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(-) Description

Title :  CRYSTAL STRUCTURE OF PTP1B WITH A MONOCYCLIC THIOPHENE INHIBITOR
 
Authors :  W. Xu, Z. -K. Wan
Date :  24 May 06  (Deposition) - 29 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein-Drug Complex Structure, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. K. Wan, J. Lee, W. Xu, D. V. Erbe, D. Joseph-Mccarthy, B. C. Follows, Y. L. Zhang
Monocyclic Thiophenes As Protein Tyrosine Phosphatase 1B Inhibitors: Capturing Interactions With Asp48.
Bioorg. Med. Chem. Lett. V. 16 4941 2006
PubMed-ID: 16806920  |  Reference-DOI: 10.1016/J.BMCL.2006.06.051
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1
    ChainsA
    EC Number3.1.3.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCATALYTIC DOMAIN OF PTP1B
    GenePTPN1, PTP1B
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROTEIN-TYROSINE PHOSPHATASE 1B, PTP-1B

 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
15091Ligand/Ion4-BROMO-3-(CARBOXYMETHOXY)-5-PHENYLTHIOPHENE-2-CARBOXYLIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:46 , VAL A:49 , LYS A:120 , PHE A:182 , SER A:216 , ILE A:219 , GLY A:220 , ARG A:221 , GLN A:262 , GLN A:266 , SER A:285 , HOH A:381BINDING SITE FOR RESIDUE 509 A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2H4K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2H4K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H4K)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_PTPPS50055 PTP type protein phosphatase family profile.PTN1_HUMAN3-277  1A:3-277
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.PTN1_HUMAN189-268  1A:189-268
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.PTN1_HUMAN213-223  1A:213-223

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003716211ENSE00001455721chr20:49126891-49127127237PTN1_HUMAN1-21211A:2-2120
1.2ENST000003716212ENSE00000509635chr20:49177900-4917799091PTN1_HUMAN22-52311A:22-5231
1.3ENST000003716213ENSE00000662794chr20:49181506-49181606101PTN1_HUMAN52-85341A:52-8534
1.4ENST000003716214ENSE00000662795chr20:49184917-4918501599PTN1_HUMAN86-118331A:86-11833
1.5ENST000003716215ENSE00000662796chr20:49191054-49191191138PTN1_HUMAN119-164461A:119-16446
1.6ENST000003716216ENSE00000662797chr20:49194957-49195166210PTN1_HUMAN165-234701A:165-23470
1.7ENST000003716217ENSE00000662798chr20:49195705-49195866162PTN1_HUMAN235-288541A:235-28854
1.8ENST000003716218ENSE00000662799chr20:49196240-49196463224PTN1_HUMAN289-363751A:289-29810
1.9ENST000003716219ENSE00001172461chr20:49197802-49197997196PTN1_HUMAN363-428660--
1.10ENST0000037162110ENSE00001455694chr20:49199229-492012992071PTN1_HUMAN429-43570--

(-) 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:297
 aligned with PTN1_HUMAN | P18031 from UniProtKB/Swiss-Prot  Length:435

    Alignment length:297
                                    11        21        31        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       
           PTN1_HUMAN     2 EMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHED 298
               SCOP domains d2h4ka_ A: Tyrosine phosphatase                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2h4kA00 A:2-298 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh...........eee.......eeeeeeeee....eeeeee......hhhhhhhhhhhh...eeee....ee..ee.............eee....eeeeeeeeee...eeeeeeeeee....eeeeeeeeee..........hhhhhhhhhhhhhhh.........eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -TYR_PHOSPHATASE_PTP  PDB: A:3-277 UniProt: 3-277                                                                                                                                                                                                                                   --------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:189-268 UniProt: 189-268                              ------------------------------ PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA--------------------------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.1  PDB: A:2-2Exon 1.2  PDB: A:22-52         ---------------------------------Exon 1.4  PDB: A:86-118          Exon 1.5  PDB: A:119-164 UniProt: 119-164     Exon 1.6  PDB: A:165-234 UniProt: 165-234                             Exon 1.7  PDB: A:235-288 UniProt: 235-288             Exon 1.8   Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------Exon 1.3  PDB: A:52-85            --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2h4k A   2 EMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHED 298
                                    11        21        31        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       

   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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H4K)

