Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ISO-CITRATE DEHYDROGENASE 1 [IDH1 (R132H)] IN COMPLEX WITH A NOVEL INHIBITOR (COMPOUND 2)
 
Authors :  C. Levy
Date :  28 May 16  (Deposition) - 14 Dec 16  (Release) - 11 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.04
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Iso-Citrate Dehydrogenase, Allosteric, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Jones, J. Ahmet, K. Ayton, M. Ball, M. Cockerill, E. Fairweather, N. Hamilton, P. Harper, J. Hitchin, A. Jordan, C. Levy, R. Lopez, E. Mckenzie, M. Packer, D. Plant, I. Simpson, P. Simpson, I. Sinclair, T. C. Somervaille, H. Small, G. J. Spencer, G. Thomson, M. Tonge, I. Waddell, J. Walsh, B. Waszkowycz, M. Wigglesworth, D. H. Wiseman, D. Ogilvie
Discovery And Optimization Of Allosteric Inhibitors Of Mutant Isocitrate Dehydrogenase 1 (R132H Idh1) Displaying Activity In Human Acute Myeloid Leukemia Cells.
J. Med. Chem. V. 59 11120 2016
PubMed-ID: 28002956

(-) Compounds

Molecule 1 - ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC
    Chains: A
    EC Number: 1.1.1.42
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: JM109 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: IDH1, PICD
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IDH,CYTOSOLIC NADP-ISOCITRATE DEHYDROGENASE,IDP,NADP(+)- SPECIFIC ICDH,OXALOSUCCINATE DECARBOXYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
16MX1Ligand/Ion2-[(3~{R})-1-[6-CYCLOHEXYLSULFANYL-5-[[(1~{R},3~{S})-5-OXIDANYL-2-ADAMANTYL]CARBAMOYL]PYRIDIN-2-YL]PYRROLIDIN-3-YL]ETHANOIC ACID
2NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
16MX2Ligand/Ion2-[(3~{R})-1-[6-CYCLOHEXYLSULFANYL-5-[[(1~{R},3~{S})-5-OXIDANYL-2-ADAMANTYL]CARBAMOYL]PYRIDIN-2-YL]PYRROLIDIN-3-YL]ETHANOIC ACID
2NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:72 , THR A:75 , THR A:77 , ARG A:82 , ASN A:96 , LEU A:288 , GLY A:289 , GLU A:306 , HIS A:309 , GLY A:310 , THR A:311 , VAL A:312 , THR A:313 , ARG A:314 , HIS A:315 , ASN A:328 , ASP A:375binding site for residue NDP A 501
2AC2SOFTWAREALA A:111 , ARG A:119 , TRP A:124 , ILE A:130 , ASP A:252 , VAL A:255 , TRP A:267 , ASN A:271 , TYR A:285binding site for residue 6MX A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5L58)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5L58)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L58)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L58)

(-) Exons   (0, 0)

(no "Exon" information available for 5L58)

(-) Sequences/Alignments

Asymmetric 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:376
                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.hhhhhhhhhhhhhhh....eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee..............eeeeeee.....eeeee...........eeeee...hhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhh..eeeeeee.........hhh.eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l58 A   3 KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDAARVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGHHAYGATDFVVPGPEITTYLVGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKKYDGRFKDIFQEIYDKQYKSQFAAAAIWYEHRLIDDMVAQAMKSEGGFIWACKNYVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL 414
                                    12        22        32        42        52        62        72        82        92       102       112       122       132   ||  146  || ||169|      185       195       205      |220       230       240       250       260       270 ||    288       298       308       318       328       338       348       358       368       378       388       398       408      
                                                                                                                                                               136|     149| ||  ||                                 212|                                                   272|                                                                                                                                     
                                                                                                                                                                141      153 ||  ||                                  218                                                    281                                                                                                                                     
                                                                                                                                                                           155|  ||                                                                                                                                                                                                                                 
                                                                                                                                                                            166  ||                                                                                                                                                                                                                                 
                                                                                                                                                                               169|                                                                                                                                                                                                                                 
                                                                                                                                                                                176
   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 5L58)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L58)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L58)

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    6MX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5l58)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  5l58
    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
  IDHC_HUMAN | O75874
    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)
  1.1.1.42
    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
  IDHC_HUMAN | O75874
    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
        IDHC_HUMAN | O75874: 1t09 1t0l 3inm 3map 3mar 3mas 4i3k 4i3l 4kzo 4l03 4l04 4l06 4umx 4umy 4xrx 4xs3 5de1 5gir 5k10 5k11 5l57 5lge 5sun 5svf 5tqh

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5L58)