Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T65889 | Target Info | |||
| Target Name | Pyruvate kinase M2 (PKM) | ||||
| Synonyms | p58; Tumor M2-PK; Thyroid hormone-binding protein 1; THBP1; Pyruvate kinase muscle isozyme; Pyruvate kinase isozymes M1/M2; Pyruvate kinase PKM; Pyruvate kinase 2/3; PKM2; PK3; PK2; Opa-interacting protein 3; OIP3; OIP-3; Cytosolic thyroid hormone-binding protein; CTHBP | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | PKM | ||||
| Biochemical Class | Kinase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Pyruvic acid | Ligand Info | |||||
| Structure Description | Crystal structure of PKM2 mutant | PDB:4YJ5 | ||||
| Method | X-ray diffraction | Resolution | 2.41 Å | Mutation | Yes | [1] |
| PDB Sequence |
QTQQLHAAMA
23 DTFLEHMCRL33 DIDSPPITAR43 NTGIICTIGP53 ASRSVETLKE63 MIKSGMNVAR 73 LNFSHGTHEY83 HAETIKNVRT93 ATESFASDPI103 LYRPVAVALD113 TKGPEIRTGL 123 IKGSGTAEVE133 LKKGATLKIT143 LDNAYMEKCD153 ENILWLDYKN163 ICKVVEVGSK 173 IYVDDGLISL183 QVKQKGADFL193 VTEVENGGSL203 GSKKGVNLPG213 AAVDLPAVSE 223 KDIQDLKFGV233 EQDVDMVFAS243 FIRKASDVHE253 VRKVLGEKGK263 NIKIISKIEN 273 HEGVRRFDEI283 LEASDGIMVA293 RGDLGIEIPA303 EKVFLAQKMM313 IGRCNRAGKP 323 VICATQMLES333 MIKKPRPTRA343 EGSDVANAVL353 DGADCIMLSG363 ETAKGDYPLE 373 AVRMQHLIAR383 EAEAAIYYLQ393 LFEELRRLAP403 ITSDPTEATA413 VGAVEASFKC 423 CSGAIIVLTK433 SGRSAHQVAR443 YRPRAPIIAV453 TRNPQTARQA463 HLYRGIFPVL 473 CKDPVQEAWA483 EDVDLRVNFA493 MNVGKARGFF503 KKGDVVIVLT513 GWRPGSGFTN 523 TMRVVPVP
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: L-phenylalanine | Ligand Info | |||||
| Structure Description | Crystal structure of M2 PYK in complex with Phenyalanine. | PDB:6GG4 | ||||
| Method | X-ray diffraction | Resolution | 2.46 Å | Mutation | No | [2] |
| PDB Sequence |
ADTFLEHMCR
32 LDIDSPPITA42 RNTGIICTIG52 PASRSVETLK62 EMIKSGMNVA72 RLNFSHGTHE 82 YHAETIKNVR92 TATESFASDP102 ILYRPVAVAL112 DTKGPEIRTG122 LIKGSGTAEV 132 ELKKGATLKI142 TLDNAYMEKC152 DENILWLDYK162 NICKVVEVGS172 KIYVDDGLIS 182 LQVKQKGADF192 LVTEVENGGS202 LGSKKGVNLP212 GAAVDLPAVS222 EKDIQDLKFG 232 VEQDVDMVFA242 SFIRKASDVH252 EVRKVLGEKG262 KNIKIISKIE272 NHEGVRRFDE 282 ILEASDGIMV292 ARGDLGIEIP302 AEKVFLAQKM312 MIGRCNRAGK322 PVICATQMLE 332 SMIKKPRPTR342 AEGSDVANAV352 LDGADCIMLS362 GETAKGDYPL372 EAVRMQHLIA 382 REAEAAIYHL392 QLFEELRRLA402 PITSDPTEAT412 AVGAVEASFK422 CCSGAIIVLT 432 KSGRSAHQVA442 RYRPRAPIIA452 VTRNPQTARQ462 AHLYRGIFPV472 LKDPVQEAWA 483 EDVDLRVNFA493 MNVGKARGFF503 KKGDVVIVLT513 GWRPGSGFTN523 TMRVVPVP |
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: L-alanine | Ligand Info | |||||
| Structure Description | Crystal structure of M2 PYK in complex with Alanine. | PDB:6GG3 | ||||
| Method | X-ray diffraction | Resolution | 3.72 Å | Mutation | No | [2] |
| PDB Sequence |
IQTQQLHAAM
