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(-) Description

Title :  WATER NETWORK DETERMINES SELECTIVITY FOR A SERIES OF PYRIMIDONE INDOLINE AMIDE PI3KBETA INHIBITORS OVER PI3K-DELTA
 
Authors :  D. Robinson, T. Bertrand, J. C. Carry, F. Halley, A. Karlsson, M. Mathie H. Minoux, M. A. Perrin, B. Robert, L. Schio, W. Sherman
Date :  16 Sep 14  (Deposition) - 30 Sep 15  (Release) - 05 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.54
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Pi3K, Kinase Selectivity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Robinson, T. Bertrand, J. Carry, F. Halley, A. Karlsson, M. Mathieu H. Minoux, M. Perrin, B. Robert, L. Schio, W. Sherman
Differential Water Thermodynamics Determine Pi3K-Beta/Delta Selectivity For Solvent-Exposed Ligand Modifications.
J. Chem. Inf. Model. V. 56 886 2016
PubMed-ID: 27144736  |  Reference-DOI: 10.1021/ACS.JCIM.5B00641

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT DELTA ISOFORM
    Chains: A, B
    EC Number: 2.7.1.153
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF21
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PACSG2
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: CATALYTIC SUBUNIT DELTA ISOFORM, RESIDUES 106-1043
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: PI3-KINASE SUBUNIT DELTA, PI3K-DELTA, PI3KDELTA, PTDINS-3-KINASE SUBUNIT DELTA, PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE 110 KDA CATALYTIC SUBUNIT DELTA, PTDINS-3-KINAS SUBUNIT P110-DELTA, P110DELTA

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1J822Ligand/Ion2-[2-(2-METHYL-2,3-DIHYDRO-INDOL-1-YL)-2-OXO-ETHYL]-6-MORPHOLIN-4-YL-3H-PYRIMIDIN-4-ONE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1J821Ligand/Ion2-[2-(2-METHYL-2,3-DIHYDRO-INDOL-1-YL)-2-OXO-ETHYL]-6-MORPHOLIN-4-YL-3H-PYRIMIDIN-4-ONE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1J821Ligand/Ion2-[2-(2-METHYL-2,3-DIHYDRO-INDOL-1-YL)-2-OXO-ETHYL]-6-MORPHOLIN-4-YL-3H-PYRIMIDIN-4-ONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:751 , MET A:752 , PRO A:758 , TRP A:760 , ILE A:777 , LYS A:779 , TYR A:813 , GLU A:826 , VAL A:827 , VAL A:828 , MET A:900 , ILE A:910 , ASP A:911 , HOH A:2054BINDING SITE FOR RESIDUE J82 A1500
2AC2SOFTWAREPHE B:751 , MET B:752 , PRO B:758 , TRP B:760 , ILE B:777 , LYS B:779 , ILE B:825 , GLU B:826 , VAL B:827 , VAL B:828 , MET B:900 , ILE B:910 , ASP B:911BINDING SITE FOR RESIDUE J82 B1500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4V0I)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ser A:186 -Asn A:187
2Thr A:434 -Gly A:435
3Thr B:434 -Gly B:435

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4V0I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4V0I)

(-) Exons   (0, 0)

(no "Exon" information available for 4V0I)