(-) Gene Ontology  (51, 51)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PTN1_HUMAN | P18031)
molecular function
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0046875    ephrin receptor binding    Interacting selectively and non-covalently with an ephrin receptor.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0005158    insulin receptor binding    Interacting selectively and non-covalently with the insulin receptor.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    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).
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0051721    protein phosphatase 2A binding    Interacting selectively and non-covalently with the enzyme protein phosphatase 2A.
    GO:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
    GO:0030971    receptor tyrosine kinase binding    Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0036498    IRE1-mediated unfolded protein response    A series of molecular signals mediated by the endoplasmic reticulum stress sensor IRE1 (Inositol-requiring transmembrane kinase/endonuclease). Begins with activation of IRE1 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. One target of activated IRE1 is the transcription factor HAC1 in yeast, or XBP1 in mammals; IRE1 cleaves an intron of a mRNA coding for HAC1/XBP1 to generate an activated HAC1/XBP1 transcription factor, which controls the up regulation of UPR-related genes. At least in mammals, IRE1 can also signal through additional intracellular pathways including JNK and NF-kappaB.
    GO:0060397    JAK-STAT cascade involved in growth hormone signaling pathway    The process in which STAT proteins (Signal Transducers and Activators of Transcription) are activated by members of the JAK (janus activated kinase) family of tyrosine kinases, following the binding of physiological ligands to the growth hormone receptor. Once activated, STATs dimerize and translocate to the nucleus and modulate the expression of target genes.
    GO:0031532    actin cytoskeleton reorganization    A process that is carried out at the cellular level which results in dynamic structural changes to the arrangement of constituent parts of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0007257    activation of JUN kinase activity    The initiation of the activity of the inactive enzyme JUN kinase (JNK).
    GO:0006987    activation of signaling protein activity involved in unfolded protein response    The conversion of a specific protein, possessing protein kinase and endoribonuclease activities, to an active form as a result of signaling via the unfolded protein response.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0030968    endoplasmic reticulum unfolded protein response    The series of molecular signals generated as a consequence of the presence of unfolded proteins in the endoplasmic reticulum (ER) or other ER-related stress; results in changes in the regulation of transcription and translation.
    GO:0008286    insulin receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
    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:0043407    negative regulation of MAP kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of MAP kinase activity.
    GO:1903898    negative regulation of PERK-mediated unfolded protein response    Any process that stops, prevents or reduces the frequency, rate or extent of the PERK-mediated unfolded protein response.
    GO:1902236    negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of an endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway.
    GO:0046627    negative regulation of insulin receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of insulin receptor signaling.
    GO:0009968    negative regulation of signal transduction    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
    GO:0030948    negative regulation of vascular endothelial growth factor receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:1990264    peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity    Any peptidyl-tyrosine dephosphorylation that is involved in inactivation of protein kinase activity.
    GO:0035791    platelet-derived growth factor receptor-beta signaling pathway    A series of molecular signals initiated by the binding of a ligand to a beta-type platelet-derived growth factor receptor (PDGFbeta) on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:1903896    positive regulation of IRE1-mediated unfolded protein response    Any process that activates or increases the frequency, rate or extent of the IRE1-mediated unfolded protein response.
    GO:0061098    positive regulation of protein tyrosine kinase activity    Any process that increases the rate, frequency, or extent of protein tyrosine kinase activity.
    GO:2000646    positive regulation of receptor catabolic process    Any process that activates or increases the frequency, rate or extent of receptor catabolic process.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0030100    regulation of endocytosis    Any process that modulates the frequency, rate or extent of endocytosis.
    GO:1902202    regulation of hepatocyte growth factor receptor signaling pathway    Any process that modulates the frequency, rate or extent of hepatocyte growth factor receptor signaling pathway.
    GO:0046626    regulation of insulin receptor signaling pathway    Any process that modulates the frequency, rate or extent of insulin receptor signaling.
    GO:0033157    regulation of intracellular protein transport    Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells.
    GO:0009966    regulation of signal transduction    Any process that modulates the frequency, rate or extent of signal transduction.
    GO:0060338    regulation of type I interferon-mediated signaling pathway    Any process that modulates the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor.
    GO:0034976    response to endoplasmic reticulum stress    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0098554    cytoplasmic side of endoplasmic reticulum membrane    The side (leaflet) of the plasma membrane that faces the cytoplasm.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0097443    sorting endosome    A multivesicular body surrounded by and connected with multiple tubular compartments with associated vesicles.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PTN1_HUMAN | P180311a5y 1aax 1bzc 1bzh 1bzj 1c83 1c84 1c85 1c86 1c87 1c88 1ecv 1een 1eeo 1g1f 1g1g 1g1h 1g7f 1g7g 1gfy 1i57 1jf7 1kak 1kav 1l8g 1lqf 1nl9 1nny 1no6 1nwe 1nwl 1nz7 1oem 1oeo 1oes 1oet 1oeu 1oev 1ony 1onz 1pa1 1ph0 1ptt 1ptu 1ptv 1pty 1pxh 1pyn 1q1m 1q6j 1q6m 1q6n 1q6p 1q6s 1q6t 1qxk 1sug 1t48 1t49 1t4j 1wax 1xbo 2azr 2b07 2b4s 2bgd 2bge 2cm2 2cm3 2cm7 2cm8 2cma 2cmb 2cmc 2cne 2cnf 2cng 2cnh 2cni 2f6f 2f6t 2f6v 2f6w 2f6y 2f6z 2f70 2f71 2fjm 2fjn 2h4g 2hb1 2hnp 2hnq 2nt7 2nta 2qbp 2qbq 2qbr 2qbs 2veu 2vev 2vew 2vex 2vey 2zmm 2zn7 3a5j 3a5k 3cwe 3d9c 3eax 3eb1 3eu0 3i7z 3i80 3qkp 3qkq 3sme 3zmp 3zmq 3zv2 4bjo 4i8n 4qah 4qap 4qbe 4qbw 4y14 4zrt 5k9v 5k9w 5ka0 5ka1 5ka2 5ka3 5ka4 5ka7 5ka8 5ka9 5kaa 5kab 5kac 5kad 5t19

(-) Related Entries Specified in the PDB File

2azr CRYSTAL STRUCTURE OF PTP1B WITH BICYCLIC THIOPHENE INHIBITOR
2b07 CRYSTAL STRUCTURE OF PTP1B WITH TRICYCLIC THIOPHENE INHIBITOR
2h4g CRYSTAL STRUCTURE OF PTP1B WITH MONOCYCLIC THIOPHENE INHIBITOR