22 ADTFLEHMCR32 LDIDSPPITA42 RNTGIICTIG52 PASRSVETLK62 EMIKSGMNVA 72 RLNFSHGTHE82 YHAETIKNVR92 TATESFASDP102 ILYRPVAVAL112 DTKGPEIRTG 122 LIKGSGTAEV132 ELKKGATLKI142 TLDNAYMEKC152 DENILWLDYK162 NICKVVEVGS 172 KIYVDDGLIS182 LQVKQKGADF192 LVTEVENGGS202 LGSKKGVNLP212 GAAVDLPAVS 222 EKDIQDLKFG232 VEQDVDMVFA242 SFIRKASDVH252 EVRKVLGEKG262 KNIKIISKIE 272 NHEGVRRFDE282 ILEASDGIMV292 ARGDLGIEIP302 AEKVFLAQKM312 MIGRCNRAGK 322 PVICATQMLE332 SMIKKPRPTR342 AEGSDVANAV352 LDGADCIMLS362 GETAKGDYPL 372 EAVRMQHLIA382 REAEAAIYHL392 QLFEELRRLA402 PITSDPTEAT412 AVGAVEASFK 422 CCSGAIIVLT432 KSGRSAHQVA442 RYRPRAPIIA452 VTRNPQTARQ462 AHLYRGIFPV 472 LCKDPVQEAW482 AEDVDLRVNF492 AMNVGKARGF502 FKKGDVVIVL512 TGWRPGSGFT 522 NTMRVVPVP
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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 .ALA or .ALA2 or .ALA3 or :3ALA;style chemicals stick;color identity;select .A:14 or .A:43 or .A:44 or .A:45 or .A:46 or .A:70 or .A:464 or .A:466 or .A:468 or .A:469 or .A:470 or .A:471; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 5-hydroxynaphthalene-1-sulfonamide | Ligand Info | |||||
| Structure Description | PKM2 in complex with Compound 5 | PDB:6TTF | ||||
| Method | Electron microscopy | Resolution | 3.20 Å | Mutation | No | [3] |
| PDB Sequence |
LHAAMADTFL
27 EHMCRLDIDS37 PPITARNTGI47 ICTIGPASRS57 VETLKEMIKS67 GMNVARLNFS 77 HGTHEYHAET87 IKNVRTATES97 FASDPILYRP107 VAVALDTKGP117 EIRTGLIKGS 127 GTAEVELKKG137 ATLKITLDNA147 YMEKCDENIL157 WLDYKNICKV167 VEVGSKIYVD 177 DGLISLQVKQ187 KGADFLVTEV197 ENGGSLGSKK207 GVNLPGAAVD217 LPAVSEKDIQ 227 DLKFGVEQDV237 DMVFASFIRK247 ASDVHEVRKV257 LGEKGKNIKI267 ISKIENHEGV 277 RRFDEILEAS287 DGIMVARGDL297 GIEIPAEKVF307 LAQKMMIGRC317 NRAGKPVICA 327 TQMLESMIKK337 PRPTRAEGSD347 VANAVLDGAD357 CIMLSGETAK367 GDYPLEAVRM 377 QHLIAREAEA387 AIYHLQLFEE397 LRRLAPITSD407 PTEATAVGAV417 EASFKCCSGA 427 IIVLTKSGRS437 AHQVARYRPR447 APIIAVTRNP457 QTARQAHLYR467 GIFPVLCKDP 477 VQEAWAEDVD487 LRVNFAMNVG497 KARGFFKKGD507 VVIVLTGWRP517 GSGFTNTMRV 527 VPVP
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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 .LZ2 or .LZ22 or .LZ23 or :3LZ2;style chemicals stick;color identity;select .A:26 or .A:318 or .A:353 or .A:354 or .A:388 or .A:389 or .A:390 or .A:393 or .A:394 or .A:397; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: adenosine diphosphate | Ligand Info | |||||
| Structure Description | Activator-Bound Structure of Human Pyruvate Kinase M2 | PDB:3GR4 | ||||
| Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [4] |
| PDB Sequence |
IQTQQLHAAM
22 ADTFLEHMCR32 LDIDSPPITA42 RNTGIICTIG52 PASRSVETLK62 EMIKSGMNVA 72 RLNFSHGTHE82 YHAETIKNVR92 TATESFASDP102 ILYRPVAVAL112 DTKGPEIRTG 122 LIKGSGTAEV132 ELKKGATLKI142 TLDNAYMEKC152 DENILWLDYK162 NICKVVEVGS 172 KIYVDDGLIS182 LQVKQKGADF192 LVTEVENGGS202 LGSKKGVNLP212 GAAVDLPAVS 222 EKDIQDLKFG232 VEQDVDMVFA242 SFIRKASDVH252 EVRKVLGEKG262 KNIKIISKIE 272 NHEGVRRFDE282 ILEASDGIMV292 ARGDLGIEIP302 AEKVFLAQKM312 MIGRCNRAGK 322 PVICATQMLE332 SMIKKPRPTR342 AEGSDVANAV352 LDGADCIMLS362 GETAKGDYPL 372 EAVRMQHLIA382 REAEAAIYHL392 QLFEELRRLA402 PITSDPTEAT412 AVGAVEASFK 422 CCSGAIIVLT432 KSGRSAHQVA442 RYRPRAPIIA452 VTRNPQTARQ462 AHLYRGIFPV 472 LCKDPVQEAW482 AEDVDLRVNF492 AMNVGKARGF502 FKKGDVVIVL512 TGWRPGSGFT 522 NTMRVVPVP
