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(-) Description

Title :  CRYSTAL STRUCTURE OF PI3K DELTA IN COMPLEX WITH A TRIFLUORO-ETHYL-PYRAZOL-PYROLOTRIAZINE INHIBITOR
 
Authors :  J. S. Sack
Date :  26 Apr 17  (Deposition) - 07 Jun 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Lipid Kinase, Inhibitor, Pi3K Delta, Transferase-Transferase Inhibitor Complex, Transferase-Transferase Regulator Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Liu, Q. Shi, D. Marcoux, D. G. Batt, L. Cornelius, L. Y. Qin, Z. Ruan, J. Neels, M. Beaudoin-Bertrand, A. S. Srivastava, L. Li, R. J. Cherney H. Gong, S. H. Watterson, C. Weigelt, K. M. Gillooly, K. W. Mcintyre, J. H. Xie, M. T. Obermeier, A. Fura, B. Sleczka, K. Stefanski, R. M. Fancher, S. Padmanabhan, T. Rp, I. Kundu, K. Rajareddy, R. Smith, J. K. Hennan, D. Xing, J. Fan, P. C. Levesque, Q. Ruan, S. Pitt, R. Zhang, D. Pedicord, J. Pan, M. Yarde, H. Lu, J. Lippy, C. Goldstine, S. Skala, R. A. Rampulla, A. Mathur, A. Gupta, P. N. Arunachalam, J. S. Sack, J. K. Muckelbauer, M. E. Cvijic, L. M. Salter-Cid, R. S. Bhide, M. A. Poss, J. Hynes, P. H. Carter, J. E. Macor, S. Ruepp, G. L. Schieven, J. A. Tino
Identification Of A Potent, Selective, And Efficacious Phosphatidylinositol 3-Kinase Delta (Pi3K Delta ) Inhibitor For The Treatment Of Immunological Disorders.
J. Med. Chem. V. 60 5193 2017
PubMed-ID: 28541707  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.7B00618

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT DELTA ISOFORM
    Chains: A
    EC Number: 2.7.1.153
    Engineered: YES
    Expression System: UNIDENTIFIED BACULOVIRUS
    Expression System Taxid: 10469
    Gene: PIK3CD
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PTDINS-3-KINASE SUBUNIT DELTA,PHOSPHATIDYLINOSITOL 4,5- BISPHOSPHATE 3-KINASE 110 KDA CATALYTIC SUBUNIT DELTA,P110DELTA
 
Molecule 2 - PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT ALPHA
    Chains: B
    Engineered: YES
    Expression System: UNIDENTIFIED BACULOVIRUS
    Expression System Taxid: 10469
    Gene: PIK3R1, GRB1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PTDINS-3-KINASE REGULATORY SUBUNIT ALPHA, PHOSPHATIDYLINOSITOL 3-KINASE 85 KDA REGULATORY SUBUNIT ALPHA,PTDINS- 3-KINASE REGULATORY SUBUNIT P85-ALPHA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
19EM1Ligand/Ion4-ACETYL-1-(3-{4-AMINO-5-[1-(2,2,2-TRIFLUOROETHYL)-1H-PYRAZOL-5-YL]PYRROLO[2,1-F][1,2,4]TRIAZIN-7-YL}PHENYL)-3,3-DIMETHYLPIPERAZIN-2-ONE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
19EM1Ligand/Ion4-ACETYL-1-(3-{4-AMINO-5-[1-(2,2,2-TRIFLUOROETHYL)-1H-PYRAZOL-5-YL]PYRROLO[2,1-F][1,2,4]TRIAZIN-7-YL}PHENYL)-3,3-DIMETHYLPIPERAZIN-2-ONE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
19EM-1Ligand/Ion4-ACETYL-1-(3-{4-AMINO-5-[1-(2,2,2-TRIFLUOROETHYL)-1H-PYRAZOL-5-YL]PYRROLO[2,1-F][1,2,4]TRIAZIN-7-YL}PHENYL)-3,3-DIMETHYLPIPERAZIN-2-ONE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
19EM1Ligand/Ion4-ACETYL-1-(3-{4-AMINO-5-[1-(2,2,2-TRIFLUOROETHYL)-1H-PYRAZOL-5-YL]PYRROLO[2,1-F][1,2,4]TRIAZIN-7-YL}PHENYL)-3,3-DIMETHYLPIPERAZIN-2-ONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:750 , PHE A:751 , MET A:752 , PRO A:758 , TRP A:760 , ILE A:777 , LYS A:779 , TYR A:813 , ILE A:825 , GLU A:826 , VAL A:828 , THR A:833 , MET A:900 , ILE A:910 , ASP A:911binding site for residue 9EM A 4001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VLR)

