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 :  CYTOCHROME P450 3A4 BOUND TO IMIDAZOLE AND AN INHIBITOR
 
Authors :  I. Sevrioukova, T. Poulos
Date :  19 Nov 14  (Deposition) - 23 Sep 15  (Release) - 25 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Monooxygenase, Cytochrome P450, Human Cyp3A4, Imidazole, Inhibitory Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Kaur, R. Chamberlin, T. L. Poulos, I. F. Sevrioukova
Structure-Based Inhibitor Design For Evaluation Of A Cyp3A4 Pharmacophore Model.
J. Med. Chem. V. 59 4210 2016
PubMed-ID: 26371436  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01146

(-) Compounds

Molecule 1 - CYTOCHROME P450 3A4
    Chains: A
    EC Number: 1.14.13.157, 1.14.13.32, 1.14.13.67, 1.14.13.97
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCWORI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, UNP RESIDUES 23-503
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 1,8-CINEOLE 2-EXO-MONOOXYGENASE, ALBENDAZOLE MONOOXYGENASE, ALBENDAZOLE SULFOXIDASE, CYPIIIA3, CYPIIIA4, CYTOCHROME P450 3A3, CYTOCHROME P450 HLP, CYTOCHROME P450 NF-25, CYTOCHROME P450-PCN1, NIFEDIPINE OXIDASE, QUININE 3-MONOOXYGENASE, TAUROCHENODEOXYCHOLATE 6-ALPHA-HYDROXYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3IMD1Ligand/IonIMIDAZOLE
4PK91Ligand/IonTERT-BUTYL {6-OXO-6-[(PYRIDIN-3-YLMETHYL)AMINO]HEXYL}CARBAMATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:105 , ILE A:118 , SER A:119 , TRP A:126 , ARG A:130 , ALA A:305 , ALA A:370 , ARG A:375 , PRO A:434 , PHE A:435 , GLY A:436 , SER A:437 , ARG A:440 , ASN A:441 , CYS A:442 , ILE A:443 , GLY A:444 , ALA A:448 , MET A:452 , IMD A:1601 , HOH A:2045BINDING SITE FOR RESIDUE HEM A1500
2AC2SOFTWAREARG A:105 , SER A:119 , ARG A:212 , PHE A:215 , PHE A:304 , ILE A:369 , ALA A:370 , IMD A:1601 , HOH A:2090 , HOH A:2150BINDING SITE FOR RESIDUE PK9 A1600
3AC3SOFTWAREALA A:305 , THR A:309 , HEM A:1500 , PK9 A:1600BINDING SITE FOR RESIDUE IMD A1601
4AC4SOFTWARELYS A:55 , GLY A:56 , PHE A:57 , CYS A:58 , MET A:371 , SER A:478 , GLY A:480 , GLY A:481 , LEU A:482 , LEU A:483BINDING SITE FOR RESIDUE GOL A1602
5AC5SOFTWAREPRO A:41 , SER A:52 , GLU A:63 , LYS A:67 , TYR A:68 , HOH A:2190BINDING SITE FOR RESIDUE GOL A1603
6AC6SOFTWARETHR A:42 , LEU A:44 , ASN A:49 , LEU A:51 , SER A:52 , HOH A:2014 , HOH A:2190BINDING SITE FOR RESIDUE GOL A1604
7AC7SOFTWARETYR A:399 , ARG A:403 , GLU A:412 , LEU A:475 , LEU A:477BINDING SITE FOR RESIDUE GOL A1605

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D6Z)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ile A:473 -Pro A:474

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D6Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D6Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4D6Z)

(-) 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:460
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...........hhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh...............hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhh..........hhhhhhhh........hhhhhhhhhh..hhhhhhhh.....hhhhhhhhhhhhhhhhhh..........hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....eeee....eee..eee....eeeehhhhhhh...........hhhhhh..hhhhh................hhhhhhhhhhhhhhhhhhheeeee......................eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d6z A  29 SHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDTQKHRVDFLQLMIDSQALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVVLKVESRD 497
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278||     297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497
                                                                                                                                                                                                                                                                                    279|                                                                                                                                                                                                                
                                                                                                                                                                                                                                                                                     289
   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 4D6Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D6Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D6Z)

(-) Gene Ontology  (41, 41)

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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IMD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PK9  [ 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
    Ile A:473 - Pro A:474   [ 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
  4d6z
    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
  CP3A4_HUMAN | P08684
    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)
  1.14.13.157
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  1.14.13.32
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  1.14.13.67
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  1.14.13.97
    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
  CP3A4_HUMAN | P08684
    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
        CP3A4_HUMAN | P08684: 1tqn 1w0e 1w0f 1w0g 2j0d 2v0m 3nxu 3tjs 3ua1 4d75 4d78 4d7d 4i3q 4i4g 4i4h 4k9t 4k9u 4k9v 4k9w 4k9x 4ny4 5a1p 5a1r 5g5j 5te8 5vc0 5vcc 5vcd 5vce 5vcg

(-) Related Entries Specified in the PDB File

4d75 CYTOCHROME P450 3A4 BOUND TO AN INHIBITOR