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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 .ADP or .ADP2 or .ADP3 or :3ADP;style chemicals stick;color identity;select .A:50 or .A:51 or .A:52 or .A:53 or .A:73 or .A:75 or .A:77 or .A:78 or .A:84 or .A:118 or .A:120 or .A:362 or .A:363 or .A:366 or .A:367; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: L-serine | Ligand Info | |||||
| Structure Description | Pyruvate Kinase M2 Mutant - S437Y in Complex with L-serine | PDB:6NUB | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | Yes | [5] |
| PDB Sequence |
EAGTAFIQTQ
16 QLHAAMADTF26 LEHMCRLDID36 SPPITARNTG46 IICTIGPASR56 SVETLKEMIK 66 SGMNVARLNF76 SHGTHEYHAE86 TIKNVRTATE96 SFASDPILYR106 PVAVALDTKG 116 PEIRTGLIKG126 SGTAEVELKK136 GATLKITLDN146 AYMEKCDENI156 LWLDYKNICK 166 VVEVGSKIYV176 DDGLISLQVK186 QKGADFLVTE196 VENGGSLGSK206 KGVNLPGAAV 216 DLPAVSEKDI226 QDLKFGVEQD236 VDMVFASFIR246 KASDVHEVRK256 VLGEKGKNIK 266 IISKIENHEG276 VRRFDEILEA286 SDGIMVARGD296 LGIEIPAEKV306 FLAQKMMIGR 316 CNRAGKPVIC326 ATQMLESMIK336 KPRPTRAEGS346 DVANAVLDGA356 DCIMLSGETA 366 KGDYPLEAVR376 MQHLIAREAE386 AAIYHLQLFE396 ELRRLAPITS406 DPTEATAVGA 416 VEASFKCCSG426 AIIVLTKSGR436 YAHQVARYRP446 RAPIIAVTRN456 PQTARQAHLY 466 RGIFPVLCKD476 PVQEAWAEDV486 DLRVNFAMNV496 GKARGFFKKG506 DVVIVLTGWR 516 PFTNTMRVVP529 VP
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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 .SER or .SER2 or .SER3 or :3SER;style chemicals stick;color identity;select .A:43 or .A:44 or .A:45 or .A:46 or .A:70 or .A:106 or .A:464 or .A:466 or .A:468 or .A:469 or .A:470 or .A:471; color #f3c393; 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: L-valine | Ligand Info | |||||
| Structure Description | Crystal Structure of Human PKM2 in Complex with L-valine | PDB:6V76 | ||||
| Method | X-ray diffraction | Resolution | 2.75 Å | Mutation | No | [6] |
| PDB Sequence |
HAAMADTFLE
28 HMCRLDIDSP38 PITARNTGII48 CTIGPASRSV58 ETLKEMIKSG68 MNVARLNFSH 78 GTHEYHAETI88 KNVRTATESF98 ASDPILYRPV108 AVALDTKGPE118 IRTGLIKGSG 128 TAEVELKKGA138 TLKITLDNAY148 MEKCDENILW158 LDYKNICKVV168 EVGSKIYVDD 178 GLISLQVKQK188 GALVTEVENG200 GSLGSKKGVN210 LPGAAVDLPA220 VSEKDIQDLK 230 FGVEQDVDMV240 FASFIRKASD250 VHEVRKVLGE260 KGKNIKIISK270 IENHEGVRRF 280 DEILEASDGI290 MVARGDLGIE300 IPAEKVFLAQ310 KMMIGRCNRA320 GKPVICATQM 330 LESMIKKPRP340 TRAEGSDVAN350 AVLDGADCIM360 LSGETAKGDY370 PLEAVRMQHL 380 IAREAEAAIY390 HLQLFEELRR400 LAPITSDPTE410 ATAVGAVEAS420 FKCCSGAIIV 430 LTKSGRSAHQ440 VARYRPRAPI450 IAVTRNPQTA460 RQAHLYRGIF470 PVLCKDPVQE 480 AWAEDVDLRV490 NFAMNVGKAR500 GFFKKGDVVI510 VLTGWRPGSG520 FTNTMRVVPV 530 P
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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 .VAL or .VAL2 or .VAL3 or :3VAL;style chemicals stick;color identity;select .C:43 or .C:44 or .C:45 or .C:46 or .C:70 or .C:106 or .C:463 or .C:464 or .C:466 or .C:468 or .C:469 or .C:470 or .C:471; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: L-aspartic acid | Ligand Info | |||||
| Structure Description | Crystal Structure of Human PKM2 in Complex with L-aspartate | PDB:6V75 | ||||
| Method | X-ray diffraction | Resolution | 2.85 Å | Mutation | No | [6] |
| PDB Sequence |
TQQLHAAMAD
