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 :  CREATING NOVEL F1 INHIBITORS THROUGH FRAGMENT BASED LEAD GENERATION AND STRUCTURE AIDED DRUG DESIGN
 
Authors :  J. Sandmark, L. Oster, O. Fjellstrom, S. Akkaya, H. G. Beisel, P. O. Erik K. Erixon, D. Gustafsson, U. Jurva, D. Kang, D. Karis, W. Knecht, V. Ner I. Nilsson, T. Olsson, A. Redzic, R. Roth, A. Tigerstrom
Date :  26 Feb 14  (Deposition) - 11 Feb 15  (Release) - 11 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Fjellstrom, S. Akkaya, H. Beisel, P. Eriksson, K. Erixon, D. Gustafsson, U. Jurva, D. Kang, D. Karis, W. Knecht, V. Nerme, I. Nilsson, T. Olsson, A. Redzic, R. Roth, J. Sandmark, A. Tigerstrom, L. Oster
Creating Novel Activated Factor Xi Inhibitors Through Fragment Based Lead Generation And Structure Aided Drug Design.
Plos One V. 10 13705 2015
PubMed-ID: 25629509  |  Reference-DOI: 10.1371/JOURNAL.PONE.0113705

(-) Compounds

Molecule 1 - COAGULATION FACTOR XI
    Chains: A
    EC Number: 3.4.21.27
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Taxid: 4922
    Fragment: CATALYTIC DOMAIN, RESIDUES 388-625
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: FXI, PLASMA THROMBOPLASTIN ANTECEDENT, PTA, COAGULATION FACTOR XIA LIGHT CHAIN

 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, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1OTW1Ligand/Ion4-METHYLQUINOLINE-2,6-DIAMINE
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
1OTW2Ligand/Ion4-METHYLQUINOLINE-2,6-DIAMINE
2SO412Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:189 , ALA A:190 , LYS A:192 , SER A:195 , TRP A:215 , GLY A:216 , GLY A:218 , CYS A:219 , SO4 A:1494 , HOH A:2297BINDING SITE FOR RESIDUE OTW A1489
2AC2SOFTWARETHR A:20 , ALA A:21 , GLN A:48 , GLN A:86 , LYS A:107 , HOH A:2008 , HOH A:2071 , HOH A:2217BINDING SITE FOR RESIDUE SO4 A1490
3AC3SOFTWARELYS A:202 , TRP A:203 , HOH A:2022 , HOH A:2260BINDING SITE FOR RESIDUE SO4 A1491
4AC4SOFTWARELYS A:127 , ARG A:130BINDING SITE FOR RESIDUE SO4 A1492
5AC5SOFTWAREHIS A:91 , TRP A:237 , HOH A:2149 , HOH A:2156 , HOH A:2245 , HOH A:2285BINDING SITE FOR RESIDUE SO4 A1493
6AC6SOFTWAREHIS A:57 , LYS A:192 , GLY A:193 , SER A:195 , OTW A:1489 , HOH A:2056 , HOH A:2074 , HOH A:2298BINDING SITE FOR RESIDUE SO4 A1494
7AC7SOFTWAREASN A:113 , TYR A:143 , LYS A:149 , LYS A:192 , HOH A:2209BINDING SITE FOR RESIDUE SO4 A1495

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:40 -A:58
2A:136 -A:201
3A:168 -A:182
4A:191 -A:219

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:37 -Pro A:37A

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CR9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CR9)

(-) Exons   (0, 0)

(no "Exon" information available for 4CR9)

(-) 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:238
                                                                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee.....eeeeeeeeee..eeeehhhhhh...hhh.eeee.....hhhh......eeeeeeee.....hhhhh...eeeee................hhhhh......eeeee..............eeee..eehhhhhhhhh........eeee................eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4cr9 A   16 IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQAEIAEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYADSQRPISLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAV  245
                                    25        35  ||||  41      ||53      ||60        70        80 |      89        99       109       119|      130  |    139       149|      160       170   |   179     | 188|      197 ||| ||203||     217       227       237        
                                                37A|||         48|      59A||                    81A                                   119|        132A              149|                   173A        184A 188A       198A|| |||| ||                                    
                                                 37B||          51       59B|                                                           121                           151                                                198B| |||| ||                                    
                                                  37C|                    59C                                                                                                                                              201 |||| ||                                    
                                                   37D                                                                                                                                                                      202A||| ||                                    
                                                                                                                                                                                                                             202B|| ||                                    
                                                                                                                                                                                                                              202C| ||                                    
                                                                                                                                                                                                                               202D ||                                    
                                                                                                                                                                                                                                  204|                                    
                                                                                                                                                                                                                                   209
   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 4CR9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CR9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CR9)

(-) Gene Ontology  (19, 19)

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
    OTW  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:37 - Pro A:37A  [ RasMol ]  
 
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
  4cr9
    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
  FA11_HUMAN | P03951
    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)
  3.4.21.27
    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
  FA11_HUMAN | P03951
    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
        FA11_HUMAN | P03951: 1xx9 1xxd 1xxf 1zhm 1zhp 1zhr 1zjd 1zlr 1zmj 1zml 1zmn 1zom 1zpb 1zpc 1zpz 1zrk 1zsj 1zsk 1zsl 1ztj 1ztk 1ztl 2f83 2fda 2j8j 2j8l 3bg8 3sor 3sos 4cr5 4cra 4crb 4crc 4crd 4cre 4crf 4crg 4d76 4d7f 4d7g 4na7 4na8 4ty6 4ty7 4wxi 4x6m 4x6n 4x6o 4x6p 4y8x 4y8y 4y8z 5e2o 5e2p 5eod 5eok 5exl 5exm 5exn 5i25 5q0d 5q0e 5q0f 5q0g 5q0h 5tks 5tkt 5tku

(-) Related Entries Specified in the PDB File

4cr5 CREATING NOVEL F1 INHIBITORS THROUGH FRAGMENT BASED LEAD GENERATION AND STRUCTURE AIDED DRUG DESIGN
4cra CREATING NOVEL F1 INHIBITORS THROUGH FRAGMENT BASED LEAD GENERATION AND STRUCTURE AIDED DRUG DESIGN
4crb CREATING NOVEL F1 INHIBITORS THROUGH FRAGMENT BASED LEAD GENERATION AND STRUCTURE AIDED DRUG DESIGN
4crc CREATING NOVEL F1 INHIBITORS THROUGH FRAGMENT BASED LEAD GENERATION AND STRUCTURE AIDED DRUG DESIGN
4crd CREATING NOVEL F1 INHIBITORS THROUGH FRAGMENT BASED LEAD GENERATION AND STRUCTURE AIDED DRUG DESIGN
4cre CREATING NOVEL F1 INHIBITORS THROUGH FRAGMENT BASED LEAD GENERATION AND STRUCTURE AIDED DRUG DESIGN
4crf CREATING NOVEL F1 INHIBITORS THROUGH FRAGMENT BASED LEAD GENERATION AND STRUCTURE AIDED DRUG DESIGN
4crg CREATING NOVEL F1 INHIBITORS THROUGH FRAGMENT BASED LEAD GENERATION AND STRUCTURE AIDED DRUG DESIGN