Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF PIM-1 KINASE BOUND TO 5-(4-CYANOBENZYL)-N-(4-FLUOROPHENYL)-7-HYDROXYPYRAZOLO[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 :  2.05
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 123-399)
    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
11OB1Ligand/Ion5-(4-CYANOBENZYL)-N-(4-FLUOROPHENYL)-7-HYDROXYPYRAZOLO[1,5-A]PYRIMIDINE-3-CARBOXAMIDE
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:156 , ARG A:221 , ARG A:258 , SER A:261 , PHE A:281 , HOH A:510 , HOH A:517 , HOH A:536BINDING SITE FOR RESIDUE PO4 A 401
2AC2SOFTWAREGLY A:45 , PHE A:49 , VAL A:52 , LYS A:67 , LEU A:120 , GLU A:121 , ARG A:122 , PRO A:123 , ASP A:128 , LEU A:174 , ILE A:185 , ASP A:186 , HOH A:554BINDING SITE FOR RESIDUE 1OB A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K18)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:124 -Pro A:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K18)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K18)

(-) Exons   (0, 0)

(no "Exon" information available for 4K18)

(-) 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:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4k18a_ A: Proto-oncogene serine/threonine-protein kinase Pim-1                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhheeeeeeeee....eeeeeee.....eeeeeeee.hhh..eeee...eeeehhhhhhhhhh........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
                 4k18 A  32 EPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLS 308
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301
   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  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K18)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K18)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    1OB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:124 - Pro A:125   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4k18
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PIM1_HUMAN | P11309
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.11.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PIM1_HUMAN | P11309
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 4k1b 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 4k1b