24 TFLEHMCRLD34 IDSPPITARN44 TGIICTIGPA54 SRSVETLKEM64 IKSGMNVARL 74 NFSHGTHEYH84 AETIKNVRTA94 TESFASDPIL104 YRPVAVALDT114 KGPEIRTGLI 124 KGSGTAEVEL134 KKGATLKITL144 DNAYMEKCDE154 NILWLDYKNI164 CKVVEVGSKI 174 YVDDGLISLQ184 VKQKGADFLV194 TEVENGGSLG204 SKKGVNLPGA214 AVDLPAVSEK 224 DIQDLKFGVE234 QDVDMVFASF244 IRKASDVHEV254 RKVLGEKGKN264 IKIISKIENH 274 EGVRRFDEIL284 EASDGIMVAR294 GDLGIEIPAE304 KVFLAQKMMI314 GRCNRAGKPV 324 ICATQMLESM334 IKKPRPTRAE344 GSDVANAVLD354 GADCIMLSGE364 TAKGDYPLEA 374 VRMQHLIARE384 AEAAIYHLQL394 FEELRRLAPI404 TSDPTEATAV414 GAVEASFKCC 424 SGAIIVLTKS434 GRSAHQVARY444 RPRAPIIAVT454 RNPQTARQAH464 LYRGIFPVLC 474 KDPVQEAWAE484 DVDLRVNFAM494 NVGKARGFFK504 KGDVVIVLTG514 WRPGSGFTNT 524 MRVVPVP
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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 .ASP or .ASP2 or .ASP3 or :3ASP;style chemicals stick;color identity;select .C:43 or .C:44 or .C:45 or .C:46 or .C:70 or .C:357 or .C:358 or .C:463 or .C:464 or .C:465 or .C:466 or .C:467 or .C:468 or .C:469 or .C:470 or .C:471; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Cysteine Sulfenic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of M2 PYK in complex with Phenyalanine. | PDB:6GG4 | ||||
| Method | X-ray diffraction | Resolution | 2.46 Å | Mutation | No | [2] |
| PDB Sequence |
ADTFLEHMCR
32 LDIDSPPITA42 RNTGIICTIG52 PASRSVETLK62 EMIKSGMNVA72 RLNFSHGTHE 82 YHAETIKNVR92 TATESFASDP102 ILYRPVAVAL112 DTKGPEIRTG122 LIKGSGTAEV 132 ELKKGATLKI142 TLDNAYMEKC152 DENILWLDYK162 NICKVVEVGS172 KIYVDDGLIS 182 LQVKQKGADF192 LVTEVENGGS202 LGSKKGVNLP212 GAAVDLPAVS222 EKDIQDLKFG 232 VEQDVDMVFA242 SFIRKASDVH252 EVRKVLGEKG262 KNIKIISKIE272 NHEGVRRFDE 282 ILEASDGIMV292 ARGDLGIEIP302 AEKVFLAQKM312 MIGRCNRAGK322 PVICATQMLE 332 SMIKKPRPTR342 AEGSDVANAV352 LDGADCIMLS362 GETAKGDYPL372 EAVRMQHLIA 382 REAEAAIYHL392 QLFEELRRLA402 PITSDPTEAT412 AVGAVEASFK422 CCSGAIIVLT 432 KSGRSAHQVA442 RYRPRAPIIA452 VTRNPQTARQ462 AHLYRGIFPV472 LKDPVQEAWA 483 EDVDLRVNFA493 MNVGKARGFF503 KKGDVVIVLT513 GWRPGSGFTN523 TMRVVPVP |
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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 .CSO or .CSO2 or .CSO3 or :3CSO;style chemicals stick;color identity;select .A:453 or .A:454 or .A:455 or .A:472 or .A:473 or .A:475 or .A:476 or .A:488 or .A:489 or .A:492; 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: Oxalic acid | Ligand Info | |||||
| Structure Description | Human Pyruvate Kinase M2 Mutant C424A | PDB:4WJ8 | ||||
| Method | X-ray diffraction | Resolution | 2.87 Å | Mutation | Yes | [7] |
| PDB Sequence |
QTQQLHAAMA
23 DTFLEHMCRL33 DIDSPPITAR43 NTGIICTIGP53 ASRSVETLKE63 MIKSGMNVAR 73 LNFSHGTHEY83 HAETIKNVRT93 ATESFASDPI103 LYRPVAVALD113 TKGPEIRTGL 123 IKGSGTAEVE133 LKKGATLKIT143 LDNAYMEKCD153 ENILWLDYKN163 ICKVVEVGSK 173 IYVDDGLISL183 QVKQKGADFL193 VTEVENGGSL203 GSKKGVNLPG213 AAVDLPAVSE 223 KDIQDLKFGV233 EQDVDMVFAS243 FIRKASDVHE253 VRKVLGEKGK263 NIKIISKIEN 273 HEGVRRFDEI283 LEASDGIMVA293 RGDLGIEIPA303 EKVFLAQKMM313 IGRCNRAGKP 323 VICATQMLES333 MIKKPRPTRA343 EGSDVANAVL353 DGADCIMLSG363 ETAKGDYPLE 373 AVRMQHLIAR383 EAEAAIYHLQ393 LFEELRRLAP403 ITSDPTEATA413 VGAVEASFKC 423 ASGAIIVLTK433 SGRSAHQVAR443 YRPRAPIIAV453 TRNPQTARQA463 HLYRGIFPVL 473 CKDPVQEAWA483 EDVDLRVNFA493 MNVGKARGFF503 KKGDVVIVLT513 GWRPGSGFTN 523 TMRVVPVP