(-) 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:926
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....eeeeeee...hhhhhhhhhhhhhh...hhhhh.hhh.eeeeee.....eeee.....hhhhhh....eeeeee.....hhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeeee........eeeeee...hhhhhhhhhhhhhhh...eee......ee....hhhhhhhhhhhhhhh......eehhhhhhhhhh......eeeeeeeeee........eeeeeeeeee..ee.........ee.....eeeeeeeeeee.hhh....eeeeeeeee.......eeeeeeeee..........eeeeee.ee..........................eeeeee...........hhhhhhhhhh..hhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..ee.......ee.ee.....ee.......eeeeee.....eeeeeee...hhhhhhhhhhhhhhhhhhhhh..........eeeee..eeeee....eeehhhhh.....hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.........eeee....eee....................hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vlr A   17 NQSVVVDFLLPTGVYLNFPVSRNANLSTIKQLLWHRAQYEPLFHMLSGPEAYVFTCINQTAEQQELEDEQRRLCDVQPFLPVLRLVAREGDRVKKLINSQISLLIGKGLHEFDSLCDPEVNDFRAKMCQFCEEAAARRQQLGWEAWLQYSFPLQLEPSLPNRALLVNVKFEGSEESFTFQVSTKDVPLALMACALRKKATEDYTLQVNGRHEYLYGSYPLCQFQYICSCLHSGLTPHLTMVHSSSILAMRDLWSLEQPFRIELIQGSKVNADERMKLVVQAGLFHGNEMLCKTVSSSEVSVCSEPVWKQRLEFDINICDLPRMARLCFALYAVIEKAKADCPIAWANLMLFDYKDQLKTGERCLYMWPSVPDEKGELLNPTGTVRSNPNTDSAAALLICLPEVAPHPVYYPALEKILELGRHTEEEQLQLREILEGELYEHEKDLVWKLRHEVQEHFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCHVGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLDRALANRKIGHFLFWHLRSEMHVPSVALRFGLILEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKLSSQKTPKPQTKELMHLCMRQEAYLEALSHLQSPLDPSTLLAEVCVEQCTFMDSKMKPLWIMYSNEEASVGIIFKNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLRSDTIANIQLNFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHIDFGHFLGNFINRERVPFILTYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFNEALRESWKT 1029
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       186       196       206       216       226|      246       256       266       276       286||     324       334       344       354       364       374       384       394      |415       425       435       445       455       465       475       485       495 ||    511    || 525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765  ||   779       789       799       809       819       829       839||     858       868       878       888       898       908       918||     933       943       953       963       973       983       993      1003      1013      1023      
                                                                                                                                                                                       174|                                      226|                                               287|                                                                                  401|                                                                                 497|         516|                                                                                                                                                                                                                                                    768|                                                                840|                                                                  919|                                                                                                        
                                                                                                                                                                                        185                                       237                                                316                                                                                   413                                                                                  504          521                                                                                                                                                                                                                                                     773                                                                 850                                                                   925                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vlr B  431 YQQDQVVKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEDYTRTSQEIQMKRTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNETEIQRIMHNYEKLKSRISEIVDSRRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQKKLNEWLGN  600
                                   440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600
   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 5VLR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (106, 123)

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  5vlr
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  P85A_HUMAN | P27986
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  PK3CD_HUMAN | O00329
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  2.7.1.153
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 Related Entries

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

UniProtKB/Swiss-Prot
        P85A_HUMAN | P27986: 1a0n 1azg 1h9o 1pbw 1pht 1pic 1pks 1pkt 2iug 2iuh 2iui 2rd0 2v1y 3hhm 3hiz 3i5r 3i5s 4a55 4jps 4l1b 4l23 4l2y 4ovu 4ovv 4waf 4ykn 4zop 5aul 5fi4 5gji 5itd 5m6u 5sw8 5swg 5swo 5swp 5swr 5swt 5sx8 5sx9 5sxa 5sxb 5sxc 5sxd 5sxe 5sxf 5sxi 5sxj 5sxk 5ubt 5uk8 5ukj 5ul1
        PK3CD_HUMAN | O00329: 5dxu 5m6u 5t8f 5ubt

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5VLR)