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(-) Description

Title :  STRUCTURE OF PIM-1 KINASE BOUND TO N-(5-(2-FLUOROPHENYL)-1H-PYRROLO[2, 3-B]PYRIDIN-3-YL)-5-((((3R,4R)-3-FLUOROPIPERIDIN-4-YL)METHYL)AMINO) PYRAZOLO[1,5-A]PYRIMIDINE-3-CARBOXAMIDE
 
Authors :  J. M. Murray, H. Wallweber, M. Steffek
Date :  04 Apr 13  (Deposition) - 15 May 13  (Release) - 22 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym./Biol. Unit :  A
Keywords :  Pim-1, Kinase Domain, Ser/Thr Kinase, Atp-Competitive, Structure- Based Drug Design, Phosphorylation, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Wang, S. Magnuson, R. Pastor, E. Fan, H. Hu, V. Tsui, W. Deng, J. Murray, M. Steffek, H. Wallweber, J. Moffat, J. Drummond, G. Chan, E. Harstad, A. J. Ebens
Discovery Of Novel Pyrazolo[1, 5-A]Pyrimidines As Potent Pan-Pim Inhibitors By Structure- And Property-Based Drug Design.
Bioorg. Med. Chem. Lett. V. 23 3149 2013
PubMed-ID: 23623490  |  Reference-DOI: 10.1016/J.BMCL.2013.04.020

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE PIM-1
    Chains: A
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: KINASE DOMAIN (UNP RESIDUES 124-396)
    Gene: PIM-1, PIM1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PIM-1 KINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
11OC1Ligand/IonN-[5-(2-FLUOROPHENYL)-1H-PYRROLO[2,3-B]PYRIDIN-3-YL]-5-({[(3R,4R)-3-FLUOROPIPERIDIN-4-YL]METHYL}AMINO)PYRAZOLO[1,5-A]PYRIMIDINE-3-CARBOXAMIDE
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:156 , ARG A:258 , SER A:261 , PHE A:281 , HOH A:509 , HOH A:579 , HOH A:600BINDING SITE FOR RESIDUE PO4 A 401
2AC2SOFTWARELEU A:44 , VAL A:52 , ALA A:65 , LYS A:67 , LEU A:120 , GLU A:121 , ARG A:122 , VAL A:126 , ASP A:128 , GLU A:171 , LEU A:174 , ILE A:185 , ASP A:186 , HOH A:520 , HOH A:548 , HOH A:592BINDING SITE FOR RESIDUE 1OC A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K1B)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro A:33 -Leu A:34
2Asp A:60 -Asn A:61
3Glu A:124 -Pro A:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K1B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K1B)

(-) Exons   (0, 0)

(no "Exon" information available for 4K1B)

(-) 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:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4k1ba_ A: Proto-oncogene serine/threonine-protein kinase Pim-1                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee....eeeeeee.....eeeeeeee.hhh..eee.....eeehhhhhhhhhh........eeeeee...eeeeeee....eeehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee....eeee......ee...........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhh........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k1b A  33 PLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLH 305
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K1B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K1B)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:60 - Asn A:61   [ RasMol ]  
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    Pro A:33 - Leu A:34   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        PIM1_HUMAN | P11309: 1xqz 1xr1 1xws 1yhs 1yi3 1yi4 1ywv 1yxs 1yxt 1yxu 1yxv 1yxx 2bik 2bil 2bzh 2bzi 2bzj 2bzk 2c3i 2j2i 2o3p 2o63 2o64 2o65 2obj 2oi4 2xix 2xiy 2xiz 2xj0 2xj1 2xj2 3a99 3bgp 3bgq 3bgz 3bwf 3c4e 3cxw 3cy2 3cy3 3dcv 3f2a 3jpv 3jxw 3jy0 3jya 3ma3 3qf9 3r00 3r01 3r02 3r04 3t9i 3uix 3umw 3umx 3vbq 3vbt 3vbv 3vbw 3vbx 3vby 3vc4 3we8 4a7c 4alu 4alv 4alw 4as0 4bzn 4bzo 4dtk 4enx 4eny 4gw8 4i41 4iaa 4jx3 4jx7 4k0y 4k18 4ll5 4lm5 4lmu 4mbi 4mbl 4med 4mta 4n6y 4n6z 4n70 4rbl 4rc2 4rc3 4rc4 4rpv 4ty1 4wrs 4wsy 4wt6 4xh6 4xhk 5c1q 5dgz 5dhj 5dia 5dwr 5eol 5iis 5ipj 5kzi 5v82

(-) Related Entries Specified in the PDB File

4k0y 4k18