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(-) Description

Title :  STRUCTURE-GUIDED DESIGN OF ALPHA-AMINO ACID-DERIVED PIN1 INHIBITORS
 
Authors :  L. M. Baker, P. Dokurno, D. A. Robinson, A. E. Surgenor, J. B. Murray, A. J. Potter, J. D. Moore
Date :  19 Oct 09  (Deposition) - 22 Dec 09  (Release) - 05 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Sbdd, Ppiase, Isomerase, Rotamase, Small Molecule, Proline Directed Kinase, Cell Cycle, Oncogenic Transformation, Nucleus, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. J. Potter, S. Ray, L. Gueritz, C. L. Nunns, C. J. Bryant, S. F. Scrace, N. Matassova, L. M. Baker, P. Dokurno, D. A. Robinson, A. E. Surgenor, B. Davis, J. B. Murray, C. M. Richardson, J. D. Moore
Structure-Guided Design Of Alpha-Amino Acid-Derived Pin1 Inhibitors
Bioorg. Med. Chem. Lett. V. 20 586 2010
PubMed-ID: 19969456  |  Reference-DOI: 10.1016/J.BMCL.2009.11.090
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA- INTERACTING 1
    ChainsA
    EC Number5.2.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GenePIN1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymROTAMASE PIN1, PPIASE PIN1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
14D91Ligand/Ion3-(1H-BENZIMIDAZOL-2-YL)-N-(1-BENZOTHIOPHEN-2-YLCARBONYL)-D-ALANINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:59 , LYS A:63 , CYS A:113 , SER A:114 , LEU A:122 , MET A:130 , PHE A:134 , SER A:154 , HIS A:157 , HOH A:171 , HOH A:203BINDING SITE FOR RESIDUE 4D9 A 164

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KAF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KAF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KAF)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WW_DOMAIN_1PS01159 WW/rsp5/WWP domain signature.PIN1_HUMAN11-37  1A:11-37
2PPIC_PPIASE_2PS50198 PpiC-type peptidyl-prolyl cis-trans isomerase family profile.PIN1_HUMAN52-163  1A:52-163
3PPIC_PPIASE_1PS01096 PpiC-type peptidyl-prolyl cis-trans isomerase signature.PIN1_HUMAN103-123  1A:103-123

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002479701aENSE00000872705chr19:9945999-994607880PIN1_HUMAN1-20201A:7-2014
1.2ENST000002479702ENSE00000872706chr19:9949112-9949324213PIN1_HUMAN20-91721A:20-91 (gaps)72
1.3aENST000002479703aENSE00000872707chr19:9958706-9958816111PIN1_HUMAN91-128381A:91-12838
1.4aENST000002479704aENSE00000872708chr19:9959766-9960358593PIN1_HUMAN128-163361A:128-16336

(-) 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:145
 aligned with PIN1_HUMAN | Q13526 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:157
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       
           PIN1_HUMAN     7 LPPGWEKRMSRSSGRVYYFNHITNASQWERPSGNSSSGGKNGQGEPARVRCSHLLVKHSQSRRPSSWRQEKITRTKEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE 163
               SCOP domains d3kafa1 A:7-37                 -------------d3kafa2 A:51-163 Mitotic rotamase PIN1, domain 2                                                                  SCOP domains
               CATH domains 3kafA01 A:7-37                 ----------------3kafA02 A:54-163  [code=3.10.50.40, no name defined]                                                           CATH domains
               Pfam domains WW-3kafA02 A:7-37              ---------------------Rotamase-3kafA01 A:59-163                                                                                 Pfam domains
         Sec.struct. author ....eeeee......eeeee.....ee.....------------...eeeeeeeee..................hhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhh.eeeeee....hhhhhhhhhhh........eee..eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----WW_DOMAIN_1  PDB: A:11-37  --------------PPIC_PPIASE_2  PDB: A:52-163 UniProt: 52-163                                                                     PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------PPIC_PPIASE_1        ---------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1a     ----------------------------------------------------------------------Exon 1.3a  PDB: A:91-128              ----------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------Exon 1.2  PDB: A:20-91 (gaps) UniProt: 20-91                            ------------------------------------Exon 1.4a  PDB: A:128-163            Transcript 1 (2)
                 3kaf A   7 LPPGWEKAMSRSSGRVYYFNHITNASQWERPS------------EPARVRCSHLLVKHSQSRRPSSWRQEKITRTKEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMAKPFEDASFALRTGEMSGPVFTDSGIHIILRTE 163
                                    16        26        36 |       -    |   56        66        76        86        96       106       116       126       136       146       156       
                                                          38           51                                                                                                                

