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(-) Description

Title :  BRUTON'S TYROSINE KINASE IN COMPLEX WITH A T-BUTYL CYANOACRYLAMIDE INHIBITOR
 
Authors :  V. O. Paavilainen, J. M. Mcfarland, J. Taunton
Date :  27 Feb 15  (Deposition) - 13 May 15  (Release) - 01 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Covalent Inhibitor, Cyanoacrylamide, Cysteine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. M. Bradshaw, J. M. Mcfarland, V. O. Paavilainen, A. Bisconte, D. Tam V. T. Phan, S. Romanov, D. Finkle, J. Shu, V. Patel, T. Ton, X. Li, D. G. Loughhead, P. A. Nunn, D. E. Karr, M. E. Gerritsen, J. O. Funk, T. D. Owens, E. Verner, K. A. Brameld, R. J. Hill, D. M. Goldstein, J. Taunton
Prolonged And Tunable Residence Time Using Reversible Covalent Kinase Inhibitors.
Nat. Chem. Biol. V. 11 525 2015
PubMed-ID: 26006010  |  Reference-DOI: 10.1038/NCHEMBIO.1817

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE BTK
    ChainsA, B
    EC Number2.7.10.2
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF21
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPFASTBAC
    Expression System Taxid7108
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 382-659
    GeneBTK, AGMX1, ATK, BPK
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAGAMMAGLOBULINEMIA TYROSINE KINASE,ATK,B-CELL PROGENITOR KINASE,BPK,BRUTON TYROSINE KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 44)

Asymmetric Unit (5, 44)
No.NameCountTypeFull Name
14C92Ligand/Ion(2S)-2-({(3R)-3-[4-AMINO-3-(4-PHENOXYPHENYL)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-1-YL]PIPERIDIN-1-YL}CARBONYL)-4,4-DIMETHYLPENTANENITRILE
2CL7Ligand/IonCHLORIDE ION
3EDO8Ligand/Ion1,2-ETHANEDIOL
4NA24Ligand/IonSODIUM ION
5SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
14C91Ligand/Ion(2S)-2-({(3R)-3-[4-AMINO-3-(4-PHENOXYPHENYL)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-1-YL]PIPERIDIN-1-YL}CARBONYL)-4,4-DIMETHYLPENTANENITRILE
2CL-1Ligand/IonCHLORIDE ION
3EDO2Ligand/Ion1,2-ETHANEDIOL
4NA-1Ligand/IonSODIUM ION
5SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
14C91Ligand/Ion(2S)-2-({(3R)-3-[4-AMINO-3-(4-PHENOXYPHENYL)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-1-YL]PIPERIDIN-1-YL}CARBONYL)-4,4-DIMETHYLPENTANENITRILE
2CL-1Ligand/IonCHLORIDE ION
3EDO6Ligand/Ion1,2-ETHANEDIOL
4NA-1Ligand/IonSODIUM ION
5SO41Ligand/IonSULFATE ION

(-) Sites  (43, 43)

