nitrogen containing bisphosphonates | ||||
| REF 6 | The effects of Lysine 200 and Phenylalanine 239 Farnesyl Pyrophosphate Synthase (FPPS) mutations on the catalytic activity, crystal structure and inhibition by nitrogen containing bisphosphonates | ||||
| REF 7 | Protonation State and Hydration of Bisphosphonate Bound to Farnesyl Pyrophosphate Synthase. J Med Chem. 2015 Sep 24;58(18):7549-56. | ||||
| REF 8 | The molecular mechanism of nitrogen-containing bisphosphonates as antiosteoporosis drugs. Proc Natl Acad Sci U S A. 2006 May 16;103(20):7829-34. | ||||
| REF 9 | Structural basis for the exceptional in vivo efficacy of bisphosphonate drugs. ChemMedChem. 2006 Feb;1(2):267-73. | ||||
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