(-) 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:759
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..........eeeeeeee.....eeeeeee...hhhhhhhhhhhhhhhhhhh.eeeee.....ee....hhhhhhhhhhhhh.....eeeeeehhhhhhhhhhh.......ee..eeeeee..ee...............eeeeeee...eeeeeeee...........eee...ee.....................eee..........hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhh......hhhhhhhhhhh....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee..eeeeee.ee.hhhhee.......eeeeeee...eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhh...........eeeee..eeeee....eeehhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh........eeee....eee............hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4v0i A  110 KKLINSQISLLIGKGLHEFDSLRDPEVNDFRTKMRQFCEEAAAHRQQLGWVEWLQYSFPLQLEPVSNRALLVNVKFEGSEESFTFQVSTKDMPLALMACALRKKATVQPEEYALQVNGRHEYLYGNYPLCHFQYICSCLHSGLTPHLTMVHSSSILAMRDEQSNQPFSIELIVQAGLFHGNEMLCKTDISVCDLPRMARLCFALYADCPIAWANLMLFDYKDQLKTGERCLYMWPSLLNPAGTVRGNPNTESAAALVIYLPEVAPVYFPALEKILELEHEKDLVWKMRHEVQEHFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCYVGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLGRALANRKIGHFLFWHLRSEMHVPSVALRFGLIMEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKVSSQKTTKPQTKEMMHMCMRQETYMEALSHLQSPLDPSTLLEEVCVEQCTFMDSKMKPLWIMYSSEEAGSAGNVGIIFKNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLHSDTIANIQLTAAFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHIDFGHFLGPFILTYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFNEALRES 1026
                                   119       129       139       149       159       169   ||  190       200       210       220      |237       247       257       267       277       287   ||  326 ||    350      |380       390     ||418       428       438     ||455       465       475   ||  487      |527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837 ||    854       864       874       884       894       904       914  ||   937       947       957       967       977       987       997      1007      1017         
                                                                                         173|                                       227|                                                     291|    328|           357|               396|                          444|                        479|         494|                                                                                                                                                                                                                                                                                                                       839|                                                                   917|                                                                                               
                                                                                          185                                        235                                                      321     343            378                415                           452                         482          525                                                                                                                                                                                                                                                                                                                        847                                                                    931                                                                                               


Chain B from PDB  Type:PROTEIN  Length:792
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..............eeeeee.....eeeee.....hhhhhhhhhhhhhhhhhhh.eeeee.....ee....hhhhhhhhhhhhh.....eeeeeehhhhhhhhhhh....eeeeeeeee......eeeeeeeeee..ee....ee...ee.....eeeeeeeeeee........eeeeeee...eeeeeeee...........eee...ee....................eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhh......hhhhhhhhhhh....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..eeeeee.ee.hhhhee.......eeeeeee...eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhh...........eeeee..eeeee....eeehhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh........eeee....eee............hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4v0i B  111 KLINSQISLLIGKGLHEFDSLRDPEVNDFRTKMRQFCEEAAAHRQQLGWVEWLQYSFPLQLEPSAVSNRALLVNVKFEGSEESFTFQVSTKDMPLALMACALRKKATVQPEEYALQVNGRHEYLYGNYPLCHFQYICSCLHSGLTPHLTMVHSSSILAMRDEQSNEQPFSIELIEGRKVNAMKLVVQAGLFHGNEMLCKTVSSSEVNVCSEPVWKQRLEFDISVCDLPRMARLCFALYADCPIAWANLMLFDYKDQLKTGERCLYMWPSLLNPAGTVRGNPNTESAAALVIYLPEVAPVYFPALEKILELEHEKDLVWKMRHEVQEHFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCYVGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLGRALANRKIGHFLFWHLRSEMHVPSVALRFGLIMEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKVSSQKTTKPQTKEMMHMCMRQETYMEALSHLQSPLDPSTLLEEVCVEQCTFMDSKMKPLWIMYSSEEAGSAGNVGIIFKNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLHSDTIANIQLTAAFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHIDFGHFLGPFILTYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFNEALRES 1026
                                   120       130       140       150       160       170    || 189       199       209       219       236       246       256       266       276       286    || 324       334||     347       357       367       377       387       415       425       435       452       462       472      |484       494|      534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834    || 851       861       871       881       891       901       911     ||934       944       954       964       974       984       994      1004      1014      1024  
                                                                                          175|                                       227|                                                     291|            335|                                                      396|                          444|                        479|         494|                                                                                                                                                                                                                                                                                                                       839|                                                                   917|                                                                                               
                                                                                           185                                        235                                                      320             339                                                       415                           452                         482          525                                                                                                                                                                                                                                                                                                                        847                                                                    931
   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 4V0I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4V0I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4V0I)

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)

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  4v0i
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UniProtKB/Swiss-Prot
        PK3CD_MOUSE | O35904: 2wxf 2wxg 2wxh 2wxi 2wxj 2wxk 2wxl 2wxm 2wxn 2wxo 2wxp 2wxq 2wxr 2x38 4ajw 4xe0 5ae8 5ae9 5i4u 5i6u 5is5 5l72 5ncy 5ncz 5t27 5t28 5t2b 5t2d 5t2g 5t2i 5t2l 5t2m 5t7f 5t8i

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