Asymmetric Unit (43, 43)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:408 , VAL A:416 , ALA A:428 , LYS A:430 , MET A:449 , VAL A:458 , LEU A:460 , ILE A:472 , THR A:474 , GLU A:475 , MET A:477 , GLY A:480 , CYS A:481 , ASN A:484 , SER A:538 , ASP A:539 , PHE A:540 , LEU A:542 , HOH A:905 , HOH A:907 , HOH A:935binding site for residue 4C9 A 701
02AC2SOFTWARESER A:623 , GLU A:624 , CL A:714binding site for residue NA A 702
03AC3SOFTWAREGLN A:497 , GLU A:500 , HOH A:813 , HOH A:861binding site for residue NA A 703
04AC4SOFTWAREARG A:618binding site for residue NA A 704
05AC5SOFTWAREMET A:570 , CL A:715 , HOH A:814binding site for residue NA A 705
06AC6SOFTWAREHIS A:454 , GLU A:455 , HOH A:926binding site for residue NA A 706
07AC7SOFTWAREGLU A:567 , LYS A:573 , SER A:575 , HOH A:892binding site for residue NA A 708
08AC8SOFTWAREARG A:520 , SER A:543 , CL A:716binding site for residue NA A 709
09AC9SOFTWAREARG A:520 , ASP A:521 , TRP A:563 , SER A:564 , PHE A:574 , HOH A:854 , HOH A:860 , HOH A:931binding site for residue EDO A 710
10AD1SOFTWARETHR A:495 , GLN A:496 , TYR A:591 , VAL A:626 , GLU A:658 , HOH A:865binding site for residue EDO A 711
11AD2SOFTWARETYR A:598 , GLU A:599 , ARG A:600 , TYR A:617 , HOH A:852binding site for residue SO4 A 712
12AD3SOFTWAREHIS A:635 , GLU A:636 , HOH A:801 , HOH A:913 , HOH A:947binding site for residue SO4 A 713
13AD4SOFTWARESER A:623 , GLU A:624 , LYS A:625 , NA A:702binding site for residue CL A 714
14AD5SOFTWAREHIS A:491 , GLN A:497 , MET A:570 , NA A:705binding site for residue CL A 715
15AD6SOFTWAREARG A:520 , SER A:543 , PHE A:574 , NA A:709binding site for residue CL A 716
16AD7SOFTWARETYR B:598 , GLU B:599 , ARG B:600 , CL B:724binding site for residue NA A 717
17AD8SOFTWAREHIS A:620binding site for residue NA B 701
18AD9SOFTWAREMET A:489 , ARG A:492 , GLU B:407binding site for residue NA B 702
19AE1SOFTWARELEU B:483 , CL B:726 , CL B:727binding site for residue NA B 704
20AE2SOFTWARESER B:623 , VAL B:654binding site for residue NA B 705
21AE3SOFTWARESER B:623 , GLU B:624 , HOH B:990binding site for residue NA B 706
22AE4SOFTWARELYS B:595 , SO4 B:723 , HOH B:819binding site for residue NA B 707
23AE5SOFTWAREHOH B:826binding site for residue NA B 708
24AE6SOFTWAREMET B:501 , GLY B:533 , HOH B:891 , HOH B:940binding site for residue NA B 709
25AE7SOFTWARETYR B:591 , LEU B:621 , ALA B:622 , SER B:623 , CL B:725 , HOH B:854binding site for residue NA B 710
26AE8SOFTWARELEU B:614 , ARG B:615 , HOH B:801binding site for residue NA B 711
27AE9SOFTWAREHOH B:843 , HOH B:933binding site for residue NA B 712
28AF1SOFTWAREPRO B:399 , GLN B:467 , HOH B:932binding site for residue NA B 713
29AF2SOFTWARETYR B:545 , HOH B:880binding site for residue NA B 714
30AF3SOFTWAREASN B:603binding site for residue NA B 715
31AF4SOFTWAREGLU B:396 , THR B:465 , LYS B:466 , HOH B:919binding site for residue NA B 716
32AF5SOFTWAREARG B:520 , ASP B:521 , TRP B:563 , SER B:564 , PHE B:574 , SER B:578 , HOH B:848 , HOH B:867binding site for residue EDO B 717
33AF6SOFTWARETYR B:476binding site for residue EDO B 718
34AF7SOFTWARESER B:575 , SER B:576binding site for residue EDO B 719
35AF8SOFTWAREALA B:611 , GLY B:613 , HOH B:812 , HOH B:890 , HOH B:946binding site for residue EDO B 720
36AF9SOFTWARETRP B:588 , MET B:596 , PRO B:597 , TYR B:598 , GLU B:599 , LEU B:616 , TYR B:617 , CL B:724binding site for residue EDO B 721
37AG1SOFTWAREGLU B:445 , PHE B:517 , LEU B:518 , ARG B:520binding site for residue EDO B 722
38AG2SOFTWARELYS B:595 , TYR B:617 , PRO B:619 , HIS B:620 , NA B:707 , HOH B:852binding site for residue SO4 B 723
39AG3SOFTWARENA A:717 , TYR B:598 , EDO B:721 , HOH B:820binding site for residue CL B 724
40AG4SOFTWARENA B:710binding site for residue CL B 725
41AG5SOFTWAREARG B:487 , NA B:704binding site for residue CL B 726
42AG6SOFTWARELEU B:483 , ARG B:525 , TRP B:563 , NA B:704 , HOH B:872binding site for residue CL B 727
43AG7SOFTWARELEU B:408 , VAL B:416 , ALA B:428 , LYS B:430 , MET B:449 , ILE B:472 , THR B:474 , GLU B:475 , MET B:477 , GLY B:480 , LEU B:482 , LEU B:483 , ASN B:484 , TYR B:485 , ARG B:525 , CYS B:527 , SER B:538 , ASP B:539 , PHE B:540 , HOH B:859 , HOH B:863 , HOH B:873binding site for Di-peptide 4C9 B 703 and CYS B 481

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YHF)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:468 -Pro A:469
2Arg B:468 -Pro B:469

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YHF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YHF)

(-) Exons   (0, 0)

(no "Exon" information available for 4YHF)

(-) Sequences/Alignments

Asymmetric 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:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhh.eeeeeeeee...eeeeeeee...eeeeeeee.....hhhhhhhhhhhhhh........eeeee......eeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee...hhhhhh.hhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhh...........hhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yhf A 391 GYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEE 658
                                   400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650        

Chain B from PDB  Type:PROTEIN  Length:269
                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhh.eeeeeeeeee..eeeeeeee...eeeeeeee.....hhhhhhhhhhhhhhh.......eeeee.....eeeeee.....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhhhhee.....ee...........hhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yhf B 390 LGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEE 658
                                   399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649         

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4YHF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YHF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YHF)

(-) Gene Ontology  (49, 49)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        BTK_HUMAN | Q061871aww 1awx 1b55 1btk 1bwn 1k2p 1qly 2ge9 2z0p 3gen 3k54 3ocs 3oct 3p08 3pix 3piy 3piz 3pj1 3pj2 3pj3 4nwm 4ot5 4ot6 4otf 4otq 4otr 4rfy 4rfz 4rg0 4rx5 4z3v 4zly 4zlz 5bpy 5bq0 5fbn 5fbo 5j87 5jrs 5kup 5p9f 5p9g 5p9h 5p9i 5p9j 5p9k 5p9l 5p9m 5t18 5u9d 5vgo

(-) Related Entries Specified in the PDB File

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