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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 .OXD or .OXD2 or .OXD3 or :3OXD;style chemicals stick;color identity;select .A:73 or .A:113 or .A:270 or .A:272 or .A:291 or .A:293 or .A:294 or .A:295 or .A:296 or .A:327 or .A:328 or .A:360; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N-(4-{[4-(Pyrazin-2-Yl)piperazin-1-Yl]carbonyl}phenyl)quinoline-8-Sulfonamide | Ligand Info | |||||
| Structure Description | PKM2 in complex with an activator | PDB:4G1N | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [8] |
| PDB Sequence |
QTQQLHAAMA
23 DTFLEHMCRL33 DIDSPPITAR43 NTGIICTIGP53 ASRSVETLKE63 MIKSGMNVAR 73 LNFSHGTHEY83 HAETIKNVRT93 ATESFASDPI103 LYRPVAVALD113 TKGPEIRTGL 123 IKGSGTAEVE133 LKKGATLKIT143 LDNAYMEKCD153 ENILWLDYKN163 ICKVVEVGSK 173 IYVDDGLISL183 QVKQKGADFL193 VTEVENGGSL203 GSKKGVNLPG213 AAVDLPAVSE 223 KDIQDLKFGV233 EQDVDMVFAS243 FIRKASDVHE253 VRKVLGEKGK263 NIKIISKIEN 273 HEGVRRFDEI283 LEASDGIMVA293 RGDLGIEIPA303 EKVFLAQKMM313 IGRCNRAGKP 323 VICATQMLES333 MIKKPRPTRA343 EGSDVANAVL353 DGADCIMLSG363 ETAKGDYPLE 373 AVRMQHLIAR383 EAEAAIYHLQ393 LFEELRRLAP403 ITSDPTEATA413 VGAVEASFKC 423 CSGAIIVLTK433 SGRSAHQVAR443 YRPRAPIIAV453 TRNPQTARQA463 HLYRGIFPVL 473 CKDPVQEAWA483 EDVDLRVNFA493 MNVGKARGFF503 KKGDVVIVLT513 GWRPGSGFTN 523 TMRVVPVP
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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 .NZT or .NZT2 or .NZT3 or :3NZT;style chemicals stick;color identity;select .A:26 or .A:30 or .A:318 or .A:350 or .A:353 or .A:354 or .A:355 or .A:388 or .A:389 or .A:390 or .A:391 or .A:393 or .A:394 or .A:397; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N-[3-(trifluoromethyl)-1,2-oxazol-5-yl]acetamide | Ligand Info | |||||
| Structure Description | PKM2 in complex with Compound 6 | PDB:6TTI | ||||
| Method | Electron microscopy | Resolution | 2.50 Å | Mutation | No | [3] |
| PDB Sequence |
HAAMADTFLE
28 HMCRLDIDSP38 PITARNTGII48 CTIGPASRSV58 ETLKEMIKSG68 MNVARLNFSH 78 GTHEYHAETI88 KNVRTATESF98 ASDPILYRPV108 AVALDTKGPE118 IRLPAVSEKD 225 IQDLKFGVEQ235 DVDMVFASFI245 RKASDVHEVR255 KVLGEKGKNI265 KIISKIENHE 275 GVRRFDEILE285 ASDGIMVARG295 DLGIEIPAEK305 VFLAQKMMIG315 RCNRAGKPVI 325 CATQMLESMI335 KKPRPTRAEG345 SDVANAVLDG355 ADCIMLSGET365 AKGDYPLEAV 375 RMQHLIAREA385 EAAIYHLQLF395 EELRRLAPIT405 SDPTEATAVG415 AVEASFKCCS 425 GAIIVLTKSG435 RSAHQVARYR445 PRAPIIAVTR455 NPQTARQAHL465 YRGIFPVLCK 475 DPVQEAWAED485 VDLRVNFAMN495 VGKARGFFKK505 GDVVIVLTGW515 RPGSGFTNTM 525 RVVPVP
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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 .NXE or .NXE2 or .NXE3 or :3NXE;style chemicals stick;color identity;select .A:26 or .A:29 or .A:30 or .A:33 or .A:311 or .A:350 or .A:353 or .A:354 or .A:388 or .A:389 or .A:390; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (2S,3R)-2-azaniumyl-3-hydroxybutanoate | Ligand Info | |||||