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: FKBP (43)

(-) Gene Ontology  (42, 42)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PIN1_HUMAN | Q13526)
molecular function
    GO:0032794    GTPase activating protein binding    Interacting selectively and non-covalently with a GTPase activating protein.
    GO:0008013    beta-catenin binding    Interacting selectively and non-covalently with the beta subunit of the catenin complex.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0031434    mitogen-activated protein kinase kinase binding    Interacting selectively and non-covalently with a mitogen-activated protein kinase kinase, any protein that can phosphorylate a MAP kinase.
    GO:0003774    motor activity    Catalysis of the generation of force resulting either in movement along a microfilament or microtubule, or in torque resulting in membrane scission, coupled to the hydrolysis of a nucleoside triphosphate.
    GO:0003755    peptidyl-prolyl cis-trans isomerase activity    Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
    GO:0050815    phosphoserine residue binding    Interacting selectively and non-covalently with a phosphorylated serine residue within a protein.
    GO:0050816    phosphothreonine residue binding    Interacting selectively and non-covalently with a phosphorylated threonine residue within a protein.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0070373    negative regulation of ERK1 and ERK2 cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:2000146    negative regulation of cell motility    Any process that stops, prevents, or reduces the frequency, rate or extent of cell motility.
    GO:0043524    negative regulation of neuron apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
    GO:0032091    negative regulation of protein binding    Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
    GO:0042177    negative regulation of protein catabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0030512    negative regulation of transforming growth factor beta receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of any TGF-beta receptor signaling pathway.
    GO:0032480    negative regulation of type I interferon production    Any process that stops, prevents, or reduces the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0030182    neuron differentiation    The process in which a relatively unspecialized cell acquires specialized features of a neuron.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0090263    positive regulation of canonical Wnt signaling pathway    Any process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0061051    positive regulation of cell growth involved in cardiac muscle cell development    Any process that increases the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state.
    GO:0043525    positive regulation of neuron apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process.
    GO:0035307    positive regulation of protein dephosphorylation    Any process that activates or increases the frequency, rate or extent of removal of phosphate groups from a protein.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0051443    positive regulation of ubiquitin-protein transferase activity    Any process that activates, maintains or increases the rate of ubiquitin transferase activity.
    GO:0000413    protein peptidyl-prolyl isomerization    The modification of a protein by cis-trans isomerization of a proline residue.
    GO:0050821    protein stabilization    Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
    GO:0032465    regulation of cytokinesis    Any process that modulates the frequency, rate or extent of the division of the cytoplasm of a cell and its separation into two daughter cells.
    GO:0007088    regulation of mitotic nuclear division    Any process that modulates the frequency, rate or extent of mitosis.
    GO:0060393    regulation of pathway-restricted SMAD protein phosphorylation    Any process that modulates the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
    GO:1900180    regulation of protein localization to nucleus    Any process that modulates the frequency, rate or extent of protein localization to nucleus.
    GO:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
    GO:0050808    synapse organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030496    midbody    A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PIN1_HUMAN | Q135261f8a 1i6c 1i8g 1i8h 1nmv 1nmw 1pin 1zcn 2f21 2itk 2kbu 2kcf 2lb3 2m8i 2m8j 2m9e 2m9f 2m9i 2m9j 2n1o 2q5a 2ruc 2rud 2ruq 2rur 2xp3 2xp4 2xp5 2xp6 2xp7 2xp8 2xp9 2xpa 2xpb 2zqs 2zqt 2zqu 2zqv 2zr4 2zr5 2zr6 3i6c 3ik8 3ikd 3ikg 3jyj 3kab 3kac 3kad 3kag 3kah 3kai 3kce 3ntp 3odk 3oob 3tc5 3tcz 3tdb 3wh0 4gwt 4gwv 4qib 4tns 4tyo 4u84 4u85 4u86 5b3w 5b3x 5b3y 5b3z 5bmy 5uy9

(-) Related Entries Specified in the PDB File

3kab 3kac 3kad 3kag 3kah 3kai