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(-) Description

Title :  PKM2 IN COMPLEX WITH COMPOUND 5
 
Authors :  Y. Matsui, H. Hanzawa
Date :  27 Jan 17  (Deposition) - 31 May 17  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Activator, Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Matsui, I. Yasumatsu, T. Asahi, T. Kitamura, K. Kanai, O. Ubukata, H. Hayasaka, S. Takaishi, H. Hanzawa, S. Katakura
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. V. 25 3540 2017
PubMed-ID: 28511909  |  Reference-DOI: 10.1016/J.BMC.2017.05.004

(-) Compounds

Molecule 1 - PYRUVATE KINASE PKM
    ChainsA, B, C, D
    EC Number2.7.1.40
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePKM, OIP3, PK2, PK3, PKM2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCYTOSOLIC THYROID HORMONE-BINDING PROTEIN,CTHBP,OPA- INTERACTING PROTEIN 3,OIP-3,PYRUVATE KINASE 2/3,PYRUVATE KINASE MUSCLE ISOZYME,THYROID HORMONE-BINDING PROTEIN 1,THBP1,TUMOR M2-PK, P58

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
17Y02Ligand/Ion4-[2,3-BIS(CHLORANYL)PHENYL]CARBONYL-N-[2-[[4-[2,3-BIS(CHLORANYL)PHENYL]CARBONYL-1-METHYL-PYRROL-2-YL]CARBONYLAMINO]ETHYL]-1-METHYL-PYRROLE-2-CARBOXAMIDE
2FBP4Ligand/IonBETA-FRUCTOSE-1,6-DIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:431 , THR A:432 , LYS A:433 , SER A:434 , SER A:437 , TRP A:482 , ARG A:489 , GLY A:514 , ARG A:516 , PRO A:517 , GLY A:518 , SER A:519 , GLY A:520 , PHE A:521 , THR A:522binding site for residue FBP A 601
2AC2SOFTWAREPHE A:26 , LYS A:311 , LEU A:353 , ASP A:354 , ILE A:389 , TYR A:390 , LEU A:394 , GLU A:397 , PHE B:26 , LYS B:311 , ASN B:350 , LEU B:353 , ASP B:354 , ILE B:389 , TYR B:390 , GLN B:393 , LEU B:394 , GLU B:397binding site for residue 7Y0 B 601
3AC3SOFTWARELEU B:431 , THR B:432 , LYS B:433 , SER B:434 , ARG B:436 , SER B:437 , TRP B:482 , ARG B:489 , GLY B:514 , ARG B:516 , PRO B:517 , GLY B:518 , SER B:519 , GLY B:520 , PHE B:521 , THR B:522binding site for residue FBP B 602
4AC4SOFTWAREPHE C:26 , LYS C:311 , ASN C:350 , LEU C:353 , ASP C:354 , ALA C:388 , ILE C:389 , TYR C:390 , LEU C:394 , GLU C:397 , PHE D:26 , LEU D:27 , LYS D:311 , ASN D:350 , LEU D:353 , ALA D:388 , ILE D:389 , TYR D:390 , GLU D:397binding site for residue 7Y0 C 601
5AC5SOFTWARELEU C:431 , THR C:432 , LYS C:433 , SER C:434 , SER C:437 , TRP C:482 , ARG C:489 , GLY C:514 , ARG C:516 , PRO C:517 , GLY C:518 , SER C:519 , GLY C:520 , PHE C:521 , THR C:522binding site for residue FBP C 602
6AC6SOFTWARELEU D:431 , THR D:432 , LYS D:433 , SER D:434 , ARG D:436 , SER D:437 , TRP D:482 , ARG D:489 , GLY D:514 , ARG D:516 , PRO D:517 , GLY D:518 , SER D:519 , GLY D:520 , PHE D:521 , THR D:522binding site for residue FBP D 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5X1W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5X1W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5X1W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5X1W)

(-) Exons   (0, 0)

(no "Exon" information available for 5X1W)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:518
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..hhhhhhhh.............eeeee......hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh...........eeeee.....ee..hhhhh....eee....eeeee.hhhhh......eee....hhhhhh....eeee....eeeeeeee....eeeeeee.eee....eee...........hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhh......eeeee.hhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeeee.......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x1w A  14 QTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEASFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP 531
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523        

Chain B from PDB  Type:PROTEIN  Length:501
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..hhhhhhhh.............eeeee......hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhh.........eeeee.....ee.........eeeee.....ee....hhhhhh....eeee....eeeeeeee....eeeee..........eee...........hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhh.....eeeee.hhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeeee.......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x1w B  14 QTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLILKKGATLKITLDNAILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEASFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP 531
                                    23        33        43        53        63        73        83        93       103       113       123||     142    || 160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530 
                                                                                                                                        124|          147|                                                                                                                                                                                                                                                                                                                                                                                       
                                                                                                                                         134           156                                                                                                                                                                                                                                                                                                                                                                                       

Chain C from PDB  Type:PROTEIN  Length:518
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..hhhhhhhh.............eeeee.hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhh.......eeeee..................eee....eeeee.hhhhh......eee....hhhhhh....eeee....eeeeeeee...eeeeeeee.eee.....ee...........hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhh......eeeee.hhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeeee.......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x1w C  14 QTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEASFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP 531
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523        

Chain D from PDB  Type:PROTEIN  Length:511
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..hhhhhhhh.............eeeee......hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhh.........eeeee...........ee.....eeeee.hhhhh......eee....hhhhhh....eeee....eeeeeeee...eeeeee....ee.....ee...........hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhh......eeeee.hhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeeee.......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x1w D  14 QTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEASFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP 531
                                    23        33        43        53        63        73        83        93       103       113       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530 
                                                                                                                                      122|                                                                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                       130                                                                                                                                                                                                                                                                                                                                                                                                                 

   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5X1W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5X1W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5X1W)

(-) Gene Ontology  (40, 40)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        KPYM_HUMAN | P146181t5a 1zjh 3bjf 3bjt 3g2g 3gqy 3gr4 3h6o 3me3 3srd 3srf 3srh 3u2z 4b2d 4fxf 4fxj 4g1n 4jpg 4qg6 4qg8 4qg9 4qgc 4rpp 4wj8 4yj5 5x1v

(-) Related Entries Specified in the PDB File

5x1v