| Structure Description | PKM2 in complex with L-threonine | PDB:6TTH | ||||
| Method | Electron microscopy | Resolution | 2.60 Å | Mutation | No | [3] |
| PDB Sequence |
MADTFLEHMC
31 RLDIDSPPIT41 ARNTGIICTI51 GPASRSVETL61 KEMIKSGMNV71 ARLNFSHGTH 81 EYHAETIKNV91 RTATESFASD101 PILYRPVAVA111 LDTKGPLPAV221 SEKDIQDLKF 231 GVEQDVDMVF241 ASFIRKASDV251 HEVRKVLGEK261 GKNIKIISKI271 ENHEGVRRFD 281 EILEASDGIM291 VARGDLGIEI301 PAEKVFLAQK311 MMIGRCNRAG321 KPVICATQML 331 ESMIKKPRPT341 RAEGSDVANA351 VLDGADCIML361 SGETAKGDYP371 LEAVRMQHLI 381 AREAEAAIYH391 LQLFEELRRL401 APITSDPTEA411 TAVGAVEASF421 KCCSGAIIVL 431 TKSGRSAHQV441 ARYRPRAPII451 AVTRNPQTAR461 QAHLYRGIFP471 VLCKDPVQEA 481 WAEDVDLRVN491 FAMNVGKARG501 FFKKGDVVIV511 LTGWRPGSGF521 TNTMRVVPVP 531
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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 .THR or .THR2 or .THR3 or :3THR;style chemicals stick;color identity;select .A:43 or .A:44 or .A:45 or .A:46 or .A:70 or .A:106 or .A:464 or .A:466 or .A:468 or .A:469 or .A:470 or .A:471; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 1-Isopropyl-3-(pyridin-4-yl)urea | Ligand Info | |||||
| Structure Description | PKM2 in complex with Compound 10 | PDB:6TTQ | ||||
| Method | Electron microscopy | Resolution | 2.70 Å | Mutation | No | [3] |
| PDB Sequence |
MADTFLEHMC
31 RLDIDSPPIT41 ARNTGIICTI51 GPASRSVETL61 KEMIKSGMNV71 ARLNFSHGTH 81 EYHAETIKNV91 RTATESFASD101 PILYRPVAVA111 LDTKGPEIRT121 GLIKGSGTAE 131 VELKKGATLK141 ITLDNAYMEK151 CDENILWLDY161 KNICKVVEVG171 SKIYVDDGLI 181 SLQVKQKGAD191 FLVTEVENGG201 SLGSKKGVNL211 PGAAVDLPAV221 SEKDIQDLKF 231 GVEQDVDMVF241 ASFIRKASDV251 HEVRKVLGEK261 GKNIKIISKI271 ENHEGVRRFD 281 EILEASDGIM291 VARGDLGIEI301 PAEKVFLAQK311 MMIGRCNRAG321 KPVICATQML 331 ESMIKKPRPT341 RAEGSDVANA351 VLDGADCIML361 SGETAKGDYP371 LEAVRMQHLI 381 AREAEAAIYH391 LQLFEELRRL401 APITSDPTEA411 TAVGAVEASF421 KCCSGAIIVL 431 TKSGRSAHQV441 ARYRPRAPII451 AVTRNPQTAR461 QAHLYRGIFP471 VLCKDPVQEA 481 WAEDVDLRVN491 FAMNVGKARG501 FFKKGDVVIV511 LTGWRPGSGF521 TNTMRVVPVP 531
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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 .NXH or .NXH2 or .NXH3 or :3NXH;style chemicals stick;color identity;select .A:26 or .A:30 or .A:311 or .A:353 or .A:354 or .A:388 or .A:389 or .A:390 or .A:393 or .A:394; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 1,6-di-O-phosphono-beta-D-fructofuranose | Ligand Info | |||||
| Structure Description | Activator-Bound Structure of Human Pyruvate Kinase M2 | PDB:3GR4 | ||||
| Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [4] |
| PDB Sequence |
IQTQQLHAAM
22 ADTFLEHMCR32 LDIDSPPITA42 RNTGIICTIG52 PASRSVETLK62 EMIKSGMNVA 72 RLNFSHGTHE82 YHAETIKNVR92 TATESFASDP102 ILYRPVAVAL112 DTKGPEIRTG 122 LIKGSGTAEV132 ELKKGATLKI142 TLDNAYMEKC152 DENILWLDYK162 NICKVVEVGS 172 KIYVDDGLIS182 LQVKQKGADF192 LVTEVENGGS202 LGSKKGVNLP212 GAAVDLPAVS 222 EKDIQDLKFG232 VEQDVDMVFA242 SFIRKASDVH252 EVRKVLGEKG262 KNIKIISKIE 272 NHEGVRRFDE282 ILEASDGIMV292 ARGDLGIEIP302 AEKVFLAQKM312 MIGRCNRAGK 322 PVICATQMLE332 SMIKKPRPTR342 AEGSDVANAV352 LDGADCIMLS362 GETAKGDYPL 372 EAVRMQHLIA382 REAEAAIYHL392 QLFEELRRLA402 PITSDPTEAT412 AVGAVEASFK 422 CCSGAIIVLT432 KSGRSAHQVA442 RYRPRAPIIA452 VTRNPQTARQ462 AHLYRGIFPV 472 LCKDPVQEAW482 AEDVDLRVNF492 AMNVGKARGF502 FKKGDVVIVL512 TGWRPGSGFT 522 NTMRVVPVP
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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 .FBP or .FBP2 or .FBP3 or :3FBP;style chemicals stick;color identity;select .A:431 or .A:432 or .A:433 or .A:434 or .A:435 or .A:436 or .A:437 or .A:438 or .A:482 or .A:485 or .A:489 or .A:513 or .A:514 or .A:515 or .A:516 or .A:517 or .A:518 or .A:519 or .A:520 or .A:521 or .A:522; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LEU431
3.772
THR432
2.515
LYS433
3.149
SER434
2.536
GLY435
4.028
ARG436
3.764
SER437
2.713
ALA438
4.854
TRP482
2.708
ASP485
4.620
ARG489
2.870
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 1-[(2,6-Difluorophenyl)sulfonyl]-4-(2,3-dihydro-1,4-benzodioxin-6-ylsulfonyl)piperazine | Ligand Info | |||||
| Structure Description | Activator-Bound Structure of Human Pyruvate Kinase M2 | PDB:3GR4 | ||||
| Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [4] |
| PDB Sequence |
IQTQQLHAAM
22 ADTFLEHMCR32 LDIDSPPITA42 RNTGIICTIG52 PASRSVETLK62 EMIKSGMNVA 72 RLNFSHGTHE82 YHAETIKNVR92 TATESFASDP102 ILYRPVAVAL112 DTKGPEIRTG 122 LIKGSGTAEV132 ELKKGATLKI142 TLDNAYMEKC152 DENILWLDYK162 NICKVVEVGS 172 KIYVDDGLIS182 LQVKQKGADF192 LVTEVENGGS202 LGSKKGVNLP212 GAAVDLPAVS 222 EKDIQDLKFG232 VEQDVDMVFA242 SFIRKASDVH252 EVRKVLGEKG262 KNIKIISKIE 272 NHEGVRRFDE282 ILEASDGIMV292 ARGDLGIEIP302 AEKVFLAQKM312 MIGRCNRAGK 322 PVICATQMLE332 SMIKKPRPTR342 AEGSDVANAV352 LDGADCIMLS362 GETAKGDYPL 372 EAVRMQHLIA382 REAEAAIYHL392 QLFEELRRLA402 PITSDPTEAT412 AVGAVEASFK 422 CCSGAIIVLT432 KSGRSAHQVA442 RYRPRAPIIA452 VTRNPQTARQ462 AHLYRGIFPV 472 LCKDPVQEAW482 AEDVDLRVNF492 AMNVGKARGF502 FKKGDVVIVL512 TGWRPGSGFT 522 NTMRVVPVP
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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 .DYY or .DYY2 or .DYY3 or :3DYY;style chemicals stick;color identity;select .A:26 or .A:27 or .A:30 or .A:353 or .A:354 or .A:390 or .A:393 or .A:394 or .A:397; 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-[[4-(2,3-Dihydro-1,4-benzodioxin-6-ylsulfonyl)-1,4-diazepan-1-yl]sulfonyl]aniline | Ligand Info | |||||
| Structure Description | Activator-Bound Structure of Human Pyruvate Kinase M2 | PDB:3ME3 | ||||
| Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | No | [9] |
| PDB Sequence |
QTQQLHAAMA
23 DTFLEHMCRL33 DIDSPPITAR43 NTGIICTIGP53 ASRSVETLKE63 MIKSGMNVAR 73 LNFSHGTHEY83 HAETIKNVRT93 ATESFASDPI103 LYRPVAVALD113 TKGPEIRTGL 123 IKGSGTAEVE133 LKKGATLKIT143 LDNAYMEKCD153 ENILWLDYKN163 ICKVVEVGSK 173 IYVDDGLISL183 QVKQKGADFL193 VTEVENGGSL203 GSKKGVNLPG213 AAVDLPAVSE 223 KDIQDLKFGV233 EQDVDMVFAS243 FIRKASDVHE253 VRKVLGEKGK263 NIKIISKIEN 273 HEGVRRFDEI283 LEASDGIMVA293 RGDLGIEIPA303 EKVFLAQKMM313 IGRCNRAGKP 323 VICATQMLES333 MIKKPRPTRA343 EGSDVANAVL353 DGADCIMLSG363 ETAKGDYPLE 373 AVRMQHLIAR383 EAEAAIYHLQ393 LFEELRRLAP403 ITSDPTEATA413 VGAVEASFKC 423 CSGAIIVLTK433 SGRSAHQVAR443 YRPRAPIIAV453 TRNPQTARQA463 HLYRGIFPVL 473 CKDPVQEAWA483 EDVDLRVNFA493 MNVGKARGFF503 KKGDVVIVLT513 GWRPGSGFTN 523 TMRVVPVP
