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(-) Description

Title :  MPI3KD IN COMPLEX WITH INH1
 
Authors :  J. Petersen
Date :  06 Mar 17  (Deposition) - 21 Jun 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  A
Keywords :  Mi3Kd, Inhibitor, Complex Pi3K, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. W. D. Perry, K. Bjorhall, B. Bonn, J. Carlsson, Y. Chen, A. Eriksson, L. Fredlund, H. Hao, N. S. Holden, K. Karabelas, H. Lindmark, F. Liu, N. Pemberton, J. Petersen, S. Rodrigo Blomqvist, R. W. Smith, T. Svensson, I. Terstiege, C. Tyrchan, W. Yang, S. Zhao, L. Oster
Design And Synthesis Of Soluble And Cell-Permeable Pi3K Delta Inhibitors For Long-Acting Inhaled Administration.
J. Med. Chem. V. 60 5057 2017
PubMed-ID: 28520415  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.7B00401

(-) 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: INSECT CELL EXPRESSION VECTOR PTIE1
    Expression System Taxid: 266783
    Gene: PIK3CD
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: PTDINS-3-KINASE SUBUNIT DELTA,PHOSPHATIDYLINOSITOL 4,5- BISPHOSPHATE 3-KINASE 110 KDA CATALYTIC SUBUNIT DELTA,P110DELTA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
18TN1Ligand/Ion4-AZANYL-6-[[(1~{S})-1-[6-[3-[(DIMETHYLAMINO)METHYL]PHENYL]-3-METHYL-5-OXIDANYLIDENE-[1,3]THIAZOLO[3,2-A]PYRIDIN-7-YL]ETHYL]AMINO]PYRIMIDINE-5-CARBONITRILE
2EDO4Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:787 , TYR A:813 , ASP A:911 , PHE A:912 , 8TN A:1105binding site for residue EDO A 1101
2AC2SOFTWARELYS A:779 , ASP A:911 , 8TN A:1105binding site for residue EDO A 1102
3AC3SOFTWAREPRO A:168 , GLN A:170 , ASP A:605 , PHE A:609 , ASN A:640 , LYS A:642 , HOH A:1223binding site for residue EDO A 1103
4AC4SOFTWARELEU A:120 , TRP A:649 , ARG A:652 , GLY A:686 , HOH A:1210 , HOH A:1251 , HOH A:1259binding site for residue EDO A 1104
5AC5SOFTWAREPHE A:751 , MET A:752 , PRO A:758 , TRP A:760 , ILE A:777 , TYR A:813 , ILE A:825 , GLU A:826 , VAL A:827 , VAL A:828 , SER A:831 , ASP A:832 , MET A:900 , ILE A:910 , EDO A:1101 , EDO A:1102 , HOH A:1391binding site for residue 8TN A 1105

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:434 -Gly A:435

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5NCZ)

(-) 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:827
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh........eeeeeeee.....eeeeeee...hhhhhhhhhhhhhhhhh..hhh.eeeee.....ee....hhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhh........eeeeeeee.......eeeeeeeeee..ee....ee...ee...eeeeeeeeeee.hhh....eeeeeeeee..eeeeeeeee..........eeeeee.ee....................eeeeee.........hhhhhhhhhh..hhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.eee..eeeeee.ee.hhhhee.......eeeeeee...eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh..........eeeee..eeeee....eeehhhhhh..........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.....hhh.eeee....eee................hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ncz A  109 VKKLINSQISLLIGKGLHEFDSLRDPEVNDFRTKMRQFCEEAAAHRQQLGWVEWLQYSFPLQLEPNRALLVNVKFEGSEESFTFQVSTKDMPLALMACALRKKATVFRQQPEEYALQVNGRHEYLYGNYPLCHFQYICSCLHSGLTPHLTMVHSSSILAMRDEQSNLWSLEQPFSIELIEGRKVNAMKLVVQAGLFHGNEMLCKTVSSSEVNVEPVWKQRLEFDISVCDLPRMARLCFALYAVVDCPIAWANLMLFDYKDQLKTGERCLYMWPSVLLNPAGTVRGNPNTESAAALVIYLPEVAPVYFPALEKILELGRITEEELREILERELYEHEKDLVWKMRHEVQEHFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCYVGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLGRALANRKIGHFLFWHLRSEMHVPSVALRFGLIMEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKVSSQKTTKPQTKEMMHMCMRQETYMEALSHLQSPLDPSTLLEEVCVEQCTFMDSKMKPLWIMYSSEEAGSAGNVGIIFKNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLHSDTIANIQLNKSNMAATAAFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHIDFGHFLGNFRVPFILTYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFNEALRESW 1027
                                   118       128       138       148       158       168    || 191       201       211       221       235       245       255       265       275       285     ||319       329     ||342       352       362  ||   374       384       394   ||  420       430       440    || 456       466       476  ||   488       507       517|      531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       930       940       950       960       970       980       990      1000      1010      1020       
                                                                                          173|                                        230|                                                     291|                335|                       365|                           398|                           445|                        479|            497|       517|                                                                                                                                                                                                                                                                                                                                                                                                          919|                                                                                                  
                                                                                           187                                         235                                                      316                 339                        368                            415                            452                         482             507        522                                                                                                                                                                                                                                                                                                                                                                                                           929
   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 5NCZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Thr A:434 - Gly A:435   [ RasMol ]  
 

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

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