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(-) Description

Title :  CYTOCHROME P450 3A4 BOUND TO AN INHIBITOR
 
Authors :  I. Sevrioukova, T. Poulos
Date :  22 Nov 14  (Deposition) - 23 Sep 15  (Release) - 25 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.76
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Monooxygenase, Human Cyp3A4, 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
    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, TAUROCHENODEOXYCHOLA TE 6-ALPHA-HYDROXYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2PKT1Ligand/IonTERT-BUTYL [(2S)-1-(1H-INDOL-3-YL)-3-({3-OXO-3-[(PYRIDIN-3-YLMETHYL)AMINO]PROPYL}SULFANYL)PROPAN-2-YL]CARBAMATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:105 , ILE A:118 , SER A:119 , TRP A:126 , ARG A:130 , PHE A:137 , ALA A:305 , THR A:309 , VAL A:313 , ALA A:370 , LEU A:373 , ARG A:375 , PRO A:434 , PHE A:435 , GLY A:436 , SER A:437 , ARG A:440 , ASN A:441 , CYS A:442 , GLY A:444 , PKT A:1600BINDING SITE FOR RESIDUE HEM A1500
2AC2SOFTWAREARG A:105 , PHE A:108 , SER A:119 , LEU A:211 , PHE A:304 , ALA A:305 , THR A:309 , ILE A:369 , HEM A:1500BINDING SITE FOR RESIDUE PKT A1600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D7D)

(-) 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 4D7D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D7D)

(-) Exons   (0, 0)

(no "Exon" information available for 4D7D)

(-) 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:459
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh............hhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh...............hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhh.......hhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh......hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....eeee....eee..eee....eeeehhhhhh............hhhhhh.......................hhhhhhhhhhhhhhhhhh.eeee.......................eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d7d A  29 SHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDTHRVDFLQLMIDSQNALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVVLKVESRD 497
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258     ||270       280|      298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488         
                                                                                                                                                                                                                                                                     264|          280|                                                                                                                                                                                                                
                                                                                                                                                                                                                                                                      267           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 4D7D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D7D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D7D)

(-) Gene Ontology  (41, 41)

Asymmetric/Biological Unit(hide GO term definitions)

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  1.14.13.32
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  1.14.13.67
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 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 4d6z 4d75 4d78 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

4d6z CYTOCHROME P450 3A4 BOUND TO IMIDAZOLE AND AN INHIBITOR
4d75 CYTOCHROME P450 3A4 BOUND TO AN INHIBITOR
4d78 CYTOCHROME P450 3A4 BOUND TO AN INHIBITOR