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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 .3SZ or .3SZ2 or .3SZ3 or :33SZ;style chemicals stick;color identity;select .A:26 or .A:27 or .A:30 or .A:315 or .A:318 or .A:353 or .A:354 or .A:355 or .A:390 or .A:393 or .A:394 or .A:397; 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-(2,3-dichlorobenzoyl)-1-methyl-1H-pyrrole-2-carboxamide | Ligand Info | |||||
| Structure Description | PKM2 in complex with compound 2 | PDB:5X1V | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [10] |
| PDB Sequence |
QTQQLHAAMA
23 DTFLEHMCRL33 DIDSPPITAR43 NTGIICTIGP53 ASRSVETLKE63 MIKSGMNVAR 73 LNFSHGTHEY83 HAETIKNVRT93 ATESFASDPI103 LYRPVAVALD113 TKGPEIRTGL 123 IKGSGTAEVE133 LKKGATLKIT143 LDNAYMEKCD153 ENILWLDYKN163 ICKVVEVGSK 173 IYVDDGLISL183 QVKLVTEVEN199 GGSLGSKKGV209 NLPGAAVDLP219 AVSEKDIQDL 229 KFGVEQDVDM239 VFASFIRKAS249 DVHEVRKVLG259 EKGKNIKIIS269 KIENHEGVRR 279 FDEILEASDG289 IMVARGDLGI299 EIPAEKVFLA309 QKMMIGRCNR319 AGKPVICATQ 329 MLESMIKKPR339 PTRAEGSDVA349 NAVLDGADCI359 MLSGETAKGD369 YPLEAVRMQH 379 LIAREAEAAI389 YHLQLFEELR399 RLAPITSDPT409 EATAVGAVEA419 SFKCCSGAII 429 VLTKSGRSAH439 QVARYRPRAP449 IIAVTRNPQT459 ARQAHLYRGI469 FPVLCKDPVQ 479 EAWAEDVDLR489 VNFAMNVGKA499 RGFFKKGDVV509 IVLTGWRPGS519 GFTNTMRVVP 529 VP
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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 .7XX or .7XX2 or .7XX3 or :37XX;style chemicals stick;color identity;select .A:26 or .A:29 or .A:30 or .A:33 or .A:350 or .A:353 or .A:354 or .A:388 or .A:389 or .A:390 or .A:391 or .A:393 or .A:394 or .A:397; 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 | Mutations in the PKM2 exon-10 region are associated with reduced allostery and increased nuclear translocation. doi:10.1038/s42003-019-0343-4. | ||||
| REF 2 | An allostatic mechanism for M2 pyruvate kinase as an amino-acid sensor. Biochem J. 2018 May 31;475(10):1821-1837. | ||||
| REF 3 | Fragment-based drug discovery using cryo-EM. Drug Discov Today. 2020 Mar;25(3):485-490. | ||||
| REF 4 | Activator-Bound Structures of Human Pyruvate Kinase M2 | ||||
| REF 5 | Mechanistic and Structural Insights into Cysteine-Mediated Inhibition of Pyruvate Kinase Muscle Isoform 2. Biochemistry. 2019 Sep 3;58(35):3669-3682. | ||||
| REF 6 | Biochemical and structural insights into how amino acids regulate pyruvate kinase muscle isoform 2. J Biol Chem. 2020 Apr 17;295(16):5390-5403. | ||||
| REF 7 | Human Pyruvate Kinase M2 Mutant C424A | ||||
| REF 8 | Small molecule activation of PKM2 in cancer cells induces serine auxotrophy. Chem Biol. 2012 Sep 21;19(9):1187-98. | ||||
| REF 9 | Pyruvate kinase M2 activators promote tetramer formation and suppress tumorigenesis. Nat Chem Biol. 2012 Oct;8(10):839-47. | ||||
| REF 10 | Discovery and structure-guided fragment-linking of 4-(2,3-dichlorobenzoyl)-1-methyl-pyrrole-2-carboxamide as a pyruvate kinase M2 activator. Bioorg Med Chem. 2017 Jul 1;25(13):3540-3